Re: What is the stability of RNA/DNA duplexes at different pH's

Glenn,

An RNA-DNA hybrid forms an A-form duplex, which differs from the more 
typical B-form duplex in some subtle way that don't matter for this purpose. 
I will tell you immediately that duplex stability depends on both 
interstrand base pairing and intrastrand base stacking, with the former 
being more affected by pH changes than the latter. At pH 7, 99.99% of DNA 
and RNA bases are in the correct protonation states (keto and amino forms) 
for proper hydrogen bond formation.  There are basically three types of 
groups involved in base pairing: the exocyclic NH2 groups, the carbonyls, 
and the ring hydrogens. The exocyclic NH2 groups are always hydrogen bond 
donors and have pKas that are so far away from physiological conditions as 
to be not relevant. The same is true for the carbonyl groups, except they 
are always hydrogen bond acceptors. The ring hydrogens have pKas as follows: 
A - 3.5; C - 4.2; G - 9.4; T - 9.4.  So you can see that below pH 3 A's and 
C's start to become deprotonated and thus no longer hydrogen bond donors, 
and above pH 10 G's and T's become protonated and thus no longer hydrogen 
bond acceptors.  The loss of interstrand base pairing will reduce overall 
duplex stability.

Chris