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Oligomers isohelical to DNA: DNA-binding properties and applications for construction of nano-scaled devices

Georgy V. Gursky 1Alexei M. Nikitin 1Anna N. Surovaya Victor A. Nikolaev Natalia P. Bajulina Michail V. Golovkin Sergei L. Grokhovsky 

1. Engelhardt Institute of Molecular Biology RAS (EIMB), Vavilova 32, Moscow 119991, Russian Federation

Abstract

There are two possible applications of DNA as a structural material for construction of nano-scaled devices. Metallization of DNA was invented as a perspective method for the construction of conductive wires for nano-scaled electrical circuits. The DNA can also be used as a scaffold for the clamping of the DNA-binding ligands that possess appropriate electrical, optical and magnetic properties. An obvious advantage of this approach is that DNA is accessible for modification with an aid of different enzymes. Using a systematic computational search, new single-stranded and two-stranded structural motifs isohelical to double-stranded DNA were found. These motifs can be used for design and synthesis of new generations of sequence-specific DNA-binding oligomers. Isohelical oligomers that possess conjugated p electron systems can serve as conductive wires in nano-scaled devices.Template-assistant organic synthesis and photopolymerization can be used to generate very long oligomers. New strategies are developed for  synthesis of sequence specific DNA -binding oligomers which recognize  long DNA sequences. Bis-netropsins  were synthesized which contain two netropsin-like fragments  attached to a pair of peptides Gly-Cys-Gly-Gly-Gly  and Gly-Val-Gly-Cys-Gly-Gly-Gly bridged by S-S bonds. These conjugates  possesses a  composite binding specificity: the peptide dimers recognize sites with  sequences GCCG  and GCCCCG on DNA, whereas the  netropsin fragments bind selectively to runs of four AT-base pairs. A series of new ligands were synthesized by a modular assembly of pyrrole carboxamides and isohelical pseudopeptides  of the form (XY)n . Here Y is a glycine residue; n is the degree of polymerization. X is an unusual amino acid residue containing five - membered aromatic ring (furan, thiazole, oxazole, imidazole). Studies on binding of these compounds to DNA will be reported.

 

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Presentation: Invited oral at E-MRS Fall Meeting 2008, Symposium H, by Georgy V. Gursky
See On-line Journal of E-MRS Fall Meeting 2008

Submitted: 2008-05-08 19:10
Revised:   2009-06-07 00:48