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Nucleic Acids Research, 2001, Vol. 29, No. 3 831-840
© 2001 Oxford University Press

Multiple four-stranded conformations of human telomere sequence d(CCCTAA) in solution

Kenji Kanaori*, Naoko Shibayama, Keigo Gohda1, Kunihiko Tajima and Keisuke Makino2

Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan, 1International Research Laboratories, CIBA-GEIGY Japan Ltd, 10-66 Miyuki-cho, Takarazuka 665-8666, Japan and 2Institute of Advanced Energy, Kyoto University, Gokasho, Uji 611-0011, Japan

By detailed NMR analysis of a human telomere repeating unit, d(CCCTAA), we have found that three distinct tetramers, each of which consists of four symmetric single-strands, slowly exchange in a slightly acidic solution. Our new finding is a novel i-motif topology (T-form) where T4 is intercalated between C1 and C2 of the other duplex. The other two tetramers have a topology where C1 is intercalated between C2 and C3 of the other parallel duplex, resulting in the non-stacking T4 residues (R-form), and a topology where C1 is stacked between C3 and T4 of the other duplex (S-form). From the NMR denaturation profile, the R-form is the most stable of the three structures in the temperature range of 15–50°C, the S-form the second and the T-form the least stable. The thermodynamic parameters indicate that the T-form is the most enthalpically driven and entropically opposed, and its population is increased with decreasing temperature. The T-form structure determined by restrained molecular dynamics calculation suggests that inter-strand van der Waals contacts in the narrow grooves should contribute to the enthalpic stabilization of the T-form.

* To whom correspondence should be addressed. Tel: +81 75 724 7825; Fax: +81 75 724 7807; Email: kanaori{at}ipc.kit.ac.jpPresent address:Keigo Gohda, Research Department, Novartis Pharma K.K., 10-66 Miyuki-cho, Takarazuka 665-8666, Japan


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