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

Author

Szachniuk, M. ; Popenda, L. ; Gdaniec, Z. ; Adamiak, R.W. ; Blazewicz, J.

Author_Institution

Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznan, Poland

fYear

2005

fDate

14-15 Nov. 2005

Firstpage

1

Lastpage

7

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.

Keywords

NMR; NOE path; RNA tertiary structure; bulge motif; Crystallization; Crystallography; DNA; Magnetic analysis; Nuclear magnetic resonance; Organisms; RNA; Shape; Signal analysis; Spectroscopy; NMR; NOE path; RNA tertiary structure; bulge motif;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Intelligence in Bioinformatics and Computational Biology, 2005. CIBCB '05. Proceedings of the 2005 IEEE Symposium on

Print_ISBN

0-7803-9387-2

Type

conf

DOI

10.1109/CIBCB.2005.1594914

Filename

1594914