Structural basis for recognition of Co2+ by RNA aptamers

Wrzesinski, J and Jozwiakowski, Stanislaw (2008) Structural basis for recognition of Co2+ by RNA aptamers. FEBS Journal, 275 (8). pp. 1651-1662. ISSN 1742-464X

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Abstract

Co 2+ binding RNA aptamers were chosen as research models to reveal the structural basis underlying the recognition of Co 2+ by RNA, with the application of two distinct methods. Using the nucleotide analog interference mapping assay, we found strong interference effects after incorporation of the 7-deaza guanosine phosphorotioate analog into the RNA chain at equivalent positions G27 and G28 in aptamer no. 18 and G25 and G26 in aptamer no. 20. The results obtained by nucleotide analog interference mapping suggest that these guanine bases are crucial for the creation of Co 2+ binding sites and that they appear to be involved in the coordination of the ion to the exposed N7 atom of the tandem guanines. Additionally, most 7-deaza guanosine phosphorotioate and 7-deaza adenosine phosphorotioate interferences were located in the common motifs: loop E-like in aptamer no. 18 and kissing dimer in aptamer no. 20. We also found that purine rich stretches containing guanines with the highest interference values were the targets for hybridization of 6-mers, which are members of the semi-random oligodeoxyribonucleotide library in both aptamers. It transpired that DNA oligomer directed RNase H digestions are sensitive to Co 2+ and, at an elevated metal ion concentration, the hybridization of oligomers to aptamer targets is inhibited, probably due to higher stability and complexity of the RNA structure.

Item Type: Article
Schools and Departments: School of Life Sciences > Sussex Centre for Genome Damage and Stability
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Depositing User: Stanislaw Jozwiakowski
Date Deposited: 06 Feb 2012 20:37
Last Modified: 24 Jul 2012 10:33
URI: http://sro.sussex.ac.uk/id/eprint/27054
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