How to find which DNA is more stable

The stability of the DNA double helix depends on a fine balance of interactions including hydrogen bonds between bases, hydrogen bonds between bases and surrounding water molecules, and base-stacking interactions between adjacent bases. Slight variations in the DNA sequence can have profound implications on the stability of the DNA duplex. For example, mutations in the base sequence that result from errors that occur during DNA replication can result in mismatches that lead to relatively unstable duplexes. This instability is exploited by proofreading enzymes which recognize the mutation and replace it with the correct nucleotide (see Mutagenesis and DNA repair). To gain an insight into DNA duplex stability, and how it is affected by changes in primary structure, scientists have studied the structure and thermodynamic stability of a variety of DNA duplexes by using a combination of physical methods including X-ray crystallography, ultraviolet (UV) melting and NMR. FACTORS INFLUENCING DNA DUPLEX STABILITY DNA duplex stability is determined primarily by hydrogen bonding, but base stacking also plays an important role. Hydrogen bonding The heterocyclic bases of single-stranded DNA have polar amido, amidino, guanidino and carbonyl groups that form a complex network of hydrogen bonds with the surrounding water molecules. Some of these bonds must be broken during duplex formation as the inter-base hydrogen bonds are formed. The overall process is one of “hydrogen bond exchange“ and the net change in enthalpy upon duplex formation is partly due to ∆H(H-bonds formed) − ∆H(H-bonds broken). For duplexes of any significant length this is an exothermic process at ambient temperature. Not surprisingly the coming together of two large oligomeric molecules is entropically unfavourable (∆S is negative). Base stacking Inter-strand hydrogen bonding is clearly important in driving the formation of DNA duplexes, but it is by no means the only contributing factor. The individual bases form strong stacking interactions which are major contributors to duplex stability, as base stacking is much more prevalent in duplexes than in single strands (Figure 1). Base-stacking interactions are hydrophobic and electrostatic in nature, and depend on the aromaticity of the bases and their dipole moments. Base-stacking interactions in nucleic acid duplexes are partly inter-strand and partly intra-strand in nature. However, it is probably more informative to consider base pairs rather than individual bases as discrete units in order to visualize the stabilizing effects of base stacking. #DNA #basePairing #doubleBounds #tripleBounds #doubleHelix