Discrete length classes of DNA depend on mode of dehydration.

Abstract

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...

DNA and RNA polymerase/DNA complex imaged by scanning force microscopy: Influence of molecular‐scale friction

“…The same RNA polymerase distribution is shown by TEM in figure 2B. Under our experimental conditions, the DNA template has lost its supercoiled form in most cases as described in electron microscopic studies (Vollenweider et al 1978); however, this conformational change did not affect the protein binding. This result indicates that DNA is still flexible during the alcoholic process and goes through successive forms after its adsorption on mica surface.…”

Unfolding of nucleosomes by ethidium binding

“…After correction for lengthening of the DNA by 2.7 A per bound ethidium (Hogan et al, 1979) (r -0.06; 140 base pairs; 0 = 41°), the calculated DNA length per base pair is 3.91 A when L -430 A and is 2.86 A when L = 320 A. The former number is clearly outside the range of plausible values as judged, for example, by electron microscopy (Vollenweider et al, 1978;Griffith, 1978). Taking 3.4 A to be the maximum allowed rise per base pair, we estimate a maximum value of L = 377…”

DNA Strand Elongation Induced by Small Gold Nanoparticles at High Ethanol Content

“…Along this line, Girod et al reported that in the range of 0–65% EtOH (v/v), the CD changes reflect a DNA B-to-C transition . The progressive dehydration results in stepwise shrinkage from the B form to the progressively shorter C-forms . By comparison with the B form, C-DNA structures display considerably more inclination, destacking, and displacement of the bases toward the major groove.…”