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.

The Influence of the Thymine C5 Methyl Group on Spontaneous Base Pair Breathing in DNA

“…Furthermore, only small differences are discernable when structures with and without the C5 methyl group are compared in crystals (40,43) as well as in solution (41,42,44,45). The NOESY spectra of the d(CATA 2 T 2 ATG) 2 and d(CATA 2 U 2 ATG) 2 oligomers that have been investigated in the present study are in agreement with these earlier studies.…”

“…The lack of structural impact of C5 methylation as evidenced by Fig. 4 and previous studies (41,42,44,45) is therefore compatible with the large dynamical effects.…”

“…4). These spectral features indicate that the C5 methyl group exerts only a minor influence on the helix structure in keeping with crystal (40,43) as well as solution structure studies (41,42,44,45).…”

Structure–Function Correlations of the Insulin-linked Polymorphic Region

“…Pair-wise average distances (and their ranges) for the non-exchangeable protons of [d(G4TGTG4)]2 were obtained by refining the R-factor ( = S=Io − Ic=/SIo) with the aid of a linked-atom least-squares procedure in conjunction with full-matrix NOESY simulations with respect to the observed 100% 2 H2O NOESY data at 100, 250, and 400 ms of mixing (Gupta et al, 1988(Gupta et al, , 1993aCatasti et al, 1994); where Io and Ic are the observed and calculated NOESY intensities, respectively. Pair-wise distances involving exchangeable protons were qualitatively estimated from the NOESY (mixing time = 400 ms) of [d(G4TGTG4)]2 in 90% H2O/10% 2 H2O.…”

TWo-Dimensional1H and31P NMR Spectra and Restrained Molecular Dynamics Structure of an Oligodeoxyribonucleotide Duplex Refined via a Hybrid Relaxation Matrix Procedure

“…The development of sequence-specific, two-dimensional nuclear magnetic resonance (2D NMR) assignment methodologies (5)(6)(7)(8)(9)(10)(11)(12)(13)(14) and higher-field spectrometers have made the study of modest size oligonucleotides (10-20 base pairs) possible. Two-dimensional NMR, combined with distance geometry (15)(16)(17) or restrained molecular mechanics/dynamics (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20), is now capable of elucidating the fine structure of short DNA duplexes in solution. Unfortunately, evaluation of interproton distances from a 2D-NMR nuclear Overhauser effect spectroscopy (NOESY) experiment has relied on the so-called "two-spin approximation" (17,21).…”