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Nucleic Acids Research, 1988, Vol. 16, No. 7 2971-2986
© 1988

Articles

Extra thymidine stacks into the d(CTGGTGCGG).d(CCGCCCAG) duplex. An NMR and modelbuilding study

Yvonne Th. van den Hoogen, Aart A. van Beuzekom, Hans van den Elst, Gijs A. van der Marel, Jacques H. van Boom and Cornelis Altona*

Gorlaeus Laboratories, Leiden University PO Box 9502, 2300 RA Leiden, The Netherlands

*to whom correspondence should be addressed

Received February 9, 1988. Accepted March 2, 1988.

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)–mar 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 end {Delta}HD of -289 kJmol–1 for the duplex {rightleftarrows} 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 (becaus 0.5 ppm) for the (9+8)–mer, which indicates the absence of t/g or g/t combinations for the phoaphete dieeter torsion angles {alpha}/{varsigma}. An energy-minimized model of the (9+8)–mer, which fits the present collection of experimantal date, is presented.


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