Hairpin structures in DNA containing arabinofuranosylcytosine. A combination of nuclear magnetic resonance and molecular dynamics
- Univ. of Leiden (Netherlands)
- Univ. of Utrecht, Padulaan (Netherlands)
Nuclear magnetic resonance (NMR) and model-building studies were carried out on the hairpin form of the octamer d(CG{sup a}CTAGCG) ({sup a}C = arabinofuranosylcytosine), referred to as the TA compound. The nonexchangeable protons of the TA compound were assigned by means of nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy (COSY). Form a detailed analysis of the coupling data and of the NOESY spectra the following conclusions are reached: (i) the hairpin consists of a stem of three Watson-Crick type base pairs, and the two remaining residues, T(4) and dA(5), participate in a loop. (ii) All sugar rings show conformational flexibility although a strong preference for the S-type (C2{prime}-endo) conformer is observed. (iii) The thymine does not stack upon the 3{prime} side of the stem as expected, but swings into the minor groove. (iv) At the 5{prime}-3{prime} loop-stem junction a stacking discontinuity occurs as a consequence of a sharp turn in that part of the backbone, caused by the unusual {beta}{sup +} and {gamma}{sup t} torsion angles in residue dG(6). (v) The A base slides over the 5{prime} side of the stem to stack upon the {sup a}C(3) residue at the 3{prime} side of the stem in an antiparallel fashion. On the basis of J couplings and a set approximate proton-proton distances from NOE cross peaks, a model for the hairpin was constructed.
- OSTI ID:
- 6697988
- Journal Information:
- Biochemistry; (USA), Vol. 29:3; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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DNA
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CONFORMATIONAL CHANGES
CHEMICAL SHIFT
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MOLECULAR STRUCTURE
OVERHAUSER EFFECT
PHOSPHORUS 31
PROTONS
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AMINES
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BARYONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
HETEROCYCLIC COMPOUNDS
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LIGHT NUCLEI
MAGNETIC RESONANCE
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ODD-EVEN NUCLEI
ORGANIC COMPOUNDS
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550601* - Medicine- Unsealed Radionuclides in Diagnostics