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An investigation into the solution structure of the single-stranded DNA undecamer 5′d AAGTGTGATAT by means of nuclear Overhauser enhancement measurements

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Abstract

A 500-MHz 1H-NMR study on the single-stranded DNA undecamer (11-mer) 5′d AAGTGTGATAT is presented. Using a combination of one-dimensional pre-steady-state nuclear Overhauser enhancement (NOE) measurements and two-dimensional homonuclear J-correlated spectroscopy, virtually complete resonance assignments are obtained. The relative magnitudes of the intra- and internucleotide NOEs indicate that the overall structure of the single-stranded 11-mer is a right-handed B-type helix with extensive base stacking. Within this overall structure there is quite a large degree of variability, as exemplified by variations in glycosidic bond and sugar pucker conformations, most likely determined by base sequence.

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Abbreviations

NOE:

nuclear Overhauser effect

COSY:

twodimensional homonuclear J-correlated spectroscopy

11-mer:

undecamer

EDTA:

sodium ethylenediamine tetraacetate

HPLC:

nigh-pressure liquid chromatography

DSS:

4,4-dimethylsilapentane-1-sulfonate

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Author notes

  1. G. M. Clore & A. M. Gronenborn

    Present address: Max-Planck Institut für Biochemie, D-8033, Martinsried bei München, FRG

Authors and Affiliations

  1. Division of Physical Biochemistry, National Institute for Medical Research, Mill Hill, NW7 1AA, London, UK

    G. M. Clore & A. M. Gronenborn

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  1. G. M. Clore
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  2. A. M. Gronenborn
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Clore, G.M., Gronenborn, A.M. An investigation into the solution structure of the single-stranded DNA undecamer 5′d AAGTGTGATAT by means of nuclear Overhauser enhancement measurements. Eur Biophys J 11, 95–102 (1984). https://doi.org/10.1007/BF00276624

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  • DOI: https://doi.org/10.1007/BF00276624

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