Hairpin structures in DNA containing arabinofuranosylcytosine. A combination of nuclear magnetic resonance and molecular dynamics

Journal Article · Tue Jan 23 00:00:00 EST 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00455a029· OSTI ID:6697988

Pieters, J M.L.; de Vroom, E; van der Marel, G A; van Boom, J H; Altona, C ^[1]; Koning, T H.G.; Kaptein, R ^[2]

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1. Univ. of Leiden (Netherlands)
2. 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

Related Subjects

62 RADIOLOGY AND NUCLEAR MEDICINE
DNA
NUCLEAR MAGNETIC RESONANCE
OLIGONUCLEOTIDES
CONFORMATIONAL CHANGES
CHEMICAL SHIFT
CYTOSINE
MOLECULAR STRUCTURE
OVERHAUSER EFFECT
PHOSPHORUS 31
PROTONS
STEREOCHEMISTRY
AMINES
AZINES
BARYONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
HETEROCYCLIC COMPOUNDS
ISOTOPES
LIGHT NUCLEI
MAGNETIC RESONANCE
NUCLEI
NUCLEIC ACIDS
NUCLEONS
ODD-EVEN NUCLEI
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
ORGANIC OXYGEN COMPOUNDS
PHOSPHORUS ISOTOPES
PYRIMIDINES
RESONANCE
STABLE ISOTOPES
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