Deoxyribonucleic acid-polylysine complexes. Structure and nucleotide specificity

Shapiro, Jewel T.; Leng, Marc; Felsenfeld, Gary

doi:10.1021/bi00836a014

Cited by 252 publications

(160 citation statements)

References 24 publications

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“…These alterations, particularly the increase in optical density at the wavelengths exceeding 320 nm, the decrease of the band intensity at 260 nm in the absorption spectrum, and the appearance of a new intense negative band in the CD spectrum observed in PEG-containing WS-solutions of native DNA at room temperature, resemble the alterations occur: ing in native DNA spectra after adding certain polycations such as, for example, polyamino acids [3][4][5].…”

Section: Introductionmentioning

confidence: 99%

Viscosimetric study on compact form of DNA in water—salt solutions containing polyethyleneglycol

Akimenko¹,

Dijakowa

Evdokimov³

et al. 1973

FEBS Letters

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Section: Introductionmentioning

confidence: 99%

Viscosimetric study on compact form of DNA in water—salt solutions containing polyethyleneglycol

Akimenko¹,

Dijakowa

Evdokimov³

et al. 1973

FEBS Letters

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“…Circular dichroism (CD) studies, although at one time devoted to simple molecules (1,2), have recently been focused upon a variety of complex biological macrostructures. Much promising CD work has been contributed on the molecular conformation of DNA in chromosomes (3), chromatin (4)(5)(6)(7)(8)(9)(10)(11)(12), and related material, such as reconstituted nucleohistone (13)(14)(15)(16)(17)(18)(19) or other model systems for DNA-protein interactions (20)(21)(22)(23). The structure of virus particles has been studied with CD in this laboratory (24).…”

mentioning

confidence: 99%

Experimental Differential Light-Scattering Correction to the Circular Dichroism of Bacteriophage T2

Dorman

Maestre

1973

Proc. Natl. Acad. Sci. U.S.A.

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Experimental techniques are presented that can be used to assay and correct for differential light scattering effects in circular dichroism spectra of biological macrostructures. The assay is based upon use of variable detector geometries that collect light over large solid angles. Disrupted T2 virus suspensions and purified T2 phage DNA exhibit geometry-independent spectra; the spectrum of intact T2 virus is highly sensitive to detection geometry. On the basis of spectra obtained after light-scattering correction, the structure of T2 DNA in the phage particle is assigned to the C form. We conclude that: (i) The measured circular dichroism of a light-scattering specimen may be highly sensitive to light-detection geometry of the instrument. This effect is indicative of differential scattering intensity for left and right circularly polarized light. (ii) Some optically active particles, although they scatter light intensely, exhibit circular dichroism that is independent of detection geometry and, therefore, apparently uninfluenced by differential light scattering. We infer that whether differential light scattering arises may depend upon the presence or absence of ordered asymmetry in the organization of the scattering particle. (iii) The circular dichroism of any light-scattering specimen should be measured again in apparatus designed for differential light-scattering correction as a prerequisite to meaningful structural conclusions. (iv) Differential scattering effects in circular dichroism may be potentially useful as a probe for large-order organization of the scattering particle. Circular dichroism (CD) studies, although at one time devoted to simple molecules (1, 2), have recently been focused upon a variety of complex biological macrostructures. Much promising CD work has been contributed on the molecular conformation of DNA in chromosomes (3), chromatin (4-12), and related material, such as reconstituted nucleohistone (13)(14)(15)(16)(17)(18)(19) (25-27, 29, 30, 32, 33, 35), other concentration-obscuring effects (30, 32, 33), and differential light scattering (25,26,29,(31)(32)(33). It is the last of these with which we are concerned. (35)(36)(37)(38)(39) have appeared, and some experimental work has been presented (25,26,29,31,32) or proposed (37, 38) for particular applications.We now report a quite general experimental approach to assay the presence of differential light scattering and to correct for its effects on measurements in a circular dichrograph.The proposed assay involves determination of whether the observed CD spectrum varies with changes in the light-collection geometry of the spectropolarimeter. The collection geometry may be described in terms of the position, size, and shape of the light-detection element relative to the incident measuring beam and the sample cell.As a basis for later discussion, we consider first the measurement of normal, unpolarized light absorption spectra.For a photomultiplier tube (PMT) detector located on the optical axis, and with a sufficiently collim...

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“…During the whole heating process, the suspension was stirred with a glass stirrer of 4-cm stirring radius at about 100 rpm. In a 5-liter beaker the product obtained after decantation was washed 3 times with 2 (i) Standard procedure for chromatographic runs on hydroxyapatite: A thermostated (25°) chromatographic column of 1.6 X 40 cm (Pharmacia, type K 16) equipped with two adaptors was packed to about 12-to 15-cm height with hydroxyapatite suspended on 0.01 M phosphate buffer (pH 7.1). After loading the DNA on the column the elution with a linear sodium phosphate gradient supplied by an "Ultrograd" gradient mixer (LKB) and a peristaltic pump was started.…”

Section: Methodsmentioning

confidence: 99%

“…As a further method the preferential precipitation of (A + T)-rich DNA by poly(lysine) has been studied (2). Chromatographic and electrophoretic procedures have also been reported (3)(4)(5), in which the physical basis for the resolution is complex and unclear.…”

mentioning

confidence: 99%

Fractionation of DNA on Hydroxyapatite with a Base-Specific Complexing Agent

Pakroppa

Müller

1974

Proc. Natl. Acad. Sci. U.S.A.

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We describe a chromatographic technique for separating mixtures of DNA of varying G + C content. The method employs a specially prepared high-capacity hydroxyapatite and a G-C-specific DNA ligand (2-methyl-3-amino-7-dimethylamino-5-phenyl-phenazinium cation, abbreviated PNR). DNA molecules rich in G C pairs bind larger amounts of this dye and are eluted earlier from the hydroxyapatite column than are molecules rich in A T pairs. The dye can easily be removed from DNA by dialysis or solvent extraction after the chromatographic separation. The resolution of the method approaches that of CsCI density gradient separation, and the capacity of the column is much larger than that of a typical density gradient experiment. Elution of the DNA is not dependent on molecular weight, so samples of different molecular weight can be separated on the basis of G + C content. The technique should be especially useful for separating G C-rich minor components from DNA obtained from eukaryotic cells, as demonstrated by a fractionation of DNA from calf thymus.The separation of DNA mixtures in which the components differ in their base composition is performed in general by density gradient centrifugation (1). As a further method the preferential precipitation of (A + T)-rich DNA by poly(lysine) has been studied (2). Chromatographic and electrophoretic procedures have also been reported (3-5), in which the physical basis for the resolution is complex and unclear. The main disadvantage of these procedures, however, is the simultaneous fractionation according to base composition and molecular size. Only hydroxyapatite could be used successfully for chromatographic separations of DNAs very different in base composition (6).The discovery of the high G* C-specificity of a phenazinium dye*, the 2-methyl-3-amino-7-dimethylamino-5-phenyl-phenazinium cation, a phenylated neutral red (PNR), caused us to try its use for chromatographic separations of DNA mixtures. The basic idea was to shift selectively the binding equilibria of DNAs bound to a suitable basic adsorbant by adding the dye cation to the eluting salt dient. Concerning the basic adsorbant to be used in these experiments, hydroxyapatite seemed the most suitable to use since (i) it does not fractionate DNA molecules according to size, (ii) it does not interact appreciably with the dye, and (iii) the capacity of this adsorbant for nucleic acids is high and the recovery of the bound DNA is complete. During our studies we were soon confronted with the problem of preparing hydroxyapatite with Abbreviation: PNR, 2-methyl-3-amino-7-dimethylamino-5-phenyl-phenazinium perchlorate (phenyl neutral red). * W. Muller, H. Biinemann, and N. Dattagupta, in preparation. 699 constant properties from batch to batch. Since the flow rate, the capacity and the resolving power can vary strongly with each preparation of the adsorbant, its preparation had to be studied in detail with respect to these parameters. MATERIAL AND METHODS (a)2-Methyl-3-amino-7-dimethylamino-5-phenyl-phenazinium perchlorat...

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Deoxyribonucleic acid-polylysine complexes. Structure and nucleotide specificity

Cited by 252 publications

References 24 publications

Viscosimetric study on compact form of DNA in water—salt solutions containing polyethyleneglycol

Viscosimetric study on compact form of DNA in water—salt solutions containing polyethyleneglycol

Experimental Differential Light-Scattering Correction to the Circular Dichroism of Bacteriophage T2

Fractionation of DNA on Hydroxyapatite with a Base-Specific Complexing Agent

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