Molecular recognition by van der Waals interaction between polymers with sequence-specific polarizabilities

Abstract

We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each polymer has a quenched-in polarizability sequence which reflects, for example, the polynucleotide sequence of a double-stranded DNA molecule, we study the van der Waals interaction energy between a pair of such polymers with rod-like structure for the cases where their respective polarizability sequences are (i) distinct and (ii) identical, with both zero and non-zero correlation length of the polarizability correlator along the polymer backbones in the latter case. For identical polymers, we find a novel r −5 scaling behavior of the van der Waals interaction energy for small inter-polymer separation r, in contradistinction to the r −4 scaling behavior of distinct polymers, with furthermore a pronounced angular dependence favoring attraction between sufficiently aligned identical polymers. Such behavior can assist the molecular recognition between polymers.

Theory of phase segregation in DNA assemblies containing two different base-pair sequence types

“…Here, to follow one specific line of enquiry, we have assumed that the difference of energies relies exclusively on the base-pair sequence-dependent patterns of helical distortions away from an ideal helix. This is not to say that there could be mechanisms relying on local base pair dependent interactions [6,17,18] playing a role. The extent of such a role has yet to be ascertained.…”

“…These proposed systematic experimental investigations should allow us to better understand the interactions involved in homology recognition. Indeed, our first goal would be to try to fit the parameters of this current model to such data, before considering other possible candidate mechanisms of homology recognition [6,17,18]. Notably, such studies would be far-reaching, as the nature of such forces may be important in initiating critical biological processes such as homologous recombination.…”

“…Alternately, preferential pairing between identical DNA sequences might be, in some part, due to interactions that depend locally on the type of base pair content [6,17,18]. Here, the interaction energy between two like base pairs has lower interaction energy than two non-alike ones.…”

“…An alternate mechanism utilising secondary hydrogen bonding was proposed in [17]. Sequence specific variations in van der Waals interactions might also be responsible [18]. Such mechanisms would also be influenced by the base-pair specific pattern of DNA distortions and are manifestly helix-structure-dependent forces.…”

Equivalence between particles and fields: A general statistical mechanics theory for short and long range many‐body forces

“…In general, whether for molecules, colloids, bio‐molecules, supra‐molecules , or nano‐particles, their interaction potentials can be, to some extend, split into repulsive and attractive parts. The repulsive part for non‐charged molecules or particles is generally of the order of a couple of angstroms, while the attractive part, even if it is of long range at the molecular level , is of the order of a couple nanometers . Even for colloidal charged particles, at infinite dilution, the colloidal electrical double layer (EDL), i.e., the thickness of the electrolyte layer next to the colloidal particle that completely screen the colloidal charge, is generally below 20 nm .…”