DNA and RNA isolation and purification _course readings

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					DNA and RNA isolation and purification (course
           readings 10 and 11)

I.     Genomic DNA preparation overview

II.    Plasmid DNA preparation

III.   DNA purification
       • Phenol extraction
       • Ethanol precipitation

IV.    RNA work
What do we need DNA for?

•Detect, enumerate, clone genes
•Detect, enumerate species
•Detect/sequence specific DNA regions
•Create new DNA “constructs” (recombinant DNA)

What about RNA?
  •Which genes are being transcribed?
  •When/where are genes being transcribed?
  •What is the level of transcription?
          DNA purification: overview

                                     cell harvest
cell growth                          and lysis

          DNA concentration   DNA purification
Bacterial genomic DNA prep: cell extract

                             • Detergents
                             • Organic solvent
                             • Proteases
                             • Heat

                           “cell extract”
Genomic DNA prep: removing proteins and RNA


Need to mix gently! (to avoid shearing breakage
of the genomic DNA)
Add the enzyme RNase to degrade RNA in the
aqueous layer
   2 ways to concentrate the genomic DNA

                                   70% final conc.

“spooling”          Ethanol precipitation
Genomic DNA prep in plants --
 how get rid of carbohydrates?



  (low ionic                       N+       Br-
  )                          CH3

                            (MC 6.61-6.62)
Plasmids: vehicles of recombinant DNA

          Bacterial cell

  genomic DNA         plasmids

     Non-chromosomal DNA
     Replication: independent of the chromosome
     Many copies per cell
     Easy to isolate
     Easy to manipulate
Plasmid purification: alkaline lysis


                                 DNA can’t
                                 they never
       DNA purification: silica binding

Binding occurs in presence of
high salt concentration, and is
disrupted by elution with water
DNA purification: phenol/chloroform extraction

           1:1 phenol : chloroform
 25:24:1 phenol : chloroform : isoamyl alcohol

Phenol: denatures proteins, precipitates form at
interface between aqueous and organic layer

Chloroform: increases density of organic layer

Isoamyl alcohol: prevents foaming
                 Phenol extraction
1. Aqueous volume (at least 200 microliters)
2. Add 2 volumes of phenol:chloroform, mix well
3. Spin in centrifuge, move aqueous phase to a new
4. Repeat steps 2 and 3 until there is no precipitate at
   phase interface
5. (extract aqueous layer with 2 volumes of
       Ethanol precipitation (DNA concentration)
Ethanol depletes the hydration shell surrounding DNA…
•   Allowing cations to interact with the DNA phosphates
•   Reducing repulsive forces between DNA strands
•   Causing aggregation and precipitation of DNA

•   Aqueous volume (example: 200 microliters)
    -- add 22 microliters sodium acetate 3M pH 5.2
    -- add 1 microliter of glycogen (gives a visible pellet)
    -- add 2 volumes (446 microliters) 100% ethanol
    -- mix well, centrifuge at high speed, decant liquid
    -- wash pellet (70% ethanol), dry pellet, dissolve in
       appropriate volume (then determine DNA
          DNA purification: overview

                                     cell harvest
cell growth                          and lysis

          DNA concentration   DNA purification
     DNA -------------->         mRNA       ----------

Lots of information in mRNA:

When is gene expressed?
What is timing of gene expression?
What is the level of gene expression?

(but what does an mRNA measurement really say
about expression of the protein?)

         Isolation of RNA -- Course reading 11
RNA in a typical eukaryotic cell:
10-5 micrograms RNA

80-85% is ribosomal RNA
15-20% is small RNA (tRNA, small nuclear RNAs)

About 1-5% is mRNA

     -- variable in size
     -- but usually containing 3’ polyadenylation
The problem(s) with RNA:
RNA is chemically unstable -- spontaneous cleavage of
phosphodiester backbone via intramolecular

RNA is susceptible to nearly ubiquitous RNA-degrading
enzymes (RNases)

      RNases are released upon cell lysis
      RNases are present on the skin
      RNases are very difficult to inactivate
           -- disulfide bridges conferring stability
           -- no requirement for divalent cations for
   Common sources of RNase and how to avoid them

Contaminated solutions/buffers

       TREAT SOLUTIONS WITH DEPC (when possible)

Contaminated equipment

       BAKE GLASSWARE, 300°C, 4 hours
       USE “RNase-free” PIPET TIPS
Top 10 sources of RNAse contamination
(Ambion Scientific website)

1) Ungloved hands
2) Tips and tubes
3) Water and buffers
4) Lab surfaces
5) Endogenous cellular RNAses
6) RNA samples
7) Plasmid preps
8) RNA storage (slow action of small amounts of RNAse
9) Chemical nucleases (Mg++, Ca++ at 80°C for 5’ +)
10) Enzyme preparations
Inhibitors of Rnase
DEPC: diethylpyrocarbonate

        alkylating agent, modifying proteins and nucleic

       fill glassware with 0.1% DEPC, let stand overnight
at room temp

      solutions may be treated with DEPC -- add DEPC to
0.1%, then autoclave (DEPC breaks down to CO2 and
Inhibitors of Rnase
Vanadyl ribonucleoside complexes
     competitive inhibitors of RNAses, but need to be
removed from the final preparation of RNA

Protein inhibitors of RNAse
      horseshoe-shaped, leucine rich protein, found in
cytoplasm of most mammalian tissues
      must be replenished following phenol extraction
Making and using mRNA (1)
Making and using mRNA (2)
Purifying RNA: the key is speed

Break the cells/solubilize components/inactivate RNAses
by the addition of guanidinium thiocyanate (very powerful

Extract RNA using phenol/chloroform (at low pH)

Precipitate the RNA using ethanol/LiCl

Store RNA:
      in DEPC-treated H20 (-80°C)
      in formamide (deionized) at -20°C
Selective capture of mRNA: oligo dT-

Oligo dT is linked to cellulose matrix

RNA is washed through matrix at high salt

Non-polyadenylated RNAs are washed through

polyA RNA is removed under low-salt conditions

(not all of the non-polyadenylated RNA gets
Other methods to capture mRNA

Poly(U) sepharose chromatography

Poly(U)-coated paper filters

Streptavidin beads:

   •A biotinylated oligo dT is added to guanidinium-
   treated cells, and it anneals to the polyA tail of

   •Biotin/streptavidin interactions permit isolation
   of the mRNA/oligo dT complexes
How good is the RNA prep?

The rRNA should form 2 sharp bands in ethidium
bromide-stained gels (but mRNA will not be visible

Use radiolabelled poly dT in a pilot Northern
hybridization--should get a smear from 0.6 to 5 kb
on the blot

Use a known, “standard” gene probe (e.g. GAPDH
in mammalian cells) in Northern hybridization--
there should be a sharp band with no degradation
  In vitro amplification of DNA by PCR
I.          Theory of PCR
II.         Components of the PCR reaction
III.        A few advanced applications of PCR

       a)     Reverse transcription PCR (for RNA
       b)     Quantitative real-time PCR
       c)     PCR of long DNA fragments
       d)     Inverse PCR
       e)     MOPAC (mixed oligonucleotide priming)

 Molecular Cloning, p. 8.1-8.24
              What is PCR?

• Polymerase Chain Reaction--first described in
  1971 by Kleppe and Khorana, re-described
  and first successful use in 1985
• Allows massive amplification of specific
  sequences that have defined endpoints
• Fast, powerful, adaptable, and simple*

• Many many many applications

                                    * usually
 Why amplify specific sequences?
• To obtain material for cloning and
  sequencing, or for in vitro studies
• To verify the identity of engineered DNA
• To monitor gene expression
• To diagnose a genetic disease
• To reveal the presence of a micro-organism
• To identify an individual
• Etcetera, etcetera
        What you need for PCR:

1. Template DNA that contains the “target

2. Primers: short oligonucleotides that define
   the ends of the target sequence

3. Thermostable DNA polymerase

4. Buffer, dNTPs

5. A thermal cycler
       A typical PCR program:

Denaturation: denature template strands (94°C for
2-5 minutes), can also add your DNA polymerase at
this temp. for a “hot start” (adding DNA pol to a hot
tube can prevent false priming in the initial round of
DNA replication)

Annealing: The default is usually 55°C. This
temperature variable is the most critical one for
getting a successful PCR reaction. This is the best
variable to start with when trying to optimize a PCR
reaction for a specific set of primers. Annealing
temperatures can be dropped as low as 40-45°C,
but non-specific annealing can be a problem
      A typical PCR program:

Extension: generally 72°C, this is the operating
temperature for many thermostable DNA

Number of cycles: Depends on the number of
copies of template DNA and the desired amount
of PCR product. Generally 20-30 cycles is
          How it works:
a simple PCR reaction, first cycle
                               (Can also be
                         Cycles of
                         primer annealing,
                72°C     and primer
                         extension by
        a simple PCR reaction, second cycle

     new                               like
reactions                              first
a simple PCR reaction, third cycle

        PCR animation:
              Choosing primers:
• Should be 18-25 (17-30?) nucleotides in length (giving
• Calculated melting temperature varies depending on the
method used (55-65°C using the Wallace Rule, eg. see
MC), but should be nearly identical for both primers
• Avoid inverted repeat sequences and self-
complementary sequences in the primers, avoid
complementarity between primers (‘primer dimers’)
• Have a G or C at the 3’ end (a G/C “clamp”)
• Many computer programs exist for helping meet these
criteria (ex: Biology Workbench,
  Thermostable DNA polymerases
      (See Molecular Cloning table 8-1)

• Isolated from thermophilic bacteria and archaea (T.
  aquaticus is a bacterium, not an archaeon)
• Bacterial enzymes (e.g. Taq) good for routine
  reactions and small PCR products, fidelity of
  replication is somewhat low
• Archaeal enzymes (e.g. Pfu) also good for routine
  reactions and best for cloning: 3’--5’ exonuclease
  activity provides very high fidelity, and enzymes are
  very stable to heat
               Thermal cyclers
Standard: heat block, “ramp” times fairly long (10 -20
seconds to change temperature), 30 cycle PCR lasts 2-
3 hours.
     Advantage: easily automated, heat blocks can
PCR up to 384 samples at a time
      Disadvantage: relatively slow
New: reactions are being sped up significantly
       --capillary tubes heated and cooled by blasts of
air--30 cycle-PCR done in >30 minutes (harder to
scale up)
       --fluid flow cells: channels force liquid through
temperature gradients, very fast (but still not widely
    Sources of problems in PCR
• Inhibitors of the reaction from the the
  template DNA preparation (protease,
  phenol, EDTA, etc)
• Cross-contamination by DNA from sources
  other than the template added
  – if this becomes a problem:
      • Work in a laminar flow hood (decontaminate
        using UV light 254 nm)
      • Use PCR dedicated pipettors (with barrier
        tips), PCR dedicated reagents
      • Centrifuge tubes before opening them to
        prevent spattering, pipet contamination
    Controls to include in difficult PCRs:
           Bystander template   Target   Specific   Bystander
           DNA       DNA        DNA      primers    DNA: not
Positive                                            recognized by
controls                                            primers

1          +         -          +        +          Target DNA:
                                                    known to
2          -         -          +        +          contain primer
Negativ                                             recognition
e                                                   sequences

3          -         -          -        +
4          +         -          -        +
           Hot Start of PCR reactions

•    Witholding some component of the reaction
    until the denaturing temperature is reached
•    This helps prevent non-specific priming, which
    may occur at the low temperatures (room temp.)
    -- the non-specific priming could give
    artifactual amplification as PCR block
    temperature rises

A) Wait until 94°C to add enzyme --or--
B) Use enzyme bound to an inactivating enzyme
   antibody that releases at high temperature --
C) Use wax beads containing Mg++ that can only
                 Touchdown PCR
• Useful if your primers are not 100% complementary to
your template DNA (e.g. degenerate oligos), or when
there are multiple members of the gene family you are
• Allows you to selectively amplify only the best
sequences (with the least mismatches) while minimizing
non-specific PCR products

• Start with 2 cycles at an annealing temperature about
3°C higher than the calculated primer melting
• Progressively reduce the annealing temperature by
1°C at 2 cycle intervals

 -- Very little product
 -- No PCR product
 -- Multiple bands

(see Molecular cloning,
tables 8-4 and 8-5)
III. Special applications for PCR

     A. Reverse transcription PCR (for RNA

     B. Quantitative (real-time) PCR

     C. PCR of long DNA fragments

     D. Whole genome amplification

     E. Inverse PCR

     E. MOPAC (mixed oligonucleotide
Amplification of RNA (monitor gene expression):
     reverse transcription PCR (RT-PCR)
Step 1: generate a 1st strand cDNA using reverse transcriptase
(catalyzes synthesis of DNA from an RNA template)




  Step 2: normal PCR (from cDNA) using gene-specific primers
   (real time)
The more target DNA
there is, the more probe
anneals, the more it is
cleaved (by Taq’s 5’-3’
exonuclease activity)

Fluorescence measurements
are done simultaneously
with PCR cycles, yields an
instantaneous measurement
of product levels
 Real Time
Position of the
steep part of
the curve
depending on
the amount of
template DNA
or RNA, can        template   less
measure                       template

variation over 5
or 6 orders of
 Another quantitative measure of double stranded DNA
 in a PCR reaction: binding of SYBR Green Dye

SYBR green dye

Fluorescing SYBR
green dye

                  From the Molecular Probes website
   Use of a quenching dye to reduce measurement
   of “primer dimer” artifacts in QRT-PCR

QSY quencher dye: it
absorbs fluorescence
from sybr green dyes in
the vicinity--prevents
accumulation of signal
from primer dimers
Always do your controls!
QRT-PCR using Sybr green dye fluorescence

Standard curve: what is “threshold” for specific number
of DNA molecules?

      (From the Invitrogen website)
  PCR of long sequences (>2 kb)

Long DNAs are difficult to amplify
  – Breakage of the DNA
  – Non-processive behavior of DNA
  – Misincorporation by error prone DNA
  PCR of long sequences (>2 kb)

Changes to protocol that assist in long PCR
  – Make sure DNA is exceedingly clean
  – Use DNA polymerase “cocktail”: Taq
    for it’s high activity, and Pfu for its
    proofreading activity (it can actually
    correct Taq’s mistakes)
  – Increase time of extension reaction (5-
    20 minutes, compared to the standard 1
    minute for short PCRs)
•Amplified product longer than 3 kilobases with high
•10 times fewer mutations than with conventional PCR

•Taq DNA pol (no proofreading) plus an archaeal DNA pol
(does proofreading)

•Betaine (amino acid analogue with several small
tetraalkyammonium ions)--reduces non-specific
amplification products--reduces non-complementary
primer-template interactions? (unknown how it works)
Whole genome amplification: multiple
displacement amplification (MDA)

Applications: forensics, embryonic disease
diagnosis, microbial diversity surveys, etc.

How it works:
Strand-displacement amplification used by
rolling-circle replication systems.

Phi29 DNA polymerase (very low error rate) and
random hexamer primers, low temperature!
Whole genome amplification : multiple displacement
amplification (MDA)

20-30 micrograms human DNA can be recovered from
1-10 copies of the human genome

Distribution of products appears to be random sampling
of the available template (and this is good!)
Inverse PCR:
 “out” from
                   “Vectorette” PCR

First primer: known sequence
Vectorette primer: only in vectorette-ligated
sequence--it cannot anneal until there is a single
round of primer extension from the specific primer
MOPAC: Mixed oligonucleotide primed
      amplification of cDNA
If you only have a protein sequence, and you want to
    clone the gene for the protein:

1. Design oligonucleotides based on deduced mRNA
   (and DNA) sequence (but since multiple codons can
   encode the same amino acid, this gets complicated
2. program your oligo synthesizer to make primer sets
   that are randomized for the degenerate positions of
   each codon
3. use universal nucleotides like inosine, which base
   pairs with C, T, and A (limits degeneracy)
4. Do your PCR and hope for the best

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