Question

Hydrogen bonds can form with bases on the opposite DNA strands in the double helix, or between the bases and H2O in the single stranded conformation. Considering that the double helix is the most stable conformation in water, how does this observation support the conclusion that base stacking contributes more to helix stability than interbase hydrogen bonding?Hydrogen bonds can form with bases on the opposite DNA strands in the double helix, or between the bases and H2O in the single stranded conformation. Considering that the double helix is the most stable conformation in water, how does this observation support the conclusion that base stacking contributes more to helix stability than interbase hydrogen bonding?

Answer 1

Answer:

• The stability of DNA depends on hydrogen bonds that are formed with bases on the opposite DNA strands in the double helix, or between the bases and H2O in the single stranded conformation.
• DNA duplex stability depends primarily by hydrogen bonding, but base stacking contributes more to helix stability than interbase hydrogen bonding

First we consider hydrogen bonding:

• The bases of single-stranded DNA are heterocyclic and have polar groups( amido, amidino, guanidino and carbonyl) that forms hydrogen bonding with the surrounding water molecules.
• During duplex formation, these bonds are broken because inter-base hydrogen bonds are formed.
• This is hydrogen bond exchange and the net change in enthalpy during duplex formation is due to difference between bonds formed and bonds broken.

Now come to base stacking:

• DNA duplex stability depends primarily by hydrogen bonding, but base stacking contributes more to helix stability than interbase hydrogen bonding because base stacking is more prevalent in duplex formation than in single strand formation.
• Base stacking interactions are hydrophobic and electrostatic in nature. These interactions depend on the aromaticity of the bases and also their dipole moments.
• Base-stacking interactions in DNA and RNA are partly inter-strand and partly intra-strand in nature.
• Base stacking stabilization depends on the DNA sequence.
• Therefore, some combinations of base pairs form more stable interactions than other combinations.
• Thus, base-stacking interactions that are nearest neighbour determine more duplex DNA stability.
• Base stacking interactions in DNA is depends on conformations of five membered rings of the backbone phosphate-sugars.
• Base-stacking interactions also depends on salt concentration.
• Therefore, these interactions increases with more salt concentration because more salt concentration will mask the destabilization of repulsion of charge between the 2 negative charge phosphodiester backbone.
• Duplex DNA stability increases with high salt concentration.
• Divalent cations, for example Mg2+ are more stable than Na+ ions and metal ions bind to specific place on the DNA duplex.

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