Scattering of ultrashort laser pulses on pseudoknots RNA

The paper theoretically models the scattering spectra of ultrashort laser pulses on an RNA pseudonode and considers the possibility of using the obtained data in genome analysis. Several configurations of pseudo-RNA nodes were  selected as a sample for theoretical modeling of the interaction of a laser pulse with matter: a hairpin, a double loop, and a spiral junction. The study of such structures is interesting for the analysis of the DNA genome, as well as for  the study of functions such as viral replication, RNA splicing and RNA editing. At the moment, the study of such structural features is difficult, existing methods cannot give an accurate result, especially on long sections of the  molecule. In this paper, the interaction of an ultrashort laser pulse with a molecule of four variants is theoretically modeled, when the RNA does not have a pseudonode and when there are hairpins and loops in the structure. The  results obtained show the expediency of using laser pulses as a method for determining such structures.