DNA stability

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(New page: 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 f...)
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==Depurination==
==Depurination==
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* Depurination involves the loss of purine bases forming abasic sites.
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* Depurination involves the loss of purine bases forming abasic sites
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* Depurination is one of the two limiting factors in chemical synthesis of long DNA oligos (the other is coupling efficiency).
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* Depurination is one of the two limiting factors in chemical synthesis of long DNA oligos (the other is coupling efficiency)
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* DNA under physiological conditions has been found to depurinate at a rate of <math>4\cdot 10^{-9}</math>/sec at 70C and pH 7.4 <cite>lindahl72</cite>.
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* DNA under physiological conditions has been estimated to depurinate at a rate of <math>3\cdot 10^{-11}</math>/sec at 37C and pH 7.4 <cite>lindahl72</cite>
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* Heating DNA for 10m@100 at pH 7.0 leads to about 1 apurinic site per 1000 base pairs
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* The activation energy of depurination is around 29 kcal/mol
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* Higher temperatures lead to faster depurination
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* Denatured DNA depurinates at about 4 times the rate of dsDNA @ pH 7.4
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* Methylated As (6-methyladenine) found in bacteria are depurinated 4 times faster than the unmethylated purine bases
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* Depurination decreases at higher pH (thus acidic conditions favor depurination)
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* Depurination proceeds more rapidly in buffers of low ionic strength
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* Depurination is correlated with lower transformation efficiency
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* Depurination is independent of sequence
==Deamination==
==Deamination==

Revision as of 20:20, 17 April 2007

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

Contents

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 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.

Strand cleavage

  • 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

References

  1. Lindahl T and Nyberg B. . pmid:4626532. PubMed HubMed [lindahl72]
  2. Frederico LA, Kunkel TA, and Shaw BR. . pmid:8329382. PubMed HubMed [frederico93]
All Medline abstracts: PubMed HubMed
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