Letter to the Editor

Oligonucleotide Conjugates with Minor Groove Ligands as Probes for Hybridization Microarray Chips

A. N. Sinyakov¹, E. V. Kostina¹, G. A. Maksakova¹, O. A. Baturina¹ and V. A. Ryabinin^1 #

^#Phone: (3832) 330-46-53, e-mail: ryabinin@niboch.nsc.ru

¹Novosibirsk Institute of Bioorganic Chemistry, Siberian Division, Russian Academy of Sciences, pr. Akademika Lavrentieva 8, Novosibirsk, 630090, Russia

Received: April 12, 2007;  in final form: April 17, 2007

Abstract.  A possibility of using oligonucleotide conjugates with minor groove ligands as probes for hybridization microarray chips was studied. The oligonucleotide conjugates contain a hairpin ligand (MGB) composed of two tripyrrolcarboxamide residues with an aminocaproic acid residue as a linker and bound to the oligonucleotide duplex AT tract in a site-specific manner. We used as (5′-3′)-probes: GACAAGAp, GACAAAAp, GACAAGA-MGB, and GACAAAA-MGB. The oligonucleotides labeled with the Cy3 cyanine dye, Cy3-ACTAATTTTGTC and Cy3-ACTAATCTTGTC, were used as targets. The maximal MGB effect on the fluorescence level of microarray chip spots, which caused its fourfold increase as compared with the initial unmodified duplex, was observed for the duplex containing only AT pairs in the ligand binding site. The presence of AC and GT mutations in the binding site (imperfect duplexes) or a CG pair (perfect duplex) affect the change in fluorescence level to a considerably lesser degree.

Key words:  conjugates; microchip; minor groove binder; oligonucleotides; point mutation; single nucleotide polymorphism

Russian Journal of Bioorganic Chemistry 2007, 33(5): 531-533