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Báo cáo khoa học: Structural basis for recognition of Co2+ by RNA aptamers

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 interfer-ence mapping assay, we found strong interference effects after incorpora-tion of the 7-deaza guanosine phosphorotioate analog into the RNA chain at equivalent positions G27 and G28 in aptamer no. | ỊFEBS Journal Structural basis for recognition of Co2 by RNA aptamers Jan Wrzesinski and Stanistaw K. JOZwiakowski Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan Poland Keywords Co2 binding RNA aptamers Co2 -induced conformational changes kissing dimer NAIM oligomer hybridization RNase H digestion Correspondence J. Wrzesinski Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12 14 61-704 Poznan Poland Fax 48 61 8520532 Tel 48 61 8528503 E-mail wrzesinj@ibch.poznan.pl Received 8 October 2007 revised 27 December 2007 accepted 5 February 2008 doi 10.1111 j.1742-4658.2008.06320.x Co2 binding RNA aptamers were chosen as research models to reveal the structural basis underlying the recognition of Co2 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 Co2 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 phos-phorotioate 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 Co2 and at an elevated metal ion concentration the hybridization of oligomers to aptamer targets is inhibited probably due to higher stability and .