NMR Analysis of RNA Bulged Structures: Tabu Search Application in NOE Signal Assignment

Abstract

Bulges belong to the most frequently occurring RNA secondary structural elements of high functional importance. Complete recognition of their spatial structure in solution requires application of Nuclear Magnetic Resonance (NMR) spectroscopy methods. A considerable part of NMR analytical process for RNA is performed automatically. However, in resonance assignment, being the process’ first computational step, manual assistance is still essential. We propose a tabu search algorithm being a tool for an automatic resonance assignment. The assignment is determined by NOE (Nuclear Overhauser Effect) pathways, which can be constructed in aromatic/anomeric region of 2D-NOESY (Nuclear Overhauser Effect SpectroscopY) spectrum generated during NMR experiment. Computational tests demonstrate performance of the tabu search applied to the experimental spectra of RNA bulged duplexes.