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The nature of stabilization of the tandem DNA duplex pTGGAGCTG · (pCAGC+(Phn-NH-(CH2)3-NH)pTCCA) basing on the UV, CD, and two-dimensional NMR spectroscopy data

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Abstract

The properties and the three-dimensional structure of the tandem DNA duplex pTGGAGCTG·(pCAGC+(PhnL)pTCCA) in aqueous solution, where L is an amino linker and Phn is anN-(2-hydroxyethyl)phenazinium residue, were studied spectrophotometrically and by two-dimensional1H NMR spectroscopy (COSY and NOESY). When a tandem complex involving a Phn residue-bearing oligonucleotide is formed, the dye aromatic system intercalates into the double helix at the nick site and takes part in two stacking interactions: a strong one (3.5–4 Å) with the T5-A12 base pair of its own duplex moiety and a weak one (4–5 Å) with the C4-G13 pair of the adjoining duplex (mainly with the C4 base). This arrangement of the dye residue, providing a cross-interaction of the phenazinium moiety with the base pairs of the adjacent duplex structures, results in the stabilization of the whole tandem complex.

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Abbreviations

Phn:

N-(2-hydroxyethyl)phenazinium; prefixd in the abbreviations of oligodeoxyribonucleotides is omitted

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Authors and Affiliations

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

    A. Yu. Denisov, D. V. Pyshnyi & E. M. Ivanova

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  1. A. Yu. Denisov
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  2. D. V. Pyshnyi
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  3. E. M. Ivanova
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Correspondence to E. M. Ivanova.

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Denisov, A.Y., Pyshnyi, D.V. & Ivanova, E.M. The nature of stabilization of the tandem DNA duplex pTGGAGCTG · (pCAGC+(Phn-NH-(CH2)3-NH)pTCCA) basing on the UV, CD, and two-dimensional NMR spectroscopy data. Russ J Bioorg Chem 26, 337–349 (2000). https://doi.org/10.1007/BF02759287

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  • DOI: https://doi.org/10.1007/BF02759287

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