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Bent dsDNA with defined geometric characteristics in terms of complexes of bridged oligonucleotides

Abstract

An opportunity of designing nontypical double-stranded DNA structures containing nonnatural inserts in a regular nucleotide DNA sequence has been investigated. The looped nucleotide inserts on the basis of adenylates and thymidilates, and nonnucleotide inserts on the basis of phosphodiesters of diethyleneglycol, 1,10-decanediol, and 3-hydroxy-2(hydroxymethyl)tetrahydrofuran were introduced into the backbone of a 32-mer native DNA duplex. These inserts formed the internal loops in the modified double-stranded DNA fragments which were shown to lead to bending of the linear duplex structure by 16 to 83 degrees. The dependencies of the bend angle of dsDNA on the composition and the length of the looped regions were determined. It was established that the bend of the irregular region of dsDNA depended on the electrostatic interaction of the phosphate residues. The tension in the complex structure could be reduced by the introduction of additional nucleotide units opposite the loop, which led to some relaxation of the bent helix. The resulting parameters of the bend values were shown to be in a good agreement with the published data obtained by NMR spectroscopy. It was demonstrated that the variation of the nature or the length of the insert allowed one to regulate the level of the local perturbation of the duplex structure and, thereby, influence both the bend level of the double helix and the destabilization of the modified complex.

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Abbreviations

DEG:

diethyleneglycol phosphodiester

DD:

1,10-decanediol phosphodiester

AP:

3-hydroxy-2(hydroxymethyl)tetrahydrophuran phosphodiester

dsDNA:

double-stranded DNA

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Correspondence to D.V. Pyshnyi.

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Original Russian Text © O.A. Vinogradova, E.V. Eremeeva, A.A. Lomzov, I.A.Pyshnaya, D.V. Pyshnyi, 2009, published in Bioorganicheskaya Khimiya, 2009, Vol. 35, No. 3, pp. 384–396.

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Vinogradova, O.A., Eremeeva, E.V., Lomzov, A.A. et al. Bent dsDNA with defined geometric characteristics in terms of complexes of bridged oligonucleotides. Russ J Bioorg Chem 35, 349–359 (2009). https://doi.org/10.1134/S1068162009030108

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  • DOI: https://doi.org/10.1134/S1068162009030108

Key words

  • nonnucleotide insert
  • bridged oligonucleotide
  • modified DNA duplex
  • mobility
  • bend
  • loop (internal loop)