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| author | bryan <kanzure@gmail.com> | 2012-07-10 21:38:31 -0500 |
|---|---|---|
| committer | bryan <kanzure@gmail.com> | 2012-07-10 21:38:31 -0500 |
| commit | 08bf5fa539de2a79ca465885984bcde539e36af6 (patch) | |
| tree | 4f1d51a26b122e5efdc7d187f82c562203b4ef2d | |
| parent | 8acac5b8f9814348100ba6a44c972cc1e7cb2dca (diff) | |
| download | diyhpluswiki-08bf5fa539de2a79ca465885984bcde539e36af6.tar.gz diyhpluswiki-08bf5fa539de2a79ca465885984bcde539e36af6.zip | |
notes on enzymatic DNA synthesis
| -rw-r--r-- | polymerase/notes.mdwn | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/polymerase/notes.mdwn b/polymerase/notes.mdwn index 7bdec5b..533b6ea 100644 --- a/polymerase/notes.mdwn +++ b/polymerase/notes.mdwn @@ -5,6 +5,50 @@ * in vivo DNA synthesis * in vivo gene synthesis +# Enzymatic DNA synthesis + +http://groups.google.com/group/enzymaticsynthesis + +http://github.com/kanzure/enzymaticsynthesis + +Mechanisms of attack: + + (1) template DNA/RNA + (2) selected dNTP + - electronic control to force a specific dNTP to be selected + +Direct control of polymerase + + 1) template shams + 2) forced misincorporation + +crazy ideas: + +1. electronic control of polymerase +2. nucleotide gun made out of a nanotube pointed at the finger domain of dna polymerase +3. single-polymerase water droplet & add in a single dNTP at a time +4. physical display of dNTP as template for current base addition (i.e., on a stick) +5. a protein that can undergo conformational changes that polymerase thinks represents the template strand +6. pull/push a template through DNA polymerase to control which dNTP it should be selecting for +7. protein-template DNA polymerase, where the polymerase itself has a giant protein that enzymatically encodes dNTP information +8. graph grammar rules of valid thumb/fingers/pad/palm domains of polymerases to generate a library of possible polymerase variants +9. mechanical pressure on polymerase +10. ultrasound + +mRNA polyadenylation (addition of adenosine monophosphates to an mRNA fragment) + +"Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA or DNA primer (for temporary DNA elongation)." + +What is the actual change in DNA polymerase that decides whether a base should be accepted or not? +Is primase template-dependent? + +replicase - RNA-dependent RNA polymerase + + +In the transfer RNA (tRNA) CCA-adding enzyme, both the tRNA backbone and the protein contribute to the specificity of the incoming nucleotide (24). Eukaryotic translesion synthesis polymerases thus use a variety of means of DNA polymerization, which include Watson-Crick base-pairing by Pols n (25) and kappa (26), Hoogsteen base-pairing by Pol?? (18, 22), and protein template-directed synthesis by Rev1. + +primer-template slippage + # tdt EC2.7.7.31 -- terminal deoxynucleotidyltransferase TDT |