Conversion of B DNA between solution and fiber conformations.

Abstract

At low salt and high DNA concentration, rodlike DNA molecules form specific aggregates containing about seven parallel DNA molecules packed in a bundle. Bundle formation can be reversed by addition ofsmall amounts of EDTA, and formation of the specific aggregates can be induced at higher salt concentration by addition of trivalent ions. In contrast to monomeric DNA, the aggregated species has the optical anisotropy expected for the B form as observed in fibers.Since the proposal of a double helical structure for DNA (1), xray diffraction from fibers has provided information concerning DNA conformation. As the analysis of this data has progressed in precision and reliability (2-4), producing highly detailed structural models, the relationship ofthe results to the structure of DNA in solution has come increasingly into question.Two recent experimental observations fail to agree precisely with expectation based on the B-form structure of DNA Eisenberg and Tomkins (14). The refractive index-concentration gradient dn/dc was determined by using a Brice-Phoenix differential refractometer, and the value obtained agrees with the result ofVreugdenhil et al. (15). The DNA concentration range was 0.21-0.61 mg/ml in 1.8 mM ionic strength buffer, 20TC.Equilibrium Sedimentation Molecular Weights. These molecular weights were determined by using a Spinco model E analytical ultracentrifuge with multiplexed UV scanning optics. Standard methods (16) The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact.

DNA gelation in concentrated solutions

“…Taken together, the small changes in counterion stoichiometry and the lack of observable birefringence in the gel phase argue against the side-byside or "bundling" mode of aggregation described by Mandelkern et a1. 22 Instead, the observation that the apparent D20.u of the mobile scatterers remains unchanged across the transition suggests a relatively open structure, with few contacts between adjacent DNA molecules. In the context, values of n = l are compatible with a network model in which each DNA molecule makes two intermolecular "contacts" (the minimum number required for elimination of free translation and rotation), and in which one divalent cation or two monovalent cations are shared by phosphate anions on adjacent molecules.…”

Rad51 and RecA juxtapose dsDNA ends ready for DNA ligase-catalyzed end-joining under recombinase-suppressive conditions

“…The hexamine cobalt chloride-mediated stimulation and suppression of the ligation were attributed to DNA-bundle formation, in which the trivalent cations bridge DNA-rods (51,52). In vitro , RecA forms well-ordered bundles of filaments under various conditions independently of ATP or ADP, and under crystallization conditions (19,53,54).…”

Liquid crystalline phases in concentrated aqueous solutions of Na+ DNA.

“…Here I report microscopic observations of a cholesteric liquid crystalline phase formed in aqueous saline solutions of DNA and present a partial phase diagram for transitions of such solutions between isotropic and liquid crystalline phases. These phase transitions, which occur with only Na' as the DNA counterion, are distinct from the collapse ofDNA at low ionic strengths that is caused by heavy metals, polycations, or organic solutes (6)(7)(8)(9)(10)(11) …”