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S Hanlon

Publications and source records attributed to S Hanlon.

At least 37 records · Page 2Linked to original sources
PubMed1978

Specific cation effects on conformational transitions of DNA in aqueous solutions.

The circular dichroism (CD) and absorption spectral properties of calf thymus DNA have been examined in aqueous solutions containing varying concentrations of MgCl2, CaCl2, MnCl2, ZnCl2 and CoCl2. When the CD spectra were analyzed by methods previously described (Hanlon, S., Brundno, S., Wu, T.T. and Wolf, B. (1975) Biochemistry 14, 1648--1660), it was found that the spectral changes observed between 0 and 0.1 molal concentrations of each salt could be satisfactorily accounted for as a linear combination of two independent spectral components. One of these components had the spectrum which we had previously obtained in dilute solutions of NaCl (0.01-0.04 molal) and in 0.2 M tetramethyl ammonium chloride and attributed to a B-like structure. The other spectral endpoint was similar but not identical to the C spectrum obtained in the monovalent series. These differences were particularly pronounced for the transition metal ions, Mn2+, Zn2+ anc Co2+. Since significant band shifts were also observed in the absorption spectra of DNA in the presence of these transition metal ions, we have concluded that the differences observed between the C spectrum previously reported and that found for these ions is attributable to changes in the absorption properties of the monomers due to cation association, rather than dramatic differences in comformational properties of the C secondary structure of DNA in the presence of these ions. The greater efficiency of these divalent ions compared to the monovalent ions previously studied in effecting the B leads to C transconformational reaction is attributed to the more effective screening of electrostatic interactions, both along the phosphate backbone, and between sites on the bases which bear partial negative charges and the negatively charged phosphate groups. In the light of these present results, we believe that it is this electrostatic factor which is primarily involved in effecting the transition from a B to a more C-like state. The role of dehydration is viewed as a subsidiary one which facilitates better ion association, especially at the weaker base sites, thus effecting better damping of the repulsive electrostatic interactions.

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PubMed1977

Structural transitions of calf thymus DNA in concentrated LiCl solutions.

The solubility, sedimentation, circular dichroism, and absorption spectral characteristics of calf thymus DNA have been examined in concentrated solutions of LiCl (6-13 m) at 25 to 27 degree C. At all concentrations of LiCl, the DNA is base stacked and exhibits normal hypochromicty, At the upper end of this range of LiCl concentrations, DNA aggregates and ultimately precipitates completely from solution between 13 and 14 m LiCl. This aggregation process is dependent on concentration, base composition, and molecular weight of DNA. The sedimentation velocity data taken together with the absorbance spectral data suggest that the aggregation process leading to the formaiton of large structures beings at approximately equal to 9 m. Prior to the onset of aggregation, the circular dichroism (CD) spectra can be adequately fitted by a linear combination of contributions of the B, C, and A forms of DNA (Hanlon, S., Brudno, S., Wu, T. T., and Wolf, B. (1975), Biochemistry 14, 1648). Above 9 m LiCl, both factor analysis and a primitive version of matrix rank order analysis indicate that at least one additional spectral component is required to account for the observed CD spectra above 260 nm. The general shape of this additional component or distortion resembles the psi form of DNA.

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PubMed1976

Comparison of the phosphorus magnetic resonance and circular dichroism properties of calf thymus DNA and chromatin.

Dual measurements of the 31P magnetic resonance spectra and the circular dichroism spectra have been made on calf thymus DNA and purified chromatin. The 31P magnetic resonance signals for all samples fell at 1.2 +/- 0.1 ppm relative to 85% orthophosphoric acid. The full width at half-height of the signal of samples in which the molecular weight of the native DNA component was in the 2-9 X 10(6) range was ca. 50 Hz. This bandwidth was reduced dramatically to ca. 20 Hz by reducing the molecular weight to 140 000 (by sonication) or by heat denaturation of the high-molecular-weight DNA. The position of the signal and the bandwidth of the chromatin samples did not differ significantly from that of the DNA samples of comparable molecular weight and state of nativity. The intensities of the chromatin signals, however, were all less than those of signals of DNA in companion runs conducted under comparable experimental conditions. The reduction of the intensity of the magnetic resonance signal paralleled the lowering of the intensity of the positive band above 260 nm in the circular dichroism spectrum of the given sample of chromatin relative to the spectrum of protein-free DNA. In fact, the percent reduction of the magnetic resonance signal of chromatin relative to protein-free DNA was, within experimental error, equal to the percentage of nucleotide residues in the Watson-Crick B secondary structure. Since the latter fraction of residues can be correlated with those in the interbead regions of the superstructure of chromatin, we have concluded that the signal of the nucleotide residues in the beads, or v bodies, has been broadened to the point of extinction by a packing arrangement which maximizes phosphate-protein interactions and structural rigidity.

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PubMed1975

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. I. Reference spectra of conformational limits.

The circular dichroism properties of calf thymus DNA have been examined at 27 degrees over the wavelength range of 215-300 nm in aqueous solutions of NaCl, KCl, LiCl, CsCl, and NH4Cl at pH 7. The concentrations of these electrolytes were varied from 0.01 to ca. 5-10 m. The spectral changes induced by changes in concentration of NaCl and KCl and all but the highest concentrations of NH4Cl as well as lower concentrations of Cstcl and LiCl could be represented by a common two-state transition involving the conversion of the typical conservative spectrum commonly seen in dilute solutions of these salts to a nonconservative spectrum similar to that obtained by Tunis-Schneider and Maestre ((1970), J. Mol. Biol. 52, 521) for the C form of DNA. At higher concentrations of CsCl, LiCl, and NH4Cl, an additional component, resembling an A type spectrum, was required to account for the observed CD changes with changing concentration of electrolyte. Relying on the published spectra of the B, the C, and the A forms of DNA by Tunis-Schneider and Maestre for identification and approximate values of the molecular ellipticities of these forms, we have analyzed these spectral transitions by two least mean squares methods in order to obtain accurate reference spectra of aqueous "B", C, and "A" conformations of calf thymus DNA. The results obtained suggest that although the C form in solution is identical with that obtained in film, the aqueous B conformational limit is not identical with the crystallographic Watson-Crick structure. In addition, the A form generated in solution under our experimental conditions appears to be more similar to that assumed by low molecular weight Escherichia coli DNA at 75% relative humidity rather than calf thymus DNA at the same relative humidity.

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PubMed1975

Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration.

The data and approach reported in paper I (Hanlon et al., 1975, preceding paper) have been used to calculate the fractional changes in secondary structure of calf thymus deoxyribonucleic acid which occur in aqueous solutions as a function of the concentration of NaCl, KCl, LiCl, CsCl, and NH4Cl. There is a continuous loss in the "B" character of the nucleic acid with concomitant production of the C and, in some instances, an A form, as well, as the salt concentration increases. Sedimentation velocity studies suggest that there is an accompanying change in the hydrodynamic characteristics of the DNA molecules, as well. Utilizing the existing hydration data in the literature (Hearst and Vinograd, 1961a,b; Hearst, 1965; Tunis and Hearst, 1968a; Cohen and Eisenberg, 1968; Falk et al., 1962, 1963a,b), we have found that a gradual loss of "B" character and a decrease in the frictional coefficient of DNA occur as the net hydration of DNA is reduced from the fully hydrated from (60-80 mol of H2O/mol of nucleotide) to values of ca. 12-14 mol of H2O/mol of nucleotide. Below that value, a more precipitous decrease in these properties occurs. Extrapolation of the linear relationship observed between the fractional B content and the net hydration in the latter regions yield values of ca. 18 mol of H2O/mol of nucleotide at 100% B and ca. 4 mol of H2O/mol of nucleotide at 0% B (i.e., 100% C or C + A) for the alkali metal salts of DNA. The ammonium salt retains somewhat more H2O in the C and A forms (ca. 7). These results together with the hydration site assignments of Falk et al. (1962, 1963a,b) are interpreted in terms of a hydration model for DNA in aqueous solution in which an intact primary hydration shell of ca. 18 mol of H2O/mol of nucleotide is required for the maintenance of the "B" conformation. Removal of all but those water molecules solvating the phosphate groups results in the conversion to the C forms, predominantly, with a small amount of A structure formed as well in some salts. The accompanying changes in the sedimentation coefficients suggest that the DNA molecule assumes a more compact and/or flexible form under these conditions in which it is mainly in the C and A structures. The combination of these two events which ensue upon dehydration create a polymeric structure which can be more easily packaged in biological systems.

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PubMed1972

Mixed conformations of deoxyribonucleic acid in chromatin: a preliminary report.

We have established empirical limits for the circular dichroism spectra appropriate for aqueous solutions of the B, C, and A forms of calf-thymus DNA and have analyzed DNA conformations in biological structures. The circular dichroism spectrum above 250 nm of purified calf-thymus chromatin can be satisfactorily accounted for as a linear combination of contributions of the B and C reference spectra without invoking higher-order structures such as supercoils. The amount of A contribution, if any, is below the limit of detection (</=4%). The fraction of bases in the B conformation depends on the method of isolation of nucleohistone, and ranges from 30-50%. The B content of a given preparation is increased by addition of a chelating agent and decreased by addition of divalent ions. More radical increases ensue upon protein removal. Nuclease treatment results in a dramatic decrease in B content. The fraction of bases melting out in the lower transitions of the complex melting profile of a given chromatin preparation corresponds to its B content. We propose a model for chromatin structure in which part of the DNA duplex is exposed or accessible to the solvent and is in the B conformation. The remainder of the base pairs and ribophosphate backbone are protected from interaction with the solvent by efficient histone coverage and are in the C conformation. Divalent ions modulate the distribution of bases between these two conformations.

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