DNA stability

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 $$3\cdot 10^{-11}$$/sec at 37C and pH 7.4 lindahl72
 * 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 $$7\cdot 10^{-13}$$/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 $$(8-40)\cdot 10^{-10}$$/sec at 60C and about $$(4-13)\cdot 10^{-10}$$/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 lindahl72b
 * Abasic sites are alkali-labile. Under mildly alkaline conditions, &beta;-elimination occurs which nicks 3' to the abasic site leaving a 5'-P on the downstream fragment
 * Under strong alkaline conditions, &delta;-elimination will occur after &beta;-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