On the question of DNA bending: two-dimensional NMR studies on d(GTTTTAAAAC)2 in solution

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Abstract
It is very well documented that the presence of an An .cntdot. Tn tract causes intrinsic DNA bending. Hagerman demonstrated that the sequence in which the An .cntdot. Tn tracts are joined plays a very crucial role in determining DNA bending. For example, Hagerman showed that the polymer with a repeat of d-(GA4T4C)n.gtoreq. 10 is bent but the polymer with a repeat of d(GT4A4C)n.gtoreq. 10 is not bent [Hagerman, P.J. (1986) Nature (London) 326, 720-722]. Earlier we have shown that the decamer repeat d(GA4T4C)2 is itself bent with a finite structural discontinuity at the A.fwdarw.T sequence [Sarma, M. H., Gupta, G., and Sarma, R. H. (1988) Biochemistry 27, 3423-3432]. In the present article, we summarize our studies on the decamer repeat d(GT4A4C)2 sturcutre in solution. By employment of 1D and 2D 1H NMR studies at 500 MHz a complete sequential assignment has been made for the exchangeable and nonexchangeable protons belonging to the ten nucleotides. NOESY data were collected for d(GT4A4C)2 at 17.degree. C in D2O for three mixing times, 150, 100, and 50ms. A quantitative NOESY simulation technique was employed to arrive at a structural model of d(GT4A4C)2 in solution. Our detailed analyses revealed the following sturcutral features: (i) The duplex adopts the gross morphology of a B-DNA. (ii) All the A .cntdot. T pairs are propeller twisted (.ltoreq. -15.degree.). (iii) Although both A and T nucleotides belong to the C2''-endo, anticonformational domain, there is a mild variation in the actual conformation of the A and T residues. (iv) Even though there is a subtile conformational difference in the A and T nucleotides, two structural frames of T4 .cntdot. A4 segments are joined at the T.fwdarw.A sequence in such a way that there is no finite discontinuity at the junction; i.e., two neighboring frames exactly coincide at the T.fwdarw.A junction. Thus, our studies on d(GA4T4C) (Sarma et al., 1988) and on d(GT4A4C)2 (this article) reveal the structural peculiarity of the An .cntdot. Tn tract and the effect of A.fwdarw.T/T.fwdarw.A sequence in causing DNA bending.