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Nucleic Acids Research, 1984, Vol. 12, No. 12 5061-5078
© 1984

CHEMISTRY

Proton NMR study and confomiational analysis of d(CGT), d(TCG) and (CGTCG) in aqueous solution. The effect of a dangling thymidlne and of a tbymidine mismatch on DNA mini-duplexes

Jan-Remt Mellema, Rob van der Woerd, Gijs A.van der Marel, Jacques H.van Boom and Comelis Altona

Goriaeus Laboratories, State University of Leiden PO Box 9502, 2300 RA Leiden, The Netherlands

Received April 19, 1984. Accepted May 18, 1984.

Proton NMR studies of d(CGT), d(TCG) and d(CGTCG) were carried out at 300 and 500 MHz. The temperature and concentration dependence of the chemical shifts of various resonances indicates duplex formation only in the cases of d(TCG) and d(CGTCG). It is concluded that d(TCG) forms a mini-duplex stabilized by a 5'-dangling thymine base. Thermodynamic parameters of the duplex-to-coil equilibrium of the d(TCG) duplex are: {delta}H0 = –22.3 kcal/mol and {delta}S0 = –70 cal/mol.K, which correspond to ~ 40% duplex formation at 00C in a 2 mM nucleotide solution. Comparison of these data with thermodynamic parameters given earlier [Borer, P.N., Dengler, B., Tinoco, I. and Uhlenbeck, O.C. (1974) J. Mol. Biol. 86, 843–853] leads to the conclusion that the dangling base stabilization observed here is approximately equivalent to the stabilization caused by one or two additional A*T base pairs.

The chemical shift behaviour of various resonances in d(CGTCG) indicates duplex formation without looping out of the thymine bases. The TxT mismatch does not seem to disturb the helical structure to a large extent.

Analysis of the vicinal proton-proton coupling constants of the three compounds yielded geometrical data for the sugar rings. The data are interpreted in terms of N and S pseudorotational ranges. It is shown that a distinct conformation-transmission effect is exerted by the guanosine residues in a 5'-> 3' direction.


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