title: Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and model-building study.
abstract: NMR and model-building studies were carried out on the duplex d(CTGGTGCGG).d(CCGCCCAG), referred to as (9+8)-mer, which contains an unpaired thymidine residue. Resonances of the base and of several sugar protons of the (9+8)-mer were assigned by means of a NOESY experiment. Interresidue NOEs between dG(4) and dT(5) as well as between dT(5) and dG(6) provided evidence that the extra dT is stacked into the duplex. Thermodynamic analysis of the chemical shift vs temperature profiles yielded an average TmD value of 334 K and delta HD of -289 kJmol-1 for the duplex in equilibrium random-coil transition. The shapes of the shift profiles as well as the thermodynamic parameters obtained for the extra dT residue and its neighbours again indicate that the unpaired dT base is incorporated inside an otherwise intact duplex. This conclusion is further supported by (a) the observation of an imino-proton resonance of the unpaired dT; (b) the relatively small dispersion in 31P chemical shifts (approximately 0.5 ppm) for the (9+8)-mer, which indicates the absence of t/g or g/t combinations for the phosphate diester torsion angles alpha/zeta. An energy-minimized model of the (9+8)-mer, which fits the present collection of experimental data, is presented.
authors: Gorlaeus Laboratories, Leiden University, The Netherlands.
authors: Y T
authors: YT
authors: van den Hoogen
authors: A A
authors: AA
authors: van Beuzekom
authors: H
authors: H
authors: van den Elst
authors: G A
authors: GA
authors: van der Marel
authors: J H
authors: JH
authors: van Boom
authors: C
authors: C
authors: Altona
mesh_terms: D001482:Base Composition; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides; D012984:Software; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D013936:Thymidine
chemical_list: D009841:Oligonucleotides; D013936:Thymidine