Studium molekulových interakcí v ribosomální RNA a ribozymech

RNDr. Mgr. Arnošt Mládek, Ph.D.

Bakalářská práce

Analysis of molekular interactions in ribosomal RNA and ribozymes

Abstract:

Trans Hoogsteen/Sugar Edge (Ho/SE) pairing patterns are of key importance at stabilizing loop geometries in RNA. The goal of this thesis is to provide a detailed quantum chemical characterization of this base pair family both in gas-phase and aqueous solution. DFT-optimized geometries and RI-MP2 interaction energies is reported for the 10 crystallographically identified members of the family. Balance of intermolecular stabilizing forces in the trans Ho/SE base pairs are very similar to that of trans Watson-Crick/Sugar edge (WC/SE) base pairs. Thus, albeit the electron correlation component remarkably contributes to the stabilization, its relative importance is noticeably lower than in the cis WC/SE or cis and trans SE/SE edge base pairs. In two pairs, i.e. C/rC and G/rG, the electrostatic component is clearly superior to the correlation contribution, due to the fortunate orientation of the molecular dipoles of the component bases. In contrast, in the A/rG pair, which is the most stable and biologically most significant member of the family, the correlation component is the leading stabilizing force.

Klíčová slova

Hoogsteen, Sugar Edge, rRNA, ribozymes, isostericity

Jazyk práce: čeština

Datum vytvoření / odevzdání či podání práce: 14. 5. 2008

Obhajoba závěrečné práce

• Obhajoba proběhla 30. 6. 2008
• Vedoucí: prof. RNDr. Jiří Šponer, DrSc.

Masarykova univerzita

Přírodovědecká fakulta

Bakalářský studijní program / obor:
Fyzika / Biofyzika