Development of new parameters for structure determination and dynamic investigations on biomacromolecules by NMR

Nuclear magnetic resonance (NMR) spectroscopy is unique in the content of structural as well as dynamic information that it can provide at atomic resolution. The aim of this PhD-thesis was to contribute to the understanding of biochemical processes by means of NMR-spectroscopic techniques, targeting specific problems as well as contributing to the general understanding and providing new, widely applicable methods. The main focus was on the structural as well as dynamic study of ribonucleic acids (RNA). A new structural NMR method was developed aimed at the determination of the glycosidic torsion angle [chi] in RNA, which defines the relative orientation of the nucleobases in respect to the ribose moiety (Duchardt et al., 2004). [Chi] was derived from the angle dependence of carbon-hydrogen dipole-dipole, nitrogen chemical shift anisotropy cross-correlated relaxation rates (gamma-rates). Method development comprised the design of a novel NMR experiment, the [gamma](HCN), as well as the introduction of [gamma] versus [chi] parameterization curves. The novel method provides an accuracy of around 10 degrees or better, comparable to the precision of conventional angle determination techniques. In contrast to conventional methods, the [gamma](HCN) is sensitive to molecular size and will therefore proof beneficial in the investigation of larger RNAs by NMR Apart from this methodological contribution to RNA structure determination, the dynamic properties of the abundant YNMG RNA tetraloop motif (with Y=C or U; N= any base; M=C or A) were studied in a residue specific manner by means of ¹³C NMR relaxation measurements. The dynamics of the extraordinarily stable cUUCGg motif were compared to the less stable uCACGg hairpin, which forms the stem-loop D (SLD) in the regulatory 5'-cloverleaf of coxsackievirus 3B.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemistry.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Duchardt, Elke, 1975-

Advisor dc:contributor.advisor

• Harald J. Schwalbe.

• Chemistry.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/30207

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/30207