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

• Published in: Biochemistry (Easton) Vol. 29; no. 3; pp. 788 - 799
• Main Authors: Pieters, Jane M. L, De Vroom, Erik, Van der Marel, Gijs A, Van Boom, Jacques H, Koning, Thea M. G, Kaptein, Robert, Altona, Cornelis
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 23.01.1990
• Subjects: AMINES; Analytical, structural and metabolic biochemistry; AZINES; BARYONS; Base Sequence; Biological and medical sciences; CHEMICAL SHIFT; CONFORMATIONAL CHANGES; Cytarabine; CYTOSINE; DNA; Dna, deoxyribonucleoproteins; ELEMENTARY PARTICLES; FERMIONS; Fundamental and applied biological sciences. Psychology; HADRONS; HETEROCYCLIC COMPOUNDS; ISOTOPES; LIGHT NUCLEI; MAGNETIC RESONANCE; Magnetic Resonance Spectroscopy - methods; Models, Chemical; Molecular Sequence Data; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; NUCLEI; Nucleic Acid Conformation; NUCLEIC ACIDS; NUCLEONS; ODD-EVEN NUCLEI; OLIGONUCLEOTIDES; ORGANIC COMPOUNDS; ORGANIC NITROGEN COMPOUNDS; ORGANIC OXYGEN COMPOUNDS; OVERHAUSER EFFECT; Phosphorus; PHOSPHORUS 31; PHOSPHORUS ISOTOPES; PROTONS; PYRIMIDINES; RADIOLOGY AND NUCLEAR MEDICINE; RESONANCE; STABLE ISOTOPES 550601 > Medicine > Unsealed Radionuclides in Diagnostics; STEREOCHEMISTRY; Hairpin loop; DNA; Molecular dynamics; Cytosine; Models; NMR spectrometry; Spatial structure
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00455a029

Nuclear magnetic resonance (NMR) and model-building studies were carried out on the hairpin form of the octamer d(CGaCTAGCG) (aC = 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). From 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'-endo) conformer is observed. (iii) The thymine does not stack upon the 3' side of the stem as expected, but swings into the minor groove. (This folding principle of the loop involves an unusual alpha t conformer in residue T(4).) (iv) At the 5'-3' 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 + and gamma t torsion angles in residue dG(6). (v) The A base slides over the 5' side of the stem to stack upon the aC(3) residue at the 3' side of the stem in an antiparallel fashion. On the basis of J couplings and a set of approximate proton-proton distances from NOE cross peaks, a model for the hairpin was constructed. This model was then refined by using an iterative relaxation matrix approach (IRMA) in combination with restrained molecular dynamics calculations. The resulting final model satisfactorily explains all the distance constraints.