title: On the question of DNA bending: two-dimensional NMR studies on d(GTTTTAAAAC)2 in solution.
abstract: It is very well documented that the presence of an An.Tn tract causes intrinsic DNA bending. Hagerman demonstrated that the sequence in which the An.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 greater than or equal to 10 is bent but the polymer with a repeat of d(GT4A4C)n greater than or equal to 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----T sequence [Sarma, M. H., Gupta, G., & Sarma, R. H. (1988) Biochemistry 27, 3423-3432]. In the present article, we summarize our studies on the decamer repeat d(GT4A4C)2 structure 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 degrees C in D2O for three mixing times, 150, 100, and 50 ms. 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 structural features: (i) The duplex adopts the gross morphology of a B-DNA. (ii) All the A.T pairs are propeller twisted (less than or equal to -15 degrees). (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 subtle conformational difference in the A and T nucleotides, two structural frames of T4.A4 segments are joined at the T----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----A junction. Thus, our studies on d(GA4T4C)2 (Sarma et al., 1988) and on d(GT4A4C)2 (this article) reveal the structural peculiarity of the An.Tn tract and the effect of A----T/T----A sequence in causing DNA bending.
authors.affiliation: Institute of Biomolecular Stereodynamics, State University, Albany, New York 12222.
authors.forename: G
authors.initials: G
authors.lastname: Gupta
authors.forename: M H
authors.initials: MH
authors.lastname: Sarma
authors.forename: R H
authors.initials: RH
authors.lastname: Sarma
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D004247:DNA; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D011089:Polydeoxyribonucleotides; D012996:Solutions
chemical_list: D011089:Polydeoxyribonucleotides; D012996:Solutions; D004247:DNA