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Oligomers isohelical to DNA: DNA-binding properties and applications for construction of nano-scaled devices |
Georgy V. Gursky 1, Alexei M. Nikitin 1, Anna 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. GurskySee On-line Journal of E-MRS Fall Meeting 2008 Submitted: 2008-05-08 19:10 Revised: 2009-06-07 00:48 |