The Biophysics of DNA-Protein Interactions

DNA or deoxyribonucleic acid plays an important role in all living beings, being responsible for storage, duplication and realization of genetic information. DNA molecules possess a double-helical structure with two long polymer chains and complementary chemical structures. Genetic information is encoded through the sequence of the nitrogenous bases adenine, guanine, thymine and cytosine (A, G, T, C). Adenine and thymine are joined by a double bond and cytosine and guanine by a triple bond. Each base pair has a chemical weight of about 600 Da. Although there is enormous versatility in living creatures, the primary structure of DNA remains the same across species. The two complementary strands facilitate DNA replication during cell division, acting as templates for new polynucleotide chains.

The functions of DNA cannot be realized without protein molecules. Proteins are polymers of amino acids, folded into specific shapes and usually having 100 to 1000 amino acids in length. DNA is covered with proteins in cells which interact either with specific base-pair sequences or any sequence. These proteins have positive charge attracting them to the double helix or hydrophobic amino acids and specific hydrogen-bonding groups. Their functions vary. For example, histones in human cells help bend the double helix to allow it to fit inside the nucleus. Others mark specific sequences to trigger certain actions or burn chemical fuels to repair and replicate the double helix.

Enzymes are proteins which perform catalytic functions. They are often used to alter DNA structure in vitro for genetic engineering. In the cell, specialized enzymes are able to alter the double-helix topology and are known as topoisomerases. Proteins binding to DNA usually restructure the double helix. There are various categories of such proteins:

Regulatory: They bind to specific short DNA sequences (<20 bp in length) and act as landmarks for starting transcription and other processes.

Architectural: They help to package DNA without much sequence dependence.

Catalytic: They “cut” and “paste” DNA, helping in repair by breaking and resealing covalent bonds in the base pairs.

DNA sequence processing: They move processively along the DNA backbone for replicating or unwinding.

Binary chemical reaction kinetics for DNA-protein interactions are: P + D ↔ C where P is the protein, D is the binding site and C is the complex formed. The chemical forward rate constant for their interaction (kon) is approximately 109 M-1s-1 per unit concentration (at room temperature). This rate can be increased if there is also a ‘searching’ component involved for a particular binding site in the long DNA chain. There is also a concentration-dependent rate of dissociation of the DNA-protein complex (koff). The strength of the binding, therefore, is described through the ratio between koff and kon. The bound state has less free energy compared to the unbound state.

Salt-concentration dependence: DNA-protein interactions involve the rearrangement of many molecules. Proteins make multiple non-covalent bonds with the double helix, with the negatively charged phosphates in the DNA backbone attached to positively charged groups in the protein molecule. During the dissociation of the complex, free energy is released due to counterions, which affects the binding strength. Lower concentration of the salt leads to stronger binding.

Cooperativity: It refers to the overall effect associated with two binding events happening at the same time. For example, if the total free energy is lowered when two proteins bind to adjacent sites in the DNA molecule, the interaction is called cooperative, otherwise anticooperative. This can be used to describe polymerization in which proteins bind to adjacent sites along the DNA molecule. It has also been found that a protein bound at one site may affect the binding process of another protein up to 15 base-pairs away.

Force effect: Tension in the DNA strand has an effect on its binding with proteins. There is also mechanical change in the molecule when a protein binds to it. Possibly, kon reduces with increase in tension and koff increases. In case of DNA looping, the effect increases.

DNA-protein interactions are essential for life and cellular processes. The biophysics of DNA continues to be a promising field for further research, with studies involving the behavior of DNA under various conditions and its role in gene regulation.