The Experts below are selected from a list of 252 Experts worldwide ranked by ideXlab platform
Alexander V. Abramenkov - One of the best experts on this subject based on the ideXlab platform.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9- pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:Abstract An analysis of the results of the fluorescence spectrum investigation of all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene in an n -decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586–9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G( d , p ) levels are also reported.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:An analysis of the results of the fluorescence spectrum investigation of all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene in an n-decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586-9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G(d,p) levels are also reported. © 2012 Elsevier B.V.SCOPUS: ar.jinfo:eu-repo/semantics/publishe
Yurii N Panchenko - One of the best experts on this subject based on the ideXlab platform.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9- pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:Abstract An analysis of the results of the fluorescence spectrum investigation of all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene in an n -decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586–9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G( d , p ) levels are also reported.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:An analysis of the results of the fluorescence spectrum investigation of all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene in an n-decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586-9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G(d,p) levels are also reported. © 2012 Elsevier B.V.SCOPUS: ar.jinfo:eu-repo/semantics/publishe
Charles W. Bock - One of the best experts on this subject based on the ideXlab platform.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9- pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:Abstract An analysis of the results of the fluorescence spectrum investigation of all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene in an n -decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586–9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G( d , p ) levels are also reported.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:An analysis of the results of the fluorescence spectrum investigation of all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene in an n-decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586-9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G(d,p) levels are also reported. © 2012 Elsevier B.V.SCOPUS: ar.jinfo:eu-repo/semantics/publishe
George R. De Maré - One of the best experts on this subject based on the ideXlab platform.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9- pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:Abstract An analysis of the results of the fluorescence spectrum investigation of all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene in an n -decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586–9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all -trans -deca-1,3,5,7,9-pentaene and t , C , t , T , t , T , t -deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G( d , p ) levels are also reported.
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Structural and vibrational analyses of t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene
Vibrational Spectroscopy, 2013Co-Authors: Yurii N Panchenko, George R. De Maré, Charles W. Bock, Alexander V. AbramenkovAbstract:An analysis of the results of the fluorescence spectrum investigation of all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene in an n-decane matrix [B.E. Kohler, V. Terpougov, J. Chem. Phys. 108 (1998) 9586-9593] has been performed using scaled quantum mechanical force field (SQM-FF) methodology at the HF/6-31G level. The measured vibronic wavenumbers were assigned taking into account the results of quantum-chemical predictions of the vibrational spectra for all-trans-deca-1,3,5,7,9-pentaene and t,C,t,T,t,T,t-deca-1,3,5,7,9-pentaene. Results from additional calculations at the MP2(FC)/aug-cc-pVDZ and B3LYP/6-311++G(d,p) levels are also reported. © 2012 Elsevier B.V.SCOPUS: ar.jinfo:eu-repo/semantics/publishe
Richard E. Dickerson - One of the best experts on this subject based on the ideXlab platform.
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Crystal structure of C-T-C-T-C-G-A-G-A-G. Implications for the structure of the Holliday junction.
Biochemistry, 1995Co-Authors: David S. Goodsell, Kazimierz Grzeskowiak, Richard E. DickersonAbstract:The structure of the B-DNA decamer of sequence C-T-C-T-C-G-A-G-A-G shows a crossed arrangement of helices in the C2 crystal lattice. This is the fourth example of a crossed arrangement of B-DNA oligomers in a crystal, and in spite of the fact that each of these four crystallizes in a different lattice, all have nearly identical structures at the crossing contact. This ubiquitous crossing arrangement may be used to generate a structure for the Holliday junction that is fully consistent with the available physical data.
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The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps.
Journal of Molecular Biology, 1994Co-Authors: David S. Goodsell, Maria Kaczor-grzeskowiak, Richard E. DickersonAbstract:The single-crystal X-ray analysis of trigonal C-C-A-T-T-A-A-T-G-G, and its comparison with orthorhombic C-G-A-T-T-A-A-T-C-G, have shown that the A-T-T-A-A-T sequence has limited polymorphism under the influence of packing forces from neighboring molecules in the crystal. The T-A step is intrinsically variable. It is not inconsistent with a large propeller twist, a narrow minor groove, and a single spine of hydration, as has sometimes been claimed on theoretical grounds. The T-A step does show a persistent positive roll, in a direction that compresses the major groove, and this may be a significant factor in macroscopic DNA curvature induced by phased A-tracts. A-tracts, as understood in this paper, include A-A and A-T steps, but not the T-A step, which is disruptive. Three conclusions regarding A-tract-induced curvature can be drawn from this and other X-ray crystal structure analyses, and from key gel retardation experiments: (1) The A-tract bending model is disqualified on two grounds: (i) tilt-wedge bending within A-tracts is incompatible with the observed direction of curvature; (ii) roll-wedge bending within A-tracts is contradicted by every crystal structure analysis, and is inconsistent with gel retardation results for (G-C-A-A-A-A-T-T-T-T)n and for (A-A-A-A-A-T-T-T-T-T)n. (2) The junction bend model is contradicted by crystallography because: (i) the inclination of base-pairs does not change between A-tract and non-A-tract regions of helix; and (ii) the observed bends at GC/AT junctions are roll-wedge bends, not tilt-wedge as the junction bend model demands. (3) The non-A-tract bending model is consistent with both gel retardation data and with X-ray crystallography, and must be regarded as the only consistent model for A-tract bending.
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Structure of a B-DNA decamer with a central T-A step: C-G-A-T-T-A-A-T-C-G.
Journal of molecular biology, 1992Co-Authors: Jordi Quintana, Kazunori Yanagi, Kazimierz Grzeskowiak, Richard E. DickersonAbstract:The X-ray crystal structure analysis of the decamer C-G-A-T-T-A-A-T-C-G has been carried out to a resolution of 1.5 A. The crystals are space group P212121, cell dimensions a = 38.60 A, b = 39.10 A, c = 33.07 A. The structure was solved by molecular replacement and refined with X-PLOR and NUCLSQ. The final R factor for a model with 404 DNA atoms, 108 water molecules and one magnesium hexahydrate cation is 15.7%. The double helix is essentially isostructural with C-G-A-T-C-G-A-T-C-G, with closely similar local helix parameters. The structure of the T-T-A-A center differs from that found in C-G-C-G-T-T-A-A-C-G-C-G in that the minor groove in our decamer is wide at the central T-A step rather than narrow, and the twist angle of the T-A step is small (31.1 °) rather than large. Whereas the tetrad model provides a convenient framework for discussing local DNA helix structure, it cannot be the entire story. The articulated helix model of DNA structure proposes that certain sequence regions of DNA show preferential twisting or bending properties, whereas other regions are less capable of deformation, in a manner that may be useful in sequence recognition by drugs and protein. Further crystal structure analyses should help to delineate the precise nature of sequence-dependent articulation in the DNA double helix.
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STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-G
Journal of Molecular Biology, 1991Co-Authors: Gilbert G. Privé, Kazunori Yanagi, Richard E. DickersonAbstract:Abstract The crystal structure of the DNA decamer C-C-A-A-C-G-T-T-G-G has been solved to a resolution of 1.4 A, and is compared with the 1.3 A structure of C-C-A-A-G-A-T-T-G-G and the 1.6 A structure of C-C-A-G-G-C-C-T-G-G. All three decamers crystallize isomorphously in space group C 2 with five base-pairs per asymmetric unit, and with decamer double helices stacked atop one another along the c axis in a manner that closely approximates a continuous B helix. This efficient stacking probably accounts for the high resolution of the crystal data. Comparison of the three decamers reveals the following. 1. (1) Minor groove width is more variable than heretofore realized. Regions of A · T base-pairs tend to be narrower than average, although two successive A · T base-pairs alone may not be sufficient to produce narrowing. The minor groove is wider in regions where B II phosphate conformations are opposed diagonally across the groove. 2. (2) Narrow regions of minor groove exhibit a zig-zag spine of hydration, as was first seen in C-G-C-G-A-A-T-T-C-G-C-G, whereas wide regions show two ribbons of water molecules down the walls, connecting base edge N or O with sugar O-4′ atoms. Regions of intermediate groove width may accommodate neither pattern of hydration well, and may exhibit a less regular pattern of hydration. 3. (3) Base-pair stacking is virtually identical at equivalent positions in the three decamers. The unconnected step from the top of one decamer helix to the bottom of the next helix is a normal helix step in all respects, except for the absence of connecting phosphate groups. 4. (4) B II phosphate conformations require the unstacking of the two bases linked by the phosphate, but do not necessarily follow as an inevitable consequence of unstacking. They have an influence on minor groove width as noted in point (1) above. 5. (5) Sugar ring pseudorotation P and main-chain torsion angle δ show an excellent correlation as given by the equation: δ = 4 ° cos ( P + 144 °) + 120 °. Although centered around C-2′- endo , the conformations in these B -DNA helices are distributed broadly from C-3′- exo to O-4′- endo , unlike the tighter clustering around C-3′- endo observed in A -DNA oligomer structures.
