The structure of ψ DNA

Maniatis, Tom; Venable, John H.; Lerman, Leonard S.

doi:10.1016/0022-2836(74)90211-3

Cited by 212 publications

(143 citation statements)

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“…Is there any relationship between the observed DNA size classes and the A, B, and C conformations (Table 1)? Brain (7) and Maniatis et al (8) found that the wide-angle (Fig. 1 and Table 2).…”

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confidence: 89%

“…By using wide-angle x-ray scattering, the structure of DNA in aqueous solution was found to be close to the classical B form (7,8). CD also permits determining various forms of DNA in solution but requires a calibration to assign the CD spectra to the A, B, and C forms.…”

Section: Introductionmentioning

confidence: 97%

“…With lithium salts, the A form of DNA could not be obtained but, when the relative humidity is reduced to about 66%, the C form appears (6). Table 1 shows various parameters of the A, B, and C forms of DNA.By using wide-angle x-ray scattering, the structure of DNA in aqueous solution was found to be close to the classical B form (7,8). CD also permits determining various forms of DNA in solution but requires a calibration to assign the CD spectra to the A, B, and C forms.…”

mentioning

confidence: 99%

“…With increasing concentrations of methanol, the CD changes reflect a B-to-C transition, whereas in 80% ethanol the CD spectrum resembles what one might expect for form A DNA (9,12) (Table 1). However, it remains unclear whether aggregates of DNA molecules or mixtures of different DNA forms could mimic or mask the true spectrum and thus introduce artifacts (8,9). 'The costs of publication of this article were defrayed in part by the payment of page charges.…”

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confidence: 99%

“…'The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement " in accordance with 18 (7,8) 80% ethanol (5) CD spectra Water (low salt) (9) 90% methanol (9) 80% ethanol (9,12) 0.03 M triethanolamine-HCl (pH 7.9) IEtOH)3N], 0.05 M KCI, and 0.01 M MgCl2. The complex was then fixed (10 min, 370) by addition of one-fifth volume of fixation buffer (0.5% glutaraldehyde in the above solution at pH 7.9), as described by Portmann et For experiments using ethidium bromide, DNA was simply diluted to 0.8 Mg/ml in the elution buffer and heated for 15 min at 370 to dissociate the cohesive ends.…”

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confidence: 99%

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Discrete length classes of DNA depend on mode of dehydration.

Vollenweider¹,

James²,

Szybalski³

1978

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

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The length of double-stranded coliphage X DNA, as determined by electron microscopy using the benzyldimethylalkyl ammonium chloride technique, depends on the mode of dehydration. The freeze-dried DNA form is the longest (16.5 mr), whereas dehydration in methanol (15.9 Am) or in ethanol (three forms: 15.2 gsm, 13.9 im, and 12.4 gm) results in progressively shorter molecules. These measured lengths of the freeze-dried, methanol-dehydrated, and shortest ethanol-dehydrated forms correspond to the axial rise per nucleotide pair in the B, C, and A forms of DNA, respectively. The remaining forms of ethanol-dehydrated DNA seem to represent novel intermediary conformations of DNA. In agreement with the redicted increment, DNA exposed to ethidium bromide and ried is elongated by 39% (2.9 Am) All size classes show the same relative distribution pattern of bound Escherichia coli RNA polymerase molecules (nucleoside triphosphate:RNA nucleotidytransferase, EC 2.7.7.6), used as intramolecular markers, indicating that the dehydration-caused transitions are uniform.Although x-ray diffraction, x-ray scattering, UV The conformation of double helical DNA (1) has been studied by various methods, including x-rays, circular dichroism (CD), and electron microscopy. X-ray diffraction by oriented DNA fibers reveals three double-helical forms, depending on the relative humidity, the ionic strength, and the nature of the cation. The B form appears at relative humidity 92% for the sodium salts (2); the crystallinity of the fibers is best with lithium salts at 66% relative humidity (3). The A form (4) exists in the presence of sodium, potassium, or rubidium salt when the relative humidity is lower than 75% or after dehydration in 80% ethanol (5). With lithium salts, the A form of DNA could not be obtained but, when the relative humidity is reduced to about 66%, the C form appears (6). Table 1 shows various parameters of the A, B, and C forms of DNA.By using wide-angle x-ray scattering, the structure of DNA in aqueous solution was found to be close to the classical B form (7,8). CD also permits determining various forms of DNA in solution but requires a calibration to assign the CD spectra to the A, B, and C forms. Therefore, Tunis-Schneider and Maestre (13) obtained the CD spectra of the DNA in films under conditions of humidity and ionic strength comparable to those used in x-ray studies. These assignments of standard spectra allowed study of the transition from one form to another in different solvents-e.g., the CD spectra of a number of DNAs were studied as a function of alcohol concentration in aqueous solutions at 0.1-1.0 mM salt concentrations. With increasing concentrations of methanol, the CD changes reflect a B-to-C transition, whereas in 80% ethanol the CD spectrum resembles what one might expect for form A DNA (9, 12) (Table 1). However, it remains unclear whether aggregates of DNA molecules or mixtures of different DNA forms could mimic or mask the true spectrum and thus introduce artifacts (8, 9). 'The costs of publica...

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confidence: 89%

Section: Introductionmentioning

confidence: 97%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Discrete length classes of DNA depend on mode of dehydration.

Vollenweider¹,

James²,

Szybalski³

1978

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

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Structure of collapsed persistent macromolecule: Toroid vs. spherical globule

et al. 1997

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We studied theoretically the behavior of a collapsed persistent macromolecule in poor solvent as a model of collapse transition of single double‐stranded DNA chain, and constructed the diagram of states in the variables with contour length of a macromolecule and quality of the solvent. We found that the state of toroidal globule exists as an intermediate state between the states of elongated coil state and the spherical globule. Our theoretical result suggests that a single linear macromolecule with a high degree of polymerization can form a toroidal globule. However, the range in which the toroidal structure is stable decreases as the macromolecule length increases. Experimental observation with transmission electron microscopy has been performed to study the globular structure of single DNA chain (bacteriophage T4 DNA, λ‐DNA) collapsed by hexammine cobalt (III) at different concentrations. We found that an extremely long chain of T4 DNA (166 kbp), with a contour length of 56 μm, actually forms a toroidal globule, and that isotropic spherical globule appears at higher hexammine cobalt concentration. © 1997 John Wiley & Sons, Inc.

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Manipulation of globular DNA molecules for sizing and separation

et al. 2000

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Handling large DNA molecules, such as chromosomal DNA, has become necessary due to recent developments in genome science. However, large DNA molecules are fragile and easily broken by shear stress accompanying flow in solution. This fragility causes difficulties in the preparation and handling of large DNA molecules. This study demonstrates the transition of DNA from a coiled to a globular form, which is highly condensed. This state suppresses DNA fragmentation due to shear stress in solution. The transition enables large DNA molecules to undergo mechanical manipulation. We confirmed that the fluorescence intensity of stained globular DNA increases with increasing length, suggesting that the resistance of globular DNA to shear stress is the factor that allows analysis of large DNA by flow cytometry.

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The structure of ψ DNA

Cited by 212 publications

References 25 publications

Discrete length classes of DNA depend on mode of dehydration.

Discrete length classes of DNA depend on mode of dehydration.

Structure of collapsed persistent macromolecule: Toroid vs. spherical globule

Manipulation of globular DNA molecules for sizing and separation

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