4. Imagine yourself as a protein who would like to find your DNA sequence you’d like to bind. Consider what it would take for you to "read" a nucleotide and the atomic interactions involved (i. e. charge-charge, H-bond, or van der Waals). First and as you (a protein) approach DNA, which is the first and strongest force you’d encounter and why (if needed, you can draw a picture)? You will find details for this answer in section 3. After that, what is the order of encounter for molecular forces as protein and DNA come together? Who are the strong interactions and who are the weaker ones?

Explanation:

Protein molecules binding to DNA initiate sequences of biochemical transitions that control and regulate all major process in the living cells

These protein molecules strongly bond to special sequences of DNA known as specific binding sites

Theoretically , there are two main components of binding forces

- One of them is purely electrostatic attraction between oppositely charged DNA and protein molecules that are mostly sequence independent

- Other one comes from particular DNA sequence that strengthens the attraction of protein molecules

The origin of this increased affinity is due to combination of van der waals , hydrogen , covalent and steric interactions as well as electrostatic charge patterns recognition

Some studies has suggested that there is an additional statistical interaction potential between protein and DNA molecules. Source of this interaction is due to the specific structure and symmetry of DNA sequences to which protein molecule binds

DNA sequences with repeated homogeneous segments (A:T or G:C) have stronger affinity for association to DNA binding proteins as compared to heterogeneous sequences

3 types of interactions takes place on encounter of protein and DNA molecule which are van der waals forces , hydrogen bonds between complimentary organic bases (base pairs) and hydrophobic interactions between the nitrogenous bases and the surrounding sheath of water

Of all these forces van der waals forces are strongest and hydrophobic interaction between the nitrogenous bases and surrounding sheath of water is the weakest .