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Nucleic Acids Research, 2002, Vol. 30, No. 6 1401-1407
© 2002 Oxford University Press

Boron-containing aptamers to ATP

Susan M. Lato, Nicole D. S. Ozerova, Kaizhang He1, Zinaida Sergueeva1, Barbara Ramsay Shaw1 and Donald H. Burke*

Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, IN 47405-7102, USA and 1Department of Chemistry, P. M. Gross Chemical Laboratory, Box 90346, Duke University, Durham, NC 27708-0346, USA

Boron neutron capture therapy (BNCT), an experimental treatment for certain cancers, destroys only cells near the boron; however, there is a need to develop highly specific delivery agents. As nucleic acid aptamers recognize specific molecular targets, we investigated the influence of boronated nucleotide analogs on RNA function and on the systematic evolution of ligands by exponential enrichment (SELEX) process. Substitution of guanosine 5'-({alpha}-P-borano) triphosphate (bG) for GTP or uridine 5'-({alpha}-P-borano) triphosphate (bU) for UTP in several known aptamers diminished or eliminated target recognition by those RNAs. Specifically, ATP-binding aptamers containing the {zeta}-fold, which appears in several selections for adenosine aptamers, became inactive upon bG substitution but were only moderately affected by bU substitution. Selections were carried out using the bG or bU analogs with C8-linked ATP agarose as the binding target. The selections with bU and normal NTP yielded some {zeta}-fold aptamers, while the bG selection yielded none of this type. Non-{zeta} aptamers from bU and bG populations tolerated the borano substitution and many required it. The borano nucleotide requirement is specific; bU could not be used in bG-dependent aptamers nor vice versa. The borano group plays an essential role, as yet undefined, in target recognition or RNA structure. We conclude that the bG and bU nucleotides are fully compatible with SELEX, and that these analogs could be used to make boronated aptamers as therapeutics for BNCT.

* To whom correspondence should be addressed. Tel: +1 812 856 4977; Fax: +1 812 855 8300; Email: dhburke{at}indiana.edu Present address:Susan M. Lato, NuGen Technologies, 821 Industrial Road, Unit A, San Carlos, CA 94070, USA


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