DNA stability
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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
/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
/sec at 37C and 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
/sec at 60C and about 
/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
- Lindahl T and Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry 1972 Sep 12; 11(19) 3610-8. pmid:4626532.
- 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. pmid:4559796.
- Frederico LA, Kunkel TA, and Shaw BR. Cytosine deamination in mismatched base pairs. Biochemistry 1993 Jul 6; 32(26) 6523-30. pmid:8329382.
