Monte Carlo simulation of AB-copolymers with saturating bonds

Abstract

Structural transitions in a single AB-copolymer chain where saturating bonds canbe formed between A-and B-units are studied by means of Monte Carlo computersimulations using the bond fluctuation model. Three transitions are found,coil–globule, coil–hairpin and globule–hairpin, depending on the nature of aparticular AB-sequence: statistical random sequence, diblock sequence and‘random–complementary’ sequence (one-half of such an AB-sequence is randomwith Bernoulli statistics while the other half is complementary to the first one).The properties of random–complementary sequences are closer to those of diblocksequences than to the properties of random sequences. The model (although quiterough) is expected to represent some basic features of real RNA molecules, i.e. theformation of secondary structure of RNA due to hydrogen bonding ofcorresponding bases and stacking interactions of the base pairs in helixes. Weintroduce the notation of RNA-like copolymers and discuss in what sense thesequences studied here can be considered as RNA-like copolymers.