Question

What parameters increase the stability of a dsDNA. Briefly explain each one.

A. Environmental (extrinsic) parameters:

B. Sequence-based (intrinsic, inherent) parameters:

Answer 1

Answer:

A. Environmental (extrinsic parameters):

• Hydrogen bonding with surrounding water molecules helps in the stability of Double stranded DNA.
• High salt concentration also plays an important role in confering stability to dsDNA. Specifically, high concentrations of divalent cations such as Mg²⁺ confer stability rather than monovalent cations such as Na⁺.
• Temperature is also an important factor that determines stability of dsDNA. Increase in temperature disrupts the Hydrogen bonds between dsDNA and the surrounding water molecules as well the hydrogen bonds between the nucleotides of the complimentary strands.

B. Sequence-based (intrinsic, inherent) parameters:

Two important intrinsic parameters play key role in determining the stability of dsDNA, They are:

• Interchain Hydrogen bonding. Hydrogen bonds between the Nucleotides of the complimentary strands that make up the dsDNA. Among the nucleotides Adenine (A), Thymine (T),Guanine (G) & Cytosine (C), A & T form two hydrogen bonds while G & C form three hydrogen between them. dsDNA becomes more stable with increase in teh GC content in the DNA. The prevalence of three hydrgen bonds between the bases (G & C) keeps the two strands together more strongly than occurance of two hydrogen bonds between A & T. More the GC content, stabler will be the dsDNA.
• Base stacking interactions. These are hydrophobic and electrostatic in nature. These strong base stacking interactions between the bases present within a strand (intra-chain) and between the bases present in the complimentary strands (inter-chain) are also very crucial in confering stability to dsDNA. Base stacking interactions depend on the aromaticity of the bases.