Question

When forming a DNA double helix, why is base stacking more important compared to H-bonding? Can you please help me understand this?

Answer 1

The stability of the DNA double helix depends mainly on fine balance of interactions including hydrogen bonds between bases and surrounding water molecules and base stacking interactions between adjacent bases.

Base stacking is a common arrangement of nucleobases found in the three dimensional structure of nucleic acids.Bases are planar and these planes stacked excluding water and maximizing Van der Waals interactions.

The individual bases form strong stacking interactions which are major contributors to double strand stability,as base stacking more prevalent in double strands than in single strands.They are hydrophobic and electrostatic in nature and depend on the aromaticity of the bases and their dipole moments.Base stacking interactions increase with increasing salt concentraction.

Some of the hydrogen bonds must be broken during duplex formation as the inter base hydrogen bonds are formed.So,base stacking is more important in the formation of DNA double bond than H- bonding.