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  • Polymer and Materials Science  (5)
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  • 1
    Electronic Resource
    Electronic Resource
    Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1059-1077 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotides have been measured. The dimer spectra are quite different from the sum of the spectra of their constituent monomers. This indicates the presence of base-stacked conformations analogous to those found for ribonucleoside diphosphates. The CD spectra of several deoxytrinucleotide diphosphates and single-strand f 1 DNA can be calculated fairly well by using a semi-empirical nearest-neighbor approach. There is little or no effect of terminal phosphate or of salt concentration on the optical properties of most deoxy oligomers. The possibility of simultaneous analysis of mixtures of deoxypurine or deoxypyrimidine sequence isomers has been examined. This seems to be a viable approach for the analysis of purine runs but cannot promise much success for pyrimidine runs.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090909
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Oligonucleotide interactions. IV. Conformational differences between deoxy- and ribodinucleoside phosphates (1970)
    New York : Wiley-Blackwell
    Biopolymers 9 (1970), S. 1079-1103 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The circular dichroism spectra of all 16 ribodinudeoside phosphates containing the bases adenine, uracil, cytosine, and guanine have been measured at room temperature and neutral pH. These results are compared with the circular dichroism spectra of the corresponding deoxy compounds. From the optical properties it is clear that the geometry of the base-stacked conformation of ribo compounds must differ substantially from that of deoxy compounds. Because of this, it is not possible to draw firm conclusions about the relative extent of stacking in most ribo and deoxy compounds. The optical rotatory dispersion of about a dozen deoxy and ribodinucleoside phosphates has been studied as a function of temperature. These results confirmed the conclusions drawn earlier from measurements at a single temperature. Several dinucleoside phosphates containing a 2′ → 5′ phosphodiester bond have also been examined. These compounds have a substantial degree of base stacking at room temperature. The geometry of the stacked conformation is different from that of either the normal ribo dimer or the deoxy dimer. The role of the 2′-hydroxyl group in stabilizing base stacked geometries has been examined by studies on C-2′-O-methyl-pC. This compound has optical properties almost identical to those of CpC. This suggests that the effect of the 2′ hydroxyl is felt indirectly through its perturbation of the geometry of the sugar ring rather than directly by hydrogen bonding. It is not possible at present to identify precise conformational differences among deoxy-, ribo-and 2′ → 5′ ribodinucleoside phosphates.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1970.360090910
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Dinucleoside monophosphates. I. Optical properties and conformation in solution with one base charged (1976)
    New York : Wiley-Blackwell
    Biopolymers 15 (1976), S. 1755-1773 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A least squares analysis of the titration properties of several dinucleoside monophosphates enables calculation of the pK's for protonation. These pK's are used to resolve the spectral properties of dinucleoside monophosphates with one base charged from the apparent spectral properties of a dinucleoside monophosphate in aqueous solution. This method is applied to dinucleoside monophosphates containing adenosine and/or cytidine. Results of CD, nmr, and CD-temperature dependence measurements are presented. The results indicate that singly protonated dimers of these nucleosides stack as do their unprotonated analogs. It is suggested that this is true for all dimers with one base charged.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1976.360150911
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  • 4
    Electronic Resource
    Electronic Resource
    Dinucleoside monophosphates. II. Nearest neighbor interactions (1976)
    New York : Wiley-Blackwell
    Biopolymers 15 (1976), S. 1775-1793 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method has been developed which enables calculation and unambiguous comparison of the thermodynamics for the stacking process of dinucleoside monophosphates (dimers) from a study of their titration properties. This method has been applied to dimers containing adenosine and/or cytidine with the result that the dimers studied can be ordered with respect to their tendency to stack as ApA 〉 ApC 〉 CpA ≃ C - containing homodimers. This dependence of the relative magnitude of ΔFstacking on composition is consistent with hydrophobic interactions, as manifested by the solubility of the bases, being the main driving force toward stacking. The sequence dependence of ΔFstacking as well as of the optical properties of the dimers is related to van der Waals interaction between the bases. The lack of variation in ΔFstacking of the C-containing isomers indicates that the role of the 2′-OH in RNA versus DNA structure is not H-bonding.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1976.360150912
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  • 5
    Electronic Resource
    Electronic Resource
    The Structures and Properties of Poly-5-methylcytidylic AcidThis work was supported in part by an NSF Grant GB8569 (to M. M. W.) and by Institutional Funds from NIH Grant FR-07062 and ACS Grant 14M (to N.Y.U.). (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1269-1287 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The optical rotatory dispersion properties of poly 5MeC, poly diMeC, and 5MeCMP-(5′) in 0.1M Na+ have been studied at various pH values and temperatures. Poly 5MeC and poly diMeC have optical properties which are similar to those for poly C; however, poly 5MeC has a biphasic melting profile in the pH range from 3.8 to 5.4 similar to that observed for poly 51C. Using titration, ionic strength, and pH dependence measuements, the data for poly 5MeC are interpreted in terms of the following scheme at pH 4.0 and 0.1 ionic strength: triple-strand helix 37°C double-strand helix 79°C single-strand coil. Support for this scheme is discussed. The effect of the methyl group is discussed in terms of similar structural possibilities for other polymers of cytidylic acid.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110611
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    Paper (German National Licenses)
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