Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations

✍ Scribed by Jakub Nový; Stanislav Böhm; Jarmila Králová; Vladimír Král; Marie Urbanová

• Publisher: Wiley (John Wiley & Sons)
• Year: 2008
• Tongue: English
• Weight: 322 KB
• Volume: 89
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.20875

✦ Synopsis

Abstract

Variations in the structure of d(GGGA)~5~ oligonucleotide in the presence of Li^+^, Na^+^, and K^+^ ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3‐Lee‐Yang‐Parr functional at the 6‐31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)~5~ in the presence of Li^+^ forms a nonplanar single tetramer, with angles of 102° and 171° between neighboring guanine bases. This tetramer changes its geometry at temperatures >50°C, but does not form a quadruplex structure. In the presence of Na^+^, the d(GGGA)~5~ structure was optimized to almost planar tetramers with an angle of 177° between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60°C. The Hartree–Fock energies imply that d(GGGA)~5~ prefers to form complexes with Na^+^ rather than Li^+^. The d(GGGA)~5~ structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li^+^ < Na^+^ < K^+^. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 144–152, 2008.

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