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Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer

¹ Department of Chemistry, Brooklyn College, Ph.D. Programs of Chemistry and Biochemistry, The Graduate School of CUNY, Brooklyn, New York 11210, USA
² Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA

Reprint requests to: Zhen Huang, Department of Chemistry, Brooklyn College, Ph.D. Programs of Chemistry and Biochemistry, The Graduate School of CUNY, Brooklyn, NY 11210, USA; e-mail: zhuang{at}brooklyn.cuny.edu; fax: (718) 951-4607.

Small changes in target specificity can sometimes be achieved, without changing aptamer structure, through mutation of a few bases. Larger changes in target geometry or chemistry may require more radical changes in an aptamer. In the latter case, it is unknown whether structural and functional solutions can still be found in the region of sequence space close to the original aptamer. To investigate these questions, we designed an in vitro selection experiment aimed at evolving specificity of an ATP aptamer. The ATP aptamer makes contacts with both the nucleobase and the sugar. We used an affinity matrix in which GTP was immobilized through the sugar, thus requiring extensive changes in or loss of sugar contact, as well as changes in recognition of the nucleobase. After just five rounds of selection, the pool was dominated by new aptamers falling into three major classes, each with secondary structures distinct from that of the ATP aptamer. The average sequence identity between the original aptamer and new aptamers is 76%. Most of the mutations appear to play roles either in disrupting the original secondary structure or in forming the new secondary structure or the new recognition loops. Our results show that there are novel structures that recognize a significantly different ligand in the region of sequence space close to the ATP aptamer. These examples of the emergence of novel functions and structures from an RNA molecule with a defined specificity and fold provide a new perspective on the evolutionary flexibility and adaptability of RNA.

Keywords: Aptamer; specificity; fold; selection; RNA evolution

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