Library

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 561-584 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Matrix generator techniques have been adapted to account for precise structural features of the nucleotide repeating unit and to translate the primary sequence of DNA base pairs into three-dimensional structures. Chains have been constructed to reflect the local sequence-dependent differences of bending and twisting of adjacent residues and various overall chain properties, including the average unperturbed moments of the end-to-end vector r and the mean angular orientation (〈γ〉 between base pair normals, 〈φ1〉 between long axes, and 〈φ2〉 between short axes) of terminal chain residues, have been computed. The chain backbone is treated implicitly in terms of the spatial fluctuations of successive base pairs. Motions are limited to low-energy perturbations of the standard B-DNA helix. Approximate potential energy schemes are used to represent the rules governing the patterns of local base-base morphology and flexibility. Theoretical predictions are compared with experimental observations at both the local and the macro-molecular level. Initial applications are limited to the rodlike poly(dA) · poly(dT) and poly(dG) · poly(dC) helices. The former duplex is found to be more compressed and the latter more extended than random-sequence DNA of the same chain length. The flexibility of the duplexes as a whole is described in terms of the average higher moments of the displacement vector ρ = r - 〈r〉 and the likelihood of chain cyclization is estimated from the three-dimensional Hermite series expansions of the displacement tensors. Emphasis is placed on theoretical methodology and the practical relevance of the calculated chain moments to observed physical properties.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270403
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Base sequence effects in double-helical DNA. III. Average properties of curved dna (1988)
    New York : Wiley-Blackwell
    Biopolymers 27 (1988), S. 585-603 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The matrix-generator methods set forth in the preceding paper for treating rodlike DNA are adapted here to the calculation of average chain extension, macroscopic flexibility, and terminal residue orientation in curved duplexes. The different characteristics of curved vs rodlike chains are illustrated with the hypothetical poly[d(A5G5)] · poly[d(T5C5)] duplex. The curved helix is both more compact and macroscopically stiffer than either the poly(dA) · poly(dT) or the poly(dG) · poly(dC) chain. The calculations have also been extended to simple repetitive DNA sequences generated by synthetic ligation studies and the computed average chain properties compared with observed gel mobilities. The predicted chain extension is also checked against the measured persistence lengths of the rodlike poly[d(GC)] and poly[d(AT)] alternating copolymers, and the known cyclization tendencies of selected repeating sequences. Chains are generated from local potential energy maps describing the morphology and flexibility of adjacent base pairs. The energy maps, while approximate, are more accurate descriptors of local structure than many of the intuitive models of DNA curvature offered to date. According to the energy surfaces, the intrinsic bending of curved DNA can be traced to asymmetry in the bending of the Gs and Cs that join half-helical turn stretches of adenines in these chains. The oligo A stretches are analogous to residues of a perfectly elastic DNA that bend with equal likelihood in opposing directions. In other models of DNA curvature, the (G · C) base pairs are presumed to adopt the classical B-DNA structure, while the (A · T) base pairs are thought to be in some perturbed conformation.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360270404
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Electrostatic interactions in ionic homopolypeptides in solutions of moderate ionic strength (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 2181-2194 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: At sufficiently high ionic strength, long-range electrostatic interactions in a polyelectrolyte such as poly(L-glutamic acid) might be adequately approximated in matrix calculations by use of statistical weights representing second-order interactions. The validity of this assumption has been investigated making use of experimental observations (CD spectra and titration curves) for poly(L-glutamic acid) as a function of temperature in 0.1-0.5M sodium chloride. Theoretical analysis, using a statistical weight matrix proposed by Warashina and Ikegami, is based on the Zimm-Rice theory. Implementation differs from that of Warashina and Ikegami in one respect. Refinement of the initial estimates is achieved using a form of the configuration partition function which does not assume diagonalization of the statistical weight matrix. This difference is of no consequence for the values of σ and s, but it does produce somewhat different values for the statistical weights used to represent the electrostatic interactions. The method used to treat electrostatic interactions in poly(L-glutamic acid) in 0.1M sodium chloride can be viewed as successful in that it properly reproduces the helix-coil transition and titration curves in this solvent and the molecular-weight dependence of the titration curves yields values for s in harmony with those obtained using a treatment which is independent of model, and gives a reasonable ionic-strength dependence for the electrostatic parameters. Furthermore, the model can account for measured helix-coil transitions and titration curves in homopolypeptides in which the side chain is  - (CH2)xNHCO(CH2)yCOOH. The model, however, is not exact. It does not properly account for the molecular-weight dependence of the helical content for polymers of low degree of polymerization.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360201011
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...