Q2.1 - 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

In the structure of Nucleic acids the nucleobases (nucleotide and bases) are arranged is a specific form.This form of arrangement is called Base stacking.It simply refers to the bond formed between the adjacent bases.

These nitrogenous bases of (A,T,C.G) pairing in DNA are in planes in geometry.The bases planes stack with one another.This form of arrangement give rooms for more Van der Waals interactions in the plane of the bases.Although the Van der Waals are weak interactions,the bond ensure that these bases are braided or twisted together to give maximum energy,to maintain stability of the bases,and therefore of DNA structure

Therefore in water and other aqueous solution the stability of structure of DNA is enhanced by the base stacking,(coiling or twisting)with maximum van der waals interaction among the bases, than the hydrogen bonds formed between bases.Generally there are more stacking among G-C,than A-T,thus the former pairing contribute more the structural stability than the latter (A-T)