A GENERALISATION OF THE KAUFFMAN BRACKET POLYNOMIAL TO DETERMINE AND ANALYSE STRUCTURAL ELEMENTS IN A RNA SECONDARY STRUCTURE

Abstract

In this work, we    use methods of knot theory to describe and analyze structural elements of a RNA secondary structure by construction of a new generalisation of the classical Kauffman bracket polynomial, which factorisation characterises these structural elements. To this end, we develop a mathematical model of RNA endowed with a topology invariant (RKB polynomial) that allows to determine a type, number and characteristics of standard structural elements that form the  RNA secondary structure. In order to define the RKB polynomial, we introduce a new skein relation to smooth hydrogen bonds and a new technique to color nucleotides, and use the known skein relation of the Kauffman bracket polynomial. Note that the proposed technique to color nucleotides allows to take into account the positional relationship of structural elements, which can be used to investigate properties of RNA.   Invariance of the RKB polynomial is shown. Computation of  the   RKB polynomial by the given Dot-Bracket notation is implemented as a small Mathematica program. Using RKB polynomials calculated by our program,  we analyze some RNA secondary structures presented in the   bpRNA-1m database. The obtained results agree with the real data.