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  • 1
    Electronic Resource
    Electronic Resource
    Circular dichroism of the nucleic acid monomers (1977)
    New York : Wiley-Blackwell
    Biopolymers 16 (1977), S. 2243-2264 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Circular dichroism spectra of the nucleic acid monomers have been measured in aqueous solution and extended into the vacuum ultraviolet region to about 166 nm. Measurements were made on ribo and deoxyribo derivatives of adenine, guanine, hypoxanthine, cytosine, thymine, and uracil derivatives both with and without the 5′-phosphate (with the exception of ribosyl thymine 5′-phosphate). Absorption spectra of the deoxyribonucleotides measured to about 175 nm are also presented. The results demonstrate that both the circular dichroism and absorption spectra observed below 200 nm are no more complicated than the spectra normally recorded above 200 nm. In most cases, the circular dichroism spectra of the various derivatives of a given base are similar, indicating that the conformations are similar. On the other hand, the differences among the circular dichroism spectra of the various derivatives of a given base are sufficient to identify a particular derivative. The average circular dichroism for the deoxyribonucleotides is compared with the circular dichroism of native E. coli DNA. The comparison reveals that the circular dichroism of DNA below 200 nm is due principally to the interaction between the bases rather than the intrinsic circular dichroism of the monomers. The monomer transitions are discussed in relationship to the absorption and circular dichroism spectra presented.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1977.360161012
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  • 2
    Electronic Resource
    Electronic Resource
    Polynucleotide conformation from flow dichroism studies (1982)
    New York : Wiley-Blackwell
    Biopolymers 21 (1982), S. 1763-1780 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We demonstrate that the isotropic absorption and linear dichroism in an unknown flow field can be used to determine base tilt in polynucleotides if three transitions are measured and the directions of the corresponding dipoles are known. The method is applied here to reach conclusions about the base tilt in poly(rA), poly(rA)+·poly(rA), and poly(rC). The respective values are: 28° tilt about the axis + 50° toward C8 from the C1′ → N9, and 25° tilt about the axis + 118° toward C5 from C1′ → N1. The results for poly(rA)+·poly(rA) are consistent with the accepted model. Spectra were measured for poly(rC)+·poly(rC), but definite conclusions must await reliable directions for transition dipoles. The dipole direction for the 218-nm transition in rC is found to be +13° or +43° toward C5 from C1′ → N1. The CD spectra to about 168 nm are presented and discussed.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360210907
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  • 3
    Electronic Resource
    Electronic Resource
    Quantum-mechanical theory of CD for infinite helical polymersThis paper is dedicated to the memory of Irvin Isenberg. (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 1337-1363 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Quantum-mechanical equations are derived that are particularly well suited to actual computations of the CD for helical polymers. They make use of cyclic boundary conditions and helical symmetry, so that only two matrices with a size equal to the number of transitions considered need be diagonalized. The final equations are expressed directly in terms of monomer properties and helical parameters to invite the same input as earlier calculations, and are given as a rotational strength times a shape function for ease of comparison with the earlier work. The shape of the helix term is expressed as a derivative with respect to ω and depends on the distance between monomers along the helix axis. Other terms involving two electric transition dipoles depend on the distance from the helix axis to the transition center. These equations are directly comparable to the classical equations derived for cyclic boundary conditions and helical symmetry. We present an outline of the derivation and enough intermediate steps to clarify how the equations arise.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360240718
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  • 4
    Electronic Resource
    Electronic Resource
    Multivalent ions are necessary for poly[d(AC) · d(GT)] to assume the Z form: A CD study (1992)
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 271-276 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In previous work, it was shown that poly [d(AC) · d(GT)] could be forced into the Z form by strong dehydrating conditions, provided EDTA was not present. Presumably multivalent impurities were also necessary for the transition. In order to gain control over the B to Z transition for this DNA, we carefully removed all divalent contaminants from the sample and asked the obvious question: What ions are necessary for the transition under dehydrating conditions? We systematically investigated the effect of various multivalent ions. The common contaminants Ca2+, Mg2+, and Fe3+ will not cause the transition, but Co2+ and Ni2+ facilitate the transition, undoubtedly because of their well-known propensity to bind to purine N7. Since the transition also depends on the synergistic dehydrating action of sodium perchlorate and ethanol, we include CD spectra for the independent variations of these two factors. In addition, vacuum-uv CD spectra for the A form and various B forms of poly [d (AC) · d (GT)] are presented for the first time.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360320307
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  • 5
    Electronic Resource
    Electronic Resource
    Conformation and circular dichroism of DNA (1979)
    New York : Wiley-Blackwell
    Biopolymers 18 (1979), S. 1009-1019 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: CD spectra of calf thymus, C. perfringens, E. coli, and M. luteus DNA have been measured in the vacuum-uv region to about 168 nm for the A-, B-, and C-forms. The positive band at about 187 nm and the negative band at about 170 nm found for each type and form of DNA are sensitive to the source of the DNA and the base-base interactions of the double-stranded helix. The A-form spectra confirm that these bands are indeed sensitive to secondary structure. In the near-uv, the CD of B-form DNA is well analyzed as a linear combination of 27% A-form and 78% C-form. However, an analysis of the extended spectrum demonstrates that the near-uv analysis is not correct. The extended analysis shows that the base-base interactions are similar for B- and C-forms in solution, which implies that these two forms have nearly the same number of base pairs per turn. Various types of CD difference spectra are also discussed.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1979.360180418
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  • 6
    Electronic Resource
    Electronic Resource
    Properties of P-form DNA as revealed by circular dichroism (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 1589-1603 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Investigations of DNA using CD spectroscopy show that the P-form is available in a wide variety of methanol-ethanol mixtures when the water content is low. Increasing the temperature or the ethanol content of a 95% methanol solution causes DNA to undergo a cooperative transition to the P-form. However, this transition cannot be reversed on cooling, or on adding methanol. Thus P-form DNA appears to be stable at high methanol concentrations, but it is usually not observed because the DNA is trapped by a kinetic barrier. P-form DNA will instantaneously assume the native B-form on addition of water, confirming earlier reports that P-form DNA is not strand separated [E. Kay (1976) Biochemistry 15, 5241]. CD spectra extended to 190 nm show that there is no base-base interaction in the P-form. However, the P-form is extremely stable to heat denaturation in solvents which promote hydrogen bonding between the base pairs. A number of models that can account for the properties of P-form DNA are discussed.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1981.360200803
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  • 7
    Electronic Resource
    Electronic Resource
    Conformation of P-form DNA (1984)
    New York : Wiley-Blackwell
    Biopolymers 23 (1984), S. 1269-1281 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The P-Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P-form has little or no hydrogen bonding, while the data from EM show that the P-form has a condensed tertiary structure. In earlier work, we demonstrated that the P-form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P-Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P-form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non-hydrogen-bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P-form that have been observed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360230711
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  • 8
    Electronic Resource
    Electronic Resource
    Base tilt of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in solution determined by linear dichroism (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 825-841 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have measured the CD, isotropic absorption, and LD of poly[d(A)]-poly[d(T)] and poly[d(AT)]-poly[d(AT)] in the vacuum-uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space-filling models of poly[d(A)]-poly[d(T)] and poly[(AT)]-poly[d(AT)] are built based on our results, and the conformations of the two (A + T) polymers in solution are discussed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360240508
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  • 9
    Electronic Resource
    Electronic Resource
    Conformational transitions of calmodulin as studied by vacuum-UV CD (1987)
    New York : Wiley-Blackwell
    Biopolymers 26 (1987), S. 561-571 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: CD measurements were made for calmodulin and its calcium (Ca2+) complexes at different ionic strengths and Ca2+ concentrations. Calmodulin at an ionic strength of 0.00M and in the absence of Ca2+ exists as an α-helical protein with a negligible amount of β-sheet. An increase in ionic strength, whether or not Ca2+ is present, increases α-helix at the expense of “other” (coil) structure. The changes in β-sheet and β-turns are insignificant. Binding of Ca2+ at low ionic strength occurs in stages with at least one folding intermediate before attaining the final stable state. Binding of Ca2+ at an ionic strength of 0.165M causes only a slight increase in α-helix, so that the secondary structure of the protein depends on ionic strength and is insensitive to the nature of the cation (i.e., Ca2+). Thus, the activation of calmodulin by Ca2+ must be due to a structural reorientation rather than to a major secondary structural alteration. The CD estimation of secondary structure with 4 mol Ca2+/calmodulin (61% α-helix, 2% antiparallel β-sheet, 2% parallel β-sheet, 21% β-turns, and 14% other) is in excellent agreement with the x-ray results.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360260409
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  • 10
    Electronic Resource
    Electronic Resource
    Poly[d(Gm5C)·d(Gm5C)] can assume the Z′ form: A CD study (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 821-828 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Poly [d(Gm5C)·d(Gm5C)] can be titrated from the Z form in 30% ethanol to the Z′ form by adding either ethanol or divalents. Analysis by singular-value decomposition of CD spectra recorded during the titration reveal that ethanol and transition metal induced changes are two state with a single-step titration curve. When the change is induced by arkaline earth metals it is still two state, but in contrast the titration curve is complex, indicating two binding sites.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300717
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