|MadSci Network: Molecular Biology|
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
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