Influence of DNA Aptamer Structure on the Specificity of Binding to Taq DNA Polymerase

O. Yu. Yakimovich¹, Ya. I. Alekseev², A. V. Maksimenko¹, O. L. Voronina³, and V. G. Lunin¹

¹All-Russia Institute of Agricultural Biotechnology, ul. Timiryazevskaya 42, Moscow, 127550 Russia; fax: (095) 977-7455; E-mail: yakimovich@mk.ru

²JSC Syntol, ul. Timiryazevskaya 42, Moscow, 127550 Russia

³Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, 117871 Russia

^* To whom correspondence should be addressed.

Received May 15, 2002; Revision received July 17, 2002

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The secondary structure of DNA aptamer to Taq DNA polymerase was established as a hairpin. Both stem and loop structures of DNA ligand were shown to be involved in the interaction with Taq DNA polymerase. Moreover, the structure and sequence of DNA aptamer that was the most effective inhibitor of DNA polymerase activity were established. This crucial structure was evaluated as a GC-rich stem longer than 17 bp, and a loop consisting of 12 bases with strictly determined nucleotide sequence. It was demonstrated that nucleotide in position 23 counting from the 5´-end of DNA ligand was involved in direct contact with Taq DNA polymerase. The ability of optimized DNA aptamer TQ21-11 to form a complex with the enzyme was increased 5-fold in comparison to the initial aptamer.

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KEY WORDS: DNA ligands, DNA aptamer design, Taq DNA polymerase, DNA-protein complex, PCR

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