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									                                                      Active Nanostructures for Nucleic Directed synthesis of Organic Functional Polymers
                                                      Nadrian Seemana, William A. Goddard IIIb, James Canary a, Erik Winfreeb
                                                      aNew  York University
                                                      bCalifornia Institute of Technology




                        Synthesize and characterize functional nanomachines and devices using:
                         General strategies for synthesizing DNA structures that self organize to provide a scaffold designed to produce polymers with the diversity and precision that ribosomes exhibit in building proteins: developed by the
                        Seeman lab
                         Methods to crosslink DNA strands across the minor groove and offer the potential to develop polymers whose topology can be directed by the single-stranded DNA topology of unusual motifs: developed by the
                        Canary lab
                         Self assembled an all-single wall carbon nanotube (SWNT) field effect transistor (FET) on DNA origami using solution phase molecular linker mediated attachment: developed by the Winfree/Goddard labs
                         A Mesoscale model of DNA to investigate the structural and thermodynamics properties of these systems: developed by the Goddard lab.




                                                                                                                                                                                                                                                        Intrastrand crosslinkages                                                                                                                                                                                                     Interstrand crosslinkages over distances
                                                                                                                                                                                                                                                                                                                                                        O               R =


                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Crosslink (Uc4-Un4)                                                                                                                                                               Yield
                                                                                                                                                                                                           c m
                                                                                                                                                                                                       Q ui k Ti e™ a nd a
                                                                                                                                                                                                   TI FF ( L ZW ) d ec om pr e ss or
                                                                                                                                                                                                ar e n ee ded t o s ee t hi p i t u r e.
                                                                                                                                                                                                                          s c              Un12                               c m
                                                                                                                                                                                                                                                                          Q ui k Ti e™ a nd a
                                                                                                                                                                                                                                                                      TI FF ( L ZW ) d ec om pr e ss or


                                                                                                                                                                                                                                                                                                              Un12                                                                    O
                                                                                                                                                                                                                                                                                                                                                            NH
                                                                                                                                                                                                                                                                                             s c
                                                                                                                                                                                                                                                                   ar e n ee ded t o s ee t hi p i t u r e.




                                                                                                                                                                                                                                                                                                                                                                                          OH      Uc
                                                                                                                                                                                                                                                                                                                                                        N       O
                                                                                                                                                                                                                                                                                                                                                                                                  Un
                                                                                                                                                                                                                                                                                                                                            O       O
                                                                                                                                                                                                                                                                                                                                                                                      NH2
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           M1                                                                                                         Major groove        Good
                                                                                                                                                                                                                                                  H2N    DMT-MM                                                           HN                                                                  O               O           OH    Uc4
                                                                                                                                                                                                                                                                                                                                               O   S                              O                   O

                                                                                                                                                                                                                                           Uc4     CO2H                                                                                      O P O-
                                                                                                                                                                                                                                                                                                                                                     R                                                                O
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           M2                                                                                                         Major groove        Good
                                                                                                                                                                                                                                                                                                              U   c
                                                                                                                                                                                                                                                                                                                      4   C                    O
                                                                                                                                                                                                                                                                                                                                                                              O
                                                                                                                                                                                                                                                                                                                                                                                          O
                                                                                                                                                                                                                                                                                                                                                                                                  O
                                                                                                                                                                                                                                                                                                                                                                                                          O           NH2      Un4

                                                                                                                                                                                                                                                                                                                              O                 O
                                                                                                                                                                                                                                                                                                                                                    O
                                                                                                                                                                                                                                                                                                                                                            O
                                                                                                                                                                                                                                                                                                                                                                    O
                                                                                                                                                                                                                                                                                                                                                                        O
                                                                                                                                                                                                                                                                                                                                                                              O
                                                                                                                                                                                                                                                                                                                                                                                          O
                                                                                                                                                                                                                                                                                                                                                                                                  O
                                                                                                                                                                                                                                                                                                                                                                                                          O
                                                                                                                                                                                                                                                                                                                                                                                                                  O
                                                                                                                                                                                                                                                                                                                                                                                                                          O
                                                                                                                                                                                                                                                                                                                                                                                                                                NH2
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           M3                                                                                                         Major groove        Fair
                                                                                                                                                                                                                                                                                                                                                                                                          Un12

                                                                                                                                                                                         PEG
                                                                                                                                                                                                                                                        Sequence                                                                   Coupling Yield
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           N1                                                                                                         Minor groove        Excellent
                                                                                                                                                                                         UnUc

                                DNA duplex of strands containing pendent                                                                                                                  T1                       5’-TTUn4TTTTTTTTUc4TTTT
                                                                             Stabilities of DNA duplex of strands after           Circular dichroism spectra of                                                                                                                                                            dsNNA/DNA: no coupling;
                                groups prior to coupling are less stable     coupling are comparable to control.                  DNA duplex with 6 shows typical                         T2                       5’-TTUn4TTTTTTTTTUc4TTT                                                                                 dsNNA/RNA: T1>T2>T3;                                                                                                                                                         c m
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Q ui kTi e ™ and a
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                TI FF ( L ZW ) dec om pr es sor
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       c m
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Q ui kTi e ™ and a
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               TI FF ( L ZW ) dec om pr es sor
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       s c
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            ar e nee de d t o s ee t h i pi t ur e.



                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       Un4     NH
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         Q ui kTi e™ and a
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             c m
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     TI FF ( L ZW ) dec om pr ess or
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            s c
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ar e nee ded t o s ee t h i p i t ur e .




                                than control.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        s c
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             ar e nee de d t o s ee t h i pi t ur e.




                                                                                                                                  signature for B-like secondary                                                                                                                                                                                                                                                                                                                                                                       Un4     NH2
                                                                                                                                                                                                                                                                                                                           ssNNA: high yield.
                                                                                                                                                                                          T3                       5’-TTUn4TTTTTTTTTTUc4TT
                                                                                                                                  structure.                                                                                                                                                                                                                                                                                                                                                                                           Un4     CO2H                                                   Un4      C                                                              Un4
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    O                                                                       NH
                                                                                                                                                                                          Hs1                      5’-TGUn4ACGTGCGAUc4TTCG                                                                                                                                    NNA = nylon-nucleic acid
                                                                                                                                                                                                                                                                                                                           dsNNA/DNA: no coupling;                                                                                                                                                                                           DMT-MM                                                                                                                                         C
                                                                                                                                                                                          Hs2                      5’-TGUn4ACGTGCGATUc4TCG
                                          1 5’-GCATAGT T T T T T GTCTAC                                                                                                                                                                                                                                                    dsNNA/RNA: no coupling;                                                                                                                                                                                                                                                                                                                             Un4               O
                                                                                                                                                                                                                                                                                                                           ssNNA: high yield.
                                          2 5’-GCATAGT T Un Uc T T GTCTAC                                                                                                                 Hs3                      5’-TGUn4ACGTGCGATTUc4CG

                                          3 5’-GCATAGT T Un UccUn T GTCTAC                                                                                                                Hl1                      5’-TGUn12ACGTGCGAUc4TTCG
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      minor groove                                                          major groove
                                                                                                                                                                                          Hl2                      5’-TGUn12ACGTGCGATUc4TCG                                                                                                                                                                                                                                                                                                           crosslink                                                             crosslink
                                          4 5’-GCATAGT Uc UnnUccUn T GTCTAC                                                                                                                                                                                                                                                dsNNA/DNA: Hl1≈Hl2>Hl3.

                                          5 5’-GCATAGT Uc UnnUccUnnUcGTCTAC                           Single strand 3 in B-form                                                           Hl3                      5’-TGUn12ACGTGCGATTUc4CG                                                                                                                                                                                                                                                                                                                                                                                                                                                  Minor groove crosslink increases
                                                                                                      conformation with pendent                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              Tm by 17°C
                                          6 5’-GCATAGUcUnnUccUnnUccUnGTCTAC                                                                                                               Uc1                      5’-TGTACGTGCGAT Uc4TCG (16mer)
                                                                                                      groups in yellow.                                                                                                                                                                                                    No coupling observed
                                                                                                                                                                                          Uc2                      5’-TGACGTGCGAT Uc4TCG (15mer)                                                                           (negative control).


                              Thermal denaturing studies and circular dichroism measurements show stability of                                                                         Coupling of double strand was successful with Un12 + Uc4                                                                                                                                                                                                                                       Coupling occurs more efficiently between Uc4 and Un4
                              nylon-nucleic acid duplexes with DNA.                                                                                                                    but not with Un4 + Uc4.                                                                                                                                                                                                                                                                        across the minor groove than across the major groove.




                                                                                                                                                                                                                                                                                                                                                                                                                         Small piece of experimental origami
                                                                  DNA origami NA hooks with “red” and                                                                                                                                                                                                                                                                                                                       1856 DNA base-pairs                                                                                                                                                                                                                                                                  Backbone-base structure
                                                                  “blue” sequences on opposite faces.
                                                                  Additional DX tiles forming a DNA                                                                                                                                                                                                                                                                                                                         2.5nm x 17.7nm x 60.5nm                                                                                                                                                                                                                                                                  Bead for Phosphate/Ribose/Nucleoside
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      Bead for water molecule
                                                                  ribbon are added as structural                                                                                                                                                                                                                                                                                                                            2-d structure not known                                                                                                                                                                                                                                                                  Bead for Ions
                                                                  reinforcement. Entire scaffold is
                                                                  ligated for additional strength.                                                                                                                                                                                                                                                                                                                       Atomistic system                                                                                                                                                                                                                                                                            quasi-Bead for Hydrogens
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ▪   Bonds, angles not calculated during dynamics
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ▪
                                                                                                                                                                                                                                                                                                                                                                                                                           >360,000 atoms: 60,000 DNA atoms, 1836
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           Move as rigid body with parent nucleotide
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               Statistics obtained from explicit water atomistic
                                                                                                                                                                                                                                                                                                                                                                                                                            Na+ ions, 300,000 waters                                                                                                                                                                                                                                                            simulations
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               All beads are neutral, Morse potential for
                                                                                                                                                           Dispersal complexes are used to link                                                                                                                                                                                                                            Estimated 2 weeks for 15ns of simulation on                                                                                                                                                                                                                                         nonbonds (VDW + Coulomb)
                                                                                                                                                           SWNTs to DNA hooks. DNA hooks bind
                                                                                                                                                           to a 5 nt toehold and displace the
                                                                                                                                                                                                                                                                                                                                                                                                                            100 processors (4 years for 1.5 microseconds)                                                                                                                      Bond stretch: Harmonic
                                                                                                                                                           protection strand by branch migration.                                                                                                                                                                                                                        Coarse Grain system                                                                                                                                                         VBonds  1  (r  r eq ) 2
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               2
                      Assembled FETs are deposited on
                      SiO2 and contacted with Au covered
                                                                                                                                                           Increasing the length of the toehold to 7
                                                                                                                                                                                                                                                                                                                                                                                                                            ~100,000 atoms                                                                                                                                                    Angle bend: Cosine Harmonic
                                                                                                                                                           nt and switching the dispersal buffer                                                                                                                                                                                                                                                                                                                                                                                                      V Angles  1  (cos   cos  eq ) 2
                      Pd electrodes using standard ebeam                                      Process Overview                                             from Na+ to Mg 2+ results in extensive                                                                                                                                                                                                                           3 weeks for 1.5 microseconds (75x speedup)                                                                                                                                          2

                      lithography techniques. Device                                                                                                       formation of SWNT-DNA “ladders”.                                                                                                                                                                                                                                                                                                                                                                                                    Torsion: Harmonic
                      shown below has clear switching                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 VTorsions  1  1  cosn  d 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  2
                      and exhibits signal gain.
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            Hydrogen Bonds: Dreiding
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  D 5   6  cos 
                                                                                                                                                                                                                                                                                                                                                                                                                                       CRMS              Helical Parameters            Simulation Details                                                                                                                 r0 12                                      r0 10             4
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             V                                         HBond       0       r                                          r

                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            van der Waals: Morse Potential
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                               Meso    Crystal   Atoms      Rise          Twist          Length                                        CPU Time

                                                                                                                                                                                                                                                                                                                                                                                                               Meso              -     5.583     2.727   3.62 (1.28)   29.22 (8.06)   2.5 micro-sec                                     12.5 days                                                     VRij  D0 e
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        0.5 Rij R0 1 2                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               2e         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        0.5 Rij R0 1   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                              Atoms            2.727   3.023       -     3.5 (0.32)    34.69 (2.47)    25 nano-sec                                      14 days


                                                                                SWNTs labeled with “red” and
                                                                                “blue” sequences attach to
                                                                                respective hook positions.
                                                                                Orientation occurs through
                                                                                cooperative action of many hooks.
                                                                                In a one pot reaction, blue SWNTs
                                                                                will only attach at blue sites while
                                                                                reds will only attach at red sites.

                                                                                                                                                                                                                                                                                                                                                                                                               Meso helical parameters within acceptable range for BDNA
                                                                                                                                                                                                                                                                                                                                                                                                               Over 100x speedup

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