Download NA stabilization

Forces stabilizing Nucleic Acid Structures
Sugar –Phosphate chain: Reasonably strain free.
Conformationally relaxed arrangement of sugar phosphate
backbone in double helices.
Glycosidic bonds: syn or anti conformations. Mostly anticonformation
Sugar Ring: C2’ endo conformation in B-DNA and C3’ endo in
some RNA structures.
Base Pairing:
Standard Watson Crick base Pairind is most preferred.
Other kind of pairings do occur in certain DNA and RNA structures.
Watson Crick Base pairs are most stable as demonstrated by Lord and
Rich by IR spectroscopy.
IR spectrum of N-H bond.
But H-bonds do not stabilize DNA structure:
DNA is denatured in non-polar solvents (ethanol) which generally
stabilize the H-bonding.
Base Stacking and hydrophobic interactions:
The major force involved in the stabilization of nucleic acid
structures.
Nucleic acid bases stack in aqueous solution
The aggregation of bases can be monitored by measuring their
osmotic coefficient (a colligative property)
Destabilization of stacking by heating leads to hyperchomism
(increase in the absorbance).
The unstaking of the single stranded poly A by heat is a noncooperative conformational change
The stacking is very specific to the bases and the hydrophobic
interactions responsible for this interaction is poorly understood
Ionic interaction
Stabilization of phosphate groups by cations.
Divalent cations like Mg 2+ play significant role in stabilizing
the nuclein acis structures.