[en] Extensive studies using one- and two-dimensional ¹H NMR at 500 MHz revealed that the oligonucleotide d(CGCCGCAGC) in solution at 5⁰C forms a double helix under conditions of high salt (500 mM in NaCl, 1 mM sodium phosphate), low pH (pH 4.5), and high DNA concentration (4 mM in duplex). The presence of very strong nuclear Overhauser effects (NOEs) from base H8/H6 to sugar H2', H2'' and the absence of NOE from base H8/H6 to sugar H3' suggested that the oligomer under these solution conditions forms a right-handed B-DNA double helix. The following lines of experimental evidence were used to conclude that C4 and A7 form an integral part of the duplex: (i) the presence of a NOESY cross-peak involving H8 of A7 and H8 of G8, (ii) the presence of a two-dimensional NOE (NOESY) cross-peak between H6 of C3 and H6 of C4, (iii) base protons belonging to C4 and A7 forming a part of the H8/H6---H1' cross-connectivity route, and (iv) the pattern of H8/H6---H2',H2'' NOESY cross-connectivity based upon a B-DNA model requiring that both C4 and A7 form an integral part of the duplex. The possibility of an A-C pair involving H bonds was also examined. Two possible structural models of the duplex at pH 4.5 are proposed: in one model A-C pairing involves two H bonds, and in the other A-C involves a single H bond

[en] A hairpin structure contains two conformationally distinct domains: a double-helical stem with Watson-Crick base pairs and a single-stranded loop that connects the two arms of the stem. By extensive 1D and 2D 500-MHz ¹H NMR studies in H₂O and D₂O, it has been demonstrated that the DNA oligomers d(CGCCGCAGC) and d(CGCCGTAGC) form hairpin structures under conditions of low concentration, 0.5 mM in DNA strand, and low salt (20 mM NaCl, pH 7). From examination of the nuclear Overhauser effect (NOE) between base protons H8/H6 and sugar protons H1' and H2'/H2'', it was concluded that in D(CGCCGCAGC) and d(CGCCCTAGC) all the nine nucleotides display average (C2'-endo,anti) geometry. The NMR data in conjunction with molecular model building and solvent accessibility studies were used to derive a working model for the hairpins

[en] It is very well documented that the presence of an A_n·T_n tract causes intrinsic DNA bending. Hagerman demonstrated that the sequence in which the A_n·T_n tracts are joined plays a very crucial role in determining DNA bending. In the present article, the authors summarize their 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 degree 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. Their studies on d(GA₄T₄C)₂ and on d(GT₄A₄C)₃ reveal the structural peculiarity of the A_n·T_n tract and the effect on A→T/T→A sequence in causing DNA bending

[en] Intrinsic DNA bending is caused by specific DNA sequences. The decamer d(GA₄T₄C)², when it repeats in a synthetic polymer or in kinetoplast DNA, results in a macroscopic bending of the molecule as a whole. The authors employed high-resolution two-dimensional NMR methods to examine the intrinsic structural properties of the d(GA₄T₄C)₂ duplex in solution. Examination of the NOESY data at 50- and 100-ms mixing times indicated that the kinds of observed NOEs can originate if each of the ten nucleotidyl residues belong to the B-DNA family, i.e., C2'-endo, anti. However, the degree of observed NOE intensities from the A-T junction as well as the observed AH2-AH2 cross-peaks from adjacent AT pairs could not be rationalized on the basis of a straight B-DNA model but could be explained by only a B-DNA model with some structural discontinuity at the A-T junction-the site of 2-fold symmetry in the molecule. In view of the fact that the degree of observed NOE intensities can be complicated spin diffusion and by fine structural distortion, they have resorted to the use of quantitative theoretical NOESY simulation to delineate the structural discontinuity at the A-T junction and to arrive at a structure for the duplex d(GA₄T₄C)₂. They propose a junction B-DNA model which can quantitatively explain the 2D NOESY data at 100- and 50-ms mixing times. It is the thesis of this paper that the observed bending in polymers with a repeat of d(GA₄T₄C)₂ and the bending in natural DNAs where A/sub n/T/sub n/(centered dot)A/sub n/T/sub n/ repeats are present originate at the oligonucleotide repeat level

[en] Two-dimensional nuclear magnetic resonance (2D NMR) studies on d(GA4T4C)2 and d(GT4A4C)2 showed that A.T pairs are propeller twisted. As a result, A/T tracts form a straight rigid structural block with an array of bifurcated inter base pair H bonds in the major groove. It was demonstrated (previous paper) that replacement of methyl group by hydrogen (changing from T to U) in the major groove does not disrupt the array of bifurcated H bonds in the major groove. In this article, we summarize results of 2D NMR and molecular mechanic studies on the effect of a minor-groove-binding A.T-specific drug on the structure d(GA4T4C)2. A distamycin analogue (Dst2) was used for this study. It is shown that Dst2 binds to the minor groove of d(GA4T4C)2 mainly driven by van der Waals interaction between A.T pairs and the drug; as a consequence, an array of bifurcated H bonds can be formed in the minor groove between amide/amino protons of Dst2 and A.T pairs of DNA. NOESY data suggest that Dst2 predominantly binds at the central 5 A.T pairs. NOESY data also reveal that, upon drug binding, d(GA4T4C)2 does not undergo any significant change in conformation from the free state; i.e., propeller-twisted A.T pairs are still present in DNA and hence the array of bifurcated H bonds must be preserved in the major groove. NOESY data for the A5-T6 sequence also indicate that there is little change in junction stereochemistry upon drug binding

[en] 500 MHz ¹H NMR studies using 2D-NOESY indicate that the oligonnucleotide d(CTCTCT) at low pH forms a parallel double helix with cytosine · cytosine base pairs and thymine · thymine bulges. This unusual structure may explain the hypersensitivity of S₁ nuclease at low pH towards supercoiled plasmids containing d(CT)_n inserts. (Auth.)

[en] 1D/2D NMR studies are reported for a [1:1] complex of d(GA₄T₄C)₂ and Dst2 (an analogue of distamycin A). Full- Matrix NOESY Simulations, Molecular Mechanics and Molecular Dynamics Calculations are performed to analyze the NMR data. Results show that drug-DNA complex formation is driven by static features like H-bonding and steric interactions in the minor-groove of DNA. As a consequence of drug binding, a non-linear oscillatory mode is activated. In this mode the molecule samples equilibrium structural states of difference degrees of bending. It is noted that these structures belong to three distinctly different energy wells that satisfy the same NMR data. 14 refs., 4 figs., 2 tabs

[en] Met⁵-enkephalin - a pentapeptide (Tyr-Gly-Gly-Phe-Met) - can exist in two possible folded arrangements with a rigid two-hydrogen-bonded network. In one arrangement, a Gly 2-Gly 3 β-bend is formed and in the other a Gly 3-Phe 4 β-bend. The two conformations are distinguished by the spatial relation of Tyr 1 and Phe 4: in the Gly 2-Gly 3 β-bend, Tyr 1 and Phe 4 can be brought close to each other while in the Gly 3-Phe 4 β-bend they are far apart the authors have utilized one-dimensional nuclear Overhauser effect (NOE) measurements between the ring protons of Tyr 1 and Phe 4 to determine their proximity. The NOE data clearly show that a pair of protons, one each from Tyr 1 and Phe 4, are as close as 3.3 A while other inter-proton distances are beyond 4.5 A. Therefore, the authors propose the presence of a Gly 2-Gly 3 β-bend for Met⁵-enkephalin in solution. The structure of Met⁵-enkephalin in solution is very similar to the single crystal structure of Leu⁵-enkephalin and tends to explain the biological activity data of several modified enkephalins. (Auth.)