Watson-Crick Double Helix Research Articles

Electrochemical analysis of polynucleotides

Summary Natural and synthetic polynucleotides were studied by means of differential and normal pulse polarography (d.p.p., n.p.p.) and by cyclic voltammetry (c.v.) in connection with a d.m.e. or h.m.d.e. o a It was shown that the d.p.p. behaviour of synthetic double-stranded polydeoxyribonucleotides is markedly influenced by the nucleotide sequence; homopolymer pairs (poly(dA) · poly(dT) and poly(dG) · poly(dC)) yield almost no signal under the given conditions, whereas polynucleotides with the alternating nucleotide sequence (poly(dA-dT) · poly(dA-dT) and poly(dG-dC) · poly(dG-dC)) produce well-developed peaks. This difference may be connected with differences in the secondary structures of the two types of polynucleotides. b It was demonstrated that both synthetic and natural polynucleotides containing guanine produce a characteristic anodic c.v. peak at about −0.2 V ( vs s.c.e.). It is necessary to polarize the h.m.d.e. to potentials of about −1.8 V in order to obtain this peak. Polynucleotides which do not contain guanine (poly(A) · poly(C) and poly(U)) do not yield this anodic peak. Similar to cathodic responses, the anodic peak is substantially higher in denatured (single-stranded) DNA than in its native double-helical form. c Various polynucleotides were modified with osmium tetroxide in an attempt to introduce a new electroactive centre into the polynucleotide chain. It is known that OsO 4 reacts with pyrimidine bases in single-stranded polynucleotides. It does not react, however, with bases incorporated in an intact Watson-Crick DNA double helix; this agent can thus act as a chemical probe of DNA structure. It was found that the introduction of osmium into singlestranded poly(C), poly(U), poly(dT) and denatured DNA resulted in the appearance of several reduction signals. After the treatment of native (double-helical) DNA with O s O 4 this DNA yielded d.p.p. peaks which are substantially smaller than peaks of single-stranded polynucleotides treated in the same manner. The peaks of the modified native DNA increased if DNA was damaged by various agents such as ionizing and U.V. radiations, which introduce minor local changes into the double helix of DNA.

A sequence-independent, four-stranded, double Watson-Crick DNA helix that could solve the unwinding problem of double helices

A four-stranded DNA helix is described that consists of two Watson-Crick double helices wound about the same axis, with no restriction on sequence. Its significance is that it permits a simple topological solution to the problem of unwinding a double helix to separate its strands. If a stretch of Watson-Crick double helix is supercoiled on itself as many times as it has helical turns it has no topological winding and its strands can be separated without the ends of the strands rotating about each other. Such a helix is folded on itself to form the four-stranded helix. The dramatic possibility that this is the structure of DNA in chromatin seems to be ruled out by measurements of supercoiling in circular chromosomes, but it could perhaps occur in special situations, for example in chromosome pairing or at irregularities in palindromic DNA sequences. The helix has Watson-Crick base pairing, bases almost perpendicular to the helix axis, eleven nucleotides per strand per turn and C2-endo puckering of the deoxyribose ring. The helix axis is an axis of symmetry for the deoxyribose-phosphate backbone.

Folding of nucleic acids.

This paper describes and discusses nucleic acid conformations, the energy contributions that stabilize them, and the ways the stable conformations are formed. Preferred conformations of nucleotides and of double, triple and super helices in nucleic acids are described briefly. Next the enthalpy and entropy of nucleic acid order/disorder transitions are reviewed. It is concluded that (a) the double helix is stabilized primarily by interbase hydrogen bonds, and (h) the available thermodynamic parameters for single-strand stacking are probably incorrect. The conformation of single strands in solution is discussed briefly. The kinetics of helix formation is described; the transition state of three base pairs that has been proposed supports the idea that the strength of hydrogen bonds depends on the access of water molecules to the base pair. Hairpin formation and more complex secondary structures of nucleic acids are described and explained in terms of rate of formation, stability, and control of secondary structure. Transfer RNA has tertiary structure as well as secondary structure. Schematic diagrams are used to show how experimental evidence fixes different parts of the tRNA tertiary structure. The detailed interactions in the proposed model are supported by the sequence of cell-wall glycine tRNA, which can be charged with an amino acid without participating in protein synthesis. Sequential steps in the folding and unfolding of the proposed tRNA conformation are outlined. Finally, the abilities of nucleic acids and proteins to form stable tertiary structures are compared and the evolutionary consequences are considered. Nucleic acids and proteins have been studied intensively over the past 25 years. Although similar techniques have been used on each of these important classes of macromolecule, available information for each is very different. X-ray diffraction methods have elucidated conformations of both nucleic acids and proteins but, whereas the known conformations of different proteins are very different, those of nucleic acids are all simple variants of the Watson-Crick double helix. It is easier, however, to study nucleic acid conformations in

Fine structure observations on the chromosomes in the spermatids of the Ascidian, Boltenia villosa.

Electron micrographs of the relatively young spermatids of the Ascidian, Boltenia villosa, reveal that its chromosomes exist in the form of 120–180 A fibers which are easily seen to be composed of two subunits of about 50–70 A each. Fibers of the diameter of such subunits have never been seen as single entities without a mate. Subunits in pairs seen imbedded in areas of “fused” chromosomes only measure 30–40 A, probably due to the loss of some protein. It is pointed out that the chromatin goes into the sperm as chromosomes in two-chromatid state, and that each chromatid probably contains only one Watson-Crick double helix.

Genetic Polarity in Bacteria

The major genetic apparatus of the enteric bacteria, Escherichia coli and Salmonella typhimurium, appears at first glance to be poor material for creating phenomena which would reflect polarity. Genetically it consists of a single linkage group or chromosome forming a circle (Jacob and Wollman, 1958; Taylor and Thoman, 1964; Sanderson and Demerec, 1965). Physically it consists of DNA, a Watson-Crick (Watson and Crick, 1953) double helix (see Cavalieri and Rosenberg, 1963; Thomas, 1963; Baldwin, 1964) formed into a circle with no free ends (Cairns, 1963). The two strands of the double helix have opposite chemical polarities, and the resulting symmetry eliminates an important possible structural basis for polarity. Most polarity phenomena are those which result from the sequential nature of the functioning of the genetic material. Functioning can be considered at two levels: the sequential replication of the chromosome and the expression (transcription and translation) of the genes. This discussion will be limited to the latter. Observed polarity effects upon gene function can generally be ascribed to the fact that the genetic information consists of a linear sequence of nucleotides and that the mechanisms which transcribe the information into messenger RNA and translate the messenger RNA into the final chain of amino acids do so in a sequential manner. As a consequence, there is a beginning and an endpoint to the linear sequence of purine and pyrimidine bases which make up a gene. This polarity is reinforced at the level of translation since the messenger RNA, being a single strand, possesses a chemical polarity.

Supercoiling of polyoma virus DNA measured by its interaction with ethidium bromide

Exposure of polyoma virus DNA to increasing amounts of the intercalating drug ethidium bromide reduces the sedimentation velocity of the fast component of the DNA (supercoiled molecules) until it is equal to that of the slow component (unsupercoiled molecules). Addition of larger amounts of drug causes the reappearance of a fast component. This is interpreted as being due to the loss and then to the reversal of the supercoiling turns in the DNA molecule. The fact that intercalation of the drug into the molecules causes the loss of supercoiling shows that the supercoiling in the untreated DNA must be due to a deficiency of turns in the Watson—Crick double helix, causing the molecule to take up a conformation with right-handed twists. From the ratio of drug to DNA at the point where supercoiling disappears, it can be calculated that the untreated molecule of polyoma virus DNA has about 12 supercoiling turns. Alternative assumptions concerning the effect of intercalation on the structure of the DNA molecule lead to even higher estimates. Ways in which this amount of supercoiling could be introduced into DNA molecules are discussed.

Four-stranded DNA as determined by electron microscopy.

Pneumococcus DNA, of weight-average molecular weight 1.6 million by light scattering, had a weight-average length of 4300 A by electron microscopy. Thus, the average mass per unit length was 370 molecular-weight units per A, or approximately two times that expected (208) for a Watson-Crick double helix. This corresponds to an average of 3.6 strands per molecule, which is close to that obtained by other methods. Morphologically, all the particles in the micrographs were relatively stiff, and had a cross-sectional height of 20 to 30 A. Some divided into two stiff branches of the same height, apparently double helical. Where the branches combined into one (minimally four-stranded) structure they apparently lay side by side in close association.