Question

Describe 2 reasons why the DNA major groove offers more specificity for protein binding.

Answer 1

DNA has two grooves namely major and minor grooves. Major grooves occur where the backbones are far apart whereas minor grooves occur where they are close together. The protein binding to DNA occurs to both the major and minor grooves but there is more specificity towards the major groove for the following reasons:

1. The DNA transcription process occurs either by binding the RNA polymerase to a protein directly or through mediator proteins to begin the transcription or binding to the enzymes which alter the histones allowing the DNA to bind to the polymerase. These protein binding to the DNA bases are more available at the major groove to read the sequence of DNA.

2. The protein binding to DNA require Electrostatics forces, Hydrogen bonding and Vander waal forces. Among which the hydrogen-bonding is the main for DNA sequence reading and accounts the highest donor group for protein and acceptor group for DNA in the major groove.