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Nucleic Acids Research, 2001, Vol. 29, No. 7 1565-1573
© 2001 Oxford University Press

Enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity

Sarah E. Lee, Alexander Sidorov, Thierry Gourlain, Nathalie Mignet, Simon J. Thorpe, John A. Brazier, Mark J. Dickman1, David P. Hornby1, Jane A. Grasby and David M. Williams*

Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK and 1Transgenomic Laboratories, Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield S10 2TN, UK

The incorporation of potentially catalytic groups in DNA is of interest for the in vitro selection of novel deoxyribozymes. A series of 10 C5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality. For each series of nucleotide analogues differing degrees of flexibility of the C5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties. The imidazole function was conjugated to these C5-amino-modified nucleotides using either imidazole 4-acetic acid or imidazole 4-acrylic acid (urocanic acid). The substrate properties of the nucleotides (fully replacing dTTP) with Taq polymerase during PCR have been investigated in order to evaluate their potential applications for in vitro selection experiments. 5-(3-Aminopropynyl)dUTP and 5-(E-3-aminopropenyl)dUTP and their imidazole 4-acetic acid- and urocanic acid-modified conjugates were found to be substrates. In contrast, C5-amino-modified dUTPs with alkane or Z-alkene linkers and their corresponding conjugates were not substrates. The incorporation of these analogues during PCR has been confirmed by inhibition of restriction enzyme digestion using XbaI and by mass spectrometry of the PCR products.

* To whom correspondence should be addressed. Tel: +44 114 222 9502; Fax: +44 114 273 8673; Email: d.m.williams{at}sheffield.ac.uk Correspondence may also be addressed to Jane A. Grasby. Tel: +44 114 222 9502; Fax: +44 114 273 8673; Email: j.a.grasby{at}sheffield.ac.uk Present address: Nathalie Mignet, Aventis Pharma/UMR7001 CNRS-ENSCP, Bat. Monod 3CO1, 13 Quai Jules Guesde BP14, 94403 Vitry Cedex, France


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