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  • Polymer and Materials Science  (4)
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  • 1
    Electronic Resource
    Electronic Resource
    Molecular-mechanics studies on d(CGCGAATTCGCG)2 and dA12·dT12: An illustration of the coupling between sugar repuckering and DNA twisting (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 2345-2376 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired deoxy dodecanucleoside undecaphosphates d(CGCGAATTCGCG)2 and d(A12)·d(T12). These refinements were carried out using the model-built Arnott B-DNA geometry as initial coordinates (with a helix repaeat of 10.0 residues/turn), as well as helix repeats ranging from 9 to 12 residues/turn. There was some variation in the optimum calculated helix repeat, depending on the dielectric model, the presence or absence of counterions, and the method used for inclusion for nonbonded interactions; the most interesting general result of these calculations was the coupling between furanose sugar puckering and twist. This coupling was observed for all models. With a helix repeat of 9.0 residues/turn, all sugars remain C(2′)endo after refinement; as the helix repear increases to 12.0 residues/turn, the number of sugars repuckering to O(1′)endo and C(3′)endo increases also. With our most rigorous model (i.e., a model with no cutoff distance for nonbonded interactions) and a helix repeat of 10.0 residues/turn, we find a greater tendency for pyrimidine than purine repuckering in d(CGCGAATTCGCG)2, in agreement with the x-ray structural data of Drew et al. [(1981) Proc. Natl. Acad. Sci. USA 78, 2179-2185].We also carried out a number of calculations in which we “forced” one of two deoxy sugars to repucker or one of the C3′-O3′-P-O5′ (ω) torsion angles to change from gauche- to trans using dihedral angle constraints. After the constraints were removed, some of these structures “reverted” to the sugar pucker of the initial structures, while others remained repuckered. In all cases, the energies for repuckered structures after refinement were very similar to energies of the initial structure. Experiments and theory suggest that local conformational fluctuations play an essential role in nmr relaxation of 31P and 13C atoms in double-helical DNA. The results of our previous calculations on hexanucleoside phosphates and the calculations presented there are consistent with an important contribution to nmr relaxation processes of conformational changes in the torsion angle ω′ from gauche- to trans and deoxy sugar repuckering from C(2′)endo to C(3′)endo. Specifically, the calculations presented here indicate a very flexible phosphate backbone in helixes having an intermediate helix repeat of 10 to 11 residues/turn. These helixes may accommodate sugars of variable pucker without significantly disrupting base-base hydrogen-bonding and stacking interactions. All of the variant structures are similar in energy, suggesting that conversion between them can occur on a nanosecond time scale, as observed in nmr relaxation experiments.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360211204
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechannics (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 969-1002 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360220316
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  • 3
    Electronic Resource
    Electronic Resource
    Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2583-2621 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We present the results of molecular-mechanics studies on base-paired dinucleoside phosphates and hexanucleoside pentaphosphates. Starting from B-DNA-like conformations, we have refined the nucleic acid conformations, allowing all degrees of freedom to relax. The calculated energies of different base sequences are used to investigate the basis for the different stabilities of DNA polymers of different sequences, as found by Wells et al. [J. Mol. Biol. 54, 465-497, 1970]. Our calculations appear to reproduce the relative melting temperatures of sequence isomers as well or better than any of the previous calculations which addresssed the question of nucleotide stability. We offer a detailed physical explanation of three observations, that poly(dA)·poly(dT) melts higher than poly[d(A-T)]·poly[d(A-T)] by 6°C, that poly(dG)·poly(dC) melts lower than poly[d(G-C)]·poly[d(G-C)] by 12°C, and that poly(dA-dG)·poly(dT-dC) melts lower than poly(dA-dC)·poly(dT-dG) by 6°C. The dihedral angles found after refinement are similar to those of Levitt [Proc. Natl. Acad. Sci. USA 75, 640-644, 1978] and differ by ∼20° from the B-DNA values. We also see evidence of base tilting and twisting similar to that found by Levitt. The two main differences in the results of our calculations and Levitt's lie in the sugar puckers [we find mainly C(2′)endo] and in the tendency to stay in local “torsional” minima (we find a number of examples of C(3′)endo sugar puckering and ω′ = trans rather than gauche). Both of these results are dependent on the nature of the potential function used in our study. However, our finding of movement from local torsional minima is suggestive of the significant flexibility of double-stranded deoxynucleotides.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360201208
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular-mechanical studies of Z-DNA: A comparison of the structural and energetic properties of Z- and B-DNA (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 1945-1969 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Molecular-mechanical studies of the left-handed Z-DNA polymers have been carried out and the results compared with similar calculations on B-DNA polymers. We have studied d(CGCGCG)2, d(GCGCGC)2 (and their 5-methyl cytosine analogs), dG6·dC6, d(ATATAT)2, and d(TATATA)2 in both B- and Z-forms. For the left-handed Z helices, we considered the ZI and ZII model of Quigley and co-workers [Wang, A. H., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979) Nature (London) 282, 680-686], the actual “Z spermidine” and “Z spermine” structures of Quigley and the model-built structure of Chandresekharan et al. [Arnott, S., Chandresekharan, R., Bindsall, D. L., Leslie, A. G. W. & Ratliff, R. L. (1980) Nature 283, 743-745]. The major conclusions of this study are as follows. (1) The stabilization of Z-DNA relative to B-DNA occurs as one increases the “effective” dielectric constant or adds counterions, consistent with observations of Z-DNA only under high salt conditions. (2) The ZII polymer is calculated to be more stable than the ZI polymer. It is not yet clear whether the greater stability of ZII than ZI is a real effect or an artifact caused by the lack of inclusion of specific solvation effects in these calculations. (3) The greater tendency of the 5-methyl cytosine analog of poly(dG-dC)·poly(dG-dC) to undergo the B → Z transition is found in our calculations and is due to destabilizing base-base and base-phosphate interactions, which are greater in the B- than in the Z-form of the 5-methyl cytosine polymer. (4) There are no large sequence-dependent effects on the relative stabilities, and the AT polymers are calculated to be as likely to form Z-helices as the GC polymers. In addition, the relative stability of a nonalternating sequence in the conformation is only slightly less than that found for alternating sequences.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360211003
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    Paper (German National Licenses)
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