Thermodynamic, Kinetic, and Conformational Properties of a Parallel Intermolecular DNA Triplex Containing 5‘ and 3‘ Junctions

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Abstract
The interaction of the 11-mer oligodeoxypyrimidine d(TCTTCTUTCCT) with the 17 bp duplex d(CGCTAGAAGAAAGGACG)·d(CGTCCUTTCTTCTAGCG) in forming an intermolecular DNA triplex has been examined in solution by surface plasmon resonance (SPR), UV thermal denaturation, circular dichroism (CD), and NMR methods. Thermodynamic data were also acquired for the shorter 15 bp target duplex d(CGCTAGAAGAAAGGA)·d(TCCUTTCTTCTAGCG), which forms a 3‘ flush-ended parallel triplex. CD titrations at pH 5 gave a triplex → (duplex + strand) dissociation constant Kd of 0.5 μM at 15 °C and ∼2 μM at 25 °C for both the 11−15·15 and 11−17·17 systems, in agreement with analysis of the UV melting data and a direct calorimetric measurement. In contrast, the “apparent” Kd value determined by SPR was 10−20-fold smaller. The rate constant for dissociation (kd) of the third strand from the triplex was found to be ∼0.0002 s-1 at 25 °C by SPR. The rate constant for exchange between the triplex and duplex states determined by NMR was ∼2 s-1 at 40 °C. The dissociation kinetics measured by SPR are considerably underestimated, which largely accounts for the poor estimation of Kd using this technique. Extensive 1H NMR assignments were obtained for both the 17 bp DNA duplex and the triplex. Large changes in chemical shifts were observed in the purine strand of the host duplex, but only small shift changes were induced in the complementary pyrimidine strand. Dramatic differences in shifts were observed for the G and A residues, especially in the minor groove, consistent with only small, localized conformational changes in the underlying duplex. The magnitude of the shift changes decreased to baseline within one base of the 3‘ triplex−duplex junction and over two to three bases at the 5‘ junction. Chemical shift changes at the 5‘ junction suggest small conformational anomalies at this site. COSY and NOESY spectra indicate that the nucleotides are in the “S” domain in both the triplex and duplex states. These data rule out major conformation changes at the triplex−duplex boundaries. NOEs between pyrimidines in the third strand and those in the duplex showed proximity for these bases in the major groove, which could be ascribed to buckling of the Hoogsteen bases out of the plane of the Watson−Crick base pairs.