Biophys J, June 2002, p. 3170-3180, Vol. 82, No. 6

Proton NMR Studies of 5'-d-(TC)₃ (CT)₃ (AG)₃-3'A Paperclip Triplex: The Structural Relevance of Turns

Laura B. Pasternack,^* Shwu-Bin Lin, Tsung-Mei Chin, Wei-Chen Lin,^§ Dee-Hua Huang,^* and Lou-Sing Kan^§

 ^*Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037 USA;  The Graduate Institute of Medical Technology, National Taiwan University, Taipei, Taiwan 10002;  Institute of Applied Chemistry, Chinese Culture University, Taipei, Taiwan 11114; and  ^§Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529

In this study, we present the results of structural analysis of an 18-mer DNA 5'-T₁C₂T₃C₄T₅C₆C₇T₈C₉T₁₀C₁₁T₁₂A₁₃G₁₄A₁₅G₁₆A₁₇G₁₈-3' by proton nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. The NMR data are consistent with characteristics for triple helical structures of DNA: downfield shifting of resonance signals, typical for the H3⁺ resonances of Hoogsteen-paired cytosines; pH dependence of these H3⁺ resonance; and observed nuclear Overhauser effects consistent with Hoogsteen and Watson-Crick basepairing. A three-dimensional model for the triplex is developed based on data obtained from two-dimensional NMR studies and molecular modeling. We find that this DNA forms an intramolecular "paperclip" pyrimidine-purine-pyrimidine triple helix. The central triads resemble typical Hoogsteen and Watson-Crick basepairing. The triads at each end region can be viewed as hairpin turns stabilized by a third base. One of these turns is comprised of a hairpin turn in the Watson-Crick basepairing portion of the 18-mer with the third base coming from the Hoogsteen pairing strand. The other turn is comprised of two bases from the continuous pyrimidine portion of the 18-mer, stabilized by a hydrogen-bond from a purine. This "triad" has well defined structure as indicated by the number of nuclear Overhauser effects and is shown to play a critical role in stabilizing triplex formation of the internal triads.

Biophys J, June 2002, p. 3170-3180, Vol. 82, No. 6
© 2002 by the Biophysical Society   0006-3495/02/06/3170/11  $2.00

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