Difference between revisions of "DNA stability"

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* Single stranded DNA deaminates significantly faster (> 100 times) than double stranded DNA
 
* Single stranded DNA deaminates significantly faster (> 100 times) than double stranded DNA
 
* Mispaired Cs (C:C and T:C) are 1-2 orders of magnitude more likely to deaminate than in double stranded DNA (similar to single stranded DNA)
 
* Mispaired Cs (C:C and T:C) are 1-2 orders of magnitude more likely to deaminate than in double stranded DNA (similar to single stranded DNA)
* The rate of deamination of C mispairs was around <math>(8-40)\cdot 10^{-10}</math>/sec at 60C and at 37C, it is about <math>(4-13)\cdot 10^{-10}</math>/sec
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* The rate of deamination of C mispairs is around <math>(8-40)\cdot 10^{-10}</math>/sec at 60C and about <math>(4-13)\cdot 10^{-10}</math>/sec at 37C
  
 
==Strand cleavage==
 
==Strand cleavage==
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#lindahl72b pmid=4559796
 
#lindahl72b pmid=4559796
 
</biblio>
 
</biblio>
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[[Category:DNA]]

Latest revision as of 11:31, 27 April 2007

Although DNA is generally viewed as a stable molecule, many conditions can cause loss of DNA bases or strand breakage.

Depurination

  • Depurination involves the loss of purine bases forming abasic sites
  • Depurination is one of the two limiting factors in chemical synthesis of long DNA oligos (the other is coupling efficiency)
  • DNA under physiological conditions has been estimated to depurinate at a rate of Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 3\cdot 10^{-11}} /sec at 37C and pH 7.4 [1]
  • Heating DNA for 10m@100 at pH 7.0 leads to about 1 apurinic site per 1000 base pairs
  • The activation energy of depurination is around 29 kcal/mol
  • Higher temperatures lead to faster depurination
  • Denatured DNA depurinates at about 4 times the rate of dsDNA @ pH 7.4
  • Methylated As (6-methyladenine) found in bacteria are depurinated 4 times faster than the unmethylated purine bases
  • Depurination decreases at higher pH (thus acidic conditions favor depurination)
  • Depurination proceeds more rapidly in buffers of low ionic strength
  • Depurination is correlated with lower transformation efficiency
  • Depurination is independent of sequence

Deamination

  • Cytosine can be spontaneously deaminated to form uracil.
  • Cytosine in native DNA is estimated to deanimate with a rate constant of Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 7\cdot 10^{-13}} /sec at 37C and Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 10^{-10}} /sec at 70C
  • Single stranded DNA deaminates significantly faster (> 100 times) than double stranded DNA
  • Mispaired Cs (C:C and T:C) are 1-2 orders of magnitude more likely to deaminate than in double stranded DNA (similar to single stranded DNA)
  • The rate of deamination of C mispairs is around Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle (8-40)\cdot 10^{-10}} /sec at 60C and about Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle (4-13)\cdot 10^{-10}} /sec at 37C

Strand cleavage

  • Under physiological conditions (pH 7.4, ionic strength of 150mM with 10mM Mg++ ions), the lifetime of a phosphodiester bond at an abasic site is 190 hours @ 37C [2]
  • Abasic sites are alkali-labile. Under mildly alkaline conditions, β-elimination occurs which nicks 3' to the abasic site leaving a 5'-P on the downstream fragment
  • Under strong alkaline conditions, δ-elimination will occur after β-elimination which completely removes the abasic site leaving a 3'-P on the upstream fragment and a 5'-P on the downstream fragment
  • Amines (such as amino acids or polyamines like putrescine, spermidiine, and spermine) greatly increase the rate of strand breakage at abasic sites

References

  1. Lindahl T and Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry. 1972 Sep 12;11(19):3610-8. PubMed ID:4626532 | HubMed [lindahl72]
  2. Lindahl T and Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry. 1972 Sep 12;11(19):3618-23. PubMed ID:4559796 | HubMed [lindahl72b]
  3. Frederico LA, Kunkel TA, and Shaw BR. Cytosine deamination in mismatched base pairs. Biochemistry. 1993 Jul 6;32(26):6523-30. PubMed ID:8329382 | HubMed [frederico93]
All Medline abstracts: PubMed | HubMed