Is DNA really a double helix?

Evidence Falsifying the Double Helix Model

Through more than 40 years of reading, thinking, searching, and experimentation, we have found that the double helix model carries some defects or incorrect information. Evidence gleaned from the literature clearly indicates that the two strands of DNA are coiled ambidextrously, rather than plectonemically. It is likely that the linking number of native chromosomal Escherichia coli (E. coli) DNA is less than 960. Presently, a clear voice is necessary to break the ice formed from decades of misleading media, questionable textbooks, and expediency. For the sake of science, we are responsible and willing to share our hard-earned knowledge, experience, and knack with the public. A promising research plan is provided for the additional falsification of the right-handed double helix model. It would be a precision hit at the Achilles’ heel of the double helix model. An appropriate conceptual shift will hopefully lead to new knowledge on the secondary structure of DNA and improve understanding of its biological functions.

Scaling and Visualization of Nucleotide Sequences

Algorithms for scaling and visualization of nucleotide sequences developed in this study allow identifying relationships between the biochemical parameters of DNA and RNA molecules with scale invariance, fractal clusters, nonlinear ordering and symmetry and noise immunity of visual representations in orthogonal coordinate systems. The algorithms are capable of displaying structures of the nucleotide sequences of living organisms by visualizing them in spaces of various dimensions and scales. Approximately one hundred genes (protozoa, plants, fungi, animals, viruses) were analysed and examples of visualization of the nucleotide composition of genomes of various species have been presented. The developed method contributes to an in-depth understanding of the principles of genetic coding and simplifying the perception of genetic information due to the algorithmic interpretation of the basic properties of polynucleotide fragments with visualization of the final geometric structure of the genetic code.

Contributions of Sequence to the Higher-Order Structures of DNA

One of the critical unanswered questions in genome biophysics is how the primary sequence of DNA bases influences the global properties of very-long-chain molecules. The local sequence-dependent features of DNA found in high-resolution structures introduce irregularities in the disposition of adjacent residues that facilitate the specific binding of proteins and modulate the global folding and interactions of double helices with hundreds of basepairs. These features also determine the positions of nucleosomes on DNA and the lengths of the interspersed DNA linkers. Like the patterns of basepair association within DNA, the arrangements of nucleosomes in chromatin modulate the properties of longer polymers. The intrachromosomal loops detected in genomic studies contain hundreds of nucleosomes, and given that the simulated configurations of chromatin depend on the lengths of linker DNA, the formation of these loops may reflect sequence-dependent information encoded within the positioning of the nucleosomes. With knowledge of the positions of nucleosomes on a given genome, methods are now at hand to estimate the looping propensities of chromatin in terms of the spacing of nucleosomes and to make a direct connection between the DNA base sequence and larger-scale chromatin folding.

The birth and development of the DNA theory of inheritance: sixty years since the discovery of the structure of DNA

The development of the DNA theory of inheritance culminated in the publication of the molecular structure of DNA 60 years ago. This paper describes this development, beginning with the discovery of DNA as a chemical substance by Friedrich Miescher in 1869, followed by its basic chemical analysis and demonstration of its participation in the structure of chromosomes. Subsequently it was discovered by Oswald Avery in 1944 that DNA was the genetic material, and then Erwin Chargaff showed that the proportions of the bases included in the structure of DNA followed a certain law. These findings, in association with the biophysical studies of Maurice Wilkins and Rosalind Franklin with Raymond Gosling, led James Watson and Francis Crick to the discovery of the double-helical structure of DNA in 1953. The paper ends with a short description of the development of the DNA theory of inheritance after the discovery of the double helix.

DNA stress and strain, in silico, in vitro and in vivo

A vast literature has explored the genetic interactions among the cellular components regulating gene expression in many organisms. Early on, in the absence of any biochemical definition, regulatory modules were conceived using the strict formalism of genetics to designate the modifiers of phenotype as either cis- or trans-acting depending on whether the relevant genes were embedded in the same or separate DNA molecules. This formalism distilled gene regulation down to its essence in much the same way that consideration of an ideal gas reveals essential thermodynamic and kinetic principles. Yet just as the anomalous behavior of materials may thwart an engineer who ignores their non-ideal properties, schemes to control and manipulate the genetic and epigenetic programs of cells may falter without a fuller and more quantitative elucidation of the physical and chemical characteristics of DNA and chromatin in vivo.

An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals

The sequence of heterocyclic bases on the interior of the DNA double helix constitutes the genetic code that drives the operation of all living organisms. With this said, it is not surprising that chemical modification of cellular DNA can have profound biological consequences. Therefore, the organic chemistry of DNA damage is fundamentally important to diverse fields including medicinal chemistry, toxicology, and biotechnology. This review is designed to provide a brief overview of the common types of chemical reactions that lead to DNA damage under physiological conditions.

A journey in the world of DNA rings and beyond

I was born in China and would have remained there but for the tumultuous events that led many of my generation to the United States for graduate studies. Norman Davidson introduced me to DNA when I became a postdoctoral fellow in his group at the California Institute of Technology in 1964, and a fortuitous conversation there ignited my interest in DNA ring formation, which later led me to study different topological forms of DNA rings-catenanes, knots, and supercoils. In 1968, a chance observation led me to identify a new enzyme capable of converting one DNA ring form to another, an enzyme now known as a DNA topoisomerase. My interest in DNA rings and DNA topoisomerases continued throughout my years at the University of California, Berkeley, and Harvard. The fascinating ability of the topoisomerases in passing DNA strands or double helices through one another and their importance in cellular processes have kept me and many others excited in their studies.

A-like guanine-guanine stacking in the aqueous DNA duplex of d(GGGGCCCC)

We have used CD spectroscopy, NMR spectroscopy and unrestrained molecular dynamics to study conformational properties of a DNA duplex formed by the self-complementary octamer d(GGGGCCCC). Its unusual CD spectrum contains features indicating A-like stacking of half of the bases, whereas the other half stack in a B-like fashion. Unrestrained molecular dynamics simulations converged to a stable B-like double-helix of d(GGGGCCCC). However, the double-helix contained a central hole whose size was half of that occurring in structure A. In the canonical structure B, the hole does not exist at all because the base-pairs cross the double-helix centre. The cytosine bases were stacked in the duplex of d(GGGGCCCC) as in structure B, while stacking of the guanine bases displayed features characteristic for structure A. NMR spectroscopy revealed that the A-like guanine-guanine stacking was accompanied by an increased tendency of the deoxyribose rings attached to the guanine bases to be puckered in an A-like fashion. Otherwise, the duplex of d(GGGGCCCC) showed no clash, no bend and no other significant deviation from structure B. The present analysis demonstrates a remarkable propensity of the guanine runs to stack in an A-like fashion even within the B-DNA framework. This property explains why the oligo(dG). oligo(dC) tracts switch into structure A so easily. Secondly, this property may influence replication, because structure A is replicated more faithfully than structure B. Thirdly, the oligo(dG) runs might have played an important role in early evolution, when DNA took on functions that originally evolved on RNA. Fourthly, the present study extends the vocabulary of DNA secondary structures by the heteronomous duplex of d(GGGGCCCC) in which the B-like strand of oligo(dC) is bound to the A-like strand of oligo(dG).

Crystal studies of B-DNA: the answers and the questions

The history of DNA crystallography is reviewed and is followed by discussion of the methods used for structure determination. The features of B-DNA molecular and crystal structures are described.

Winding of the DNA helix by divalent metal ions

When supercoiled pBR322 DNA was relaxed at 0 or 22 degrees C by topoisomerase I in the presence of the divalent cations Ca2+, Mn2+ or Co2+, the resulting distributions of topoisomers observed at 22 degrees C had positive supercoils, up to an average delta Lk value of +8.6 (for Ca2+at 0 degrees C), corresponding to an overwinding of the helix by 0.7 degrees/bp. An increase of the divalent cation concentration in the reaction mixture above 50 mM completely reversed the effect. When such ions were present in agarose electrophoresis gels, they caused a relaxation of positively supercoiled DNA molecules, and thus allowed a separation of strongly positively supercoiled topoisomers. The effect of divalent cations on DNA adds a useful tool for the study of DNA topoisomers, for the generation as well as separation of positively supercoiled DNA molecules.

The structure of B-DNA in oriented fibers

Native, general sequence B-form DNA in uniaxially oriented fibers is a ten-fold helix with identical antiparallel strands: this is to say the molecular symmetry is 2 2 10(1). The diffraction patterns indicate that local variations, however significant, must be modest. This is true also for the lithium salt of calf thymus DNA in fibers that are polycrystalline as well as oriented. The contents of its orthorhombic unit cells are arranged with P2(1)2(1)2(1) symmetry which permits the molecular symmetry to be merely two-fold. The molecular structure of DNA in such conditions resembles, conformationally and molecularly, that of B-type DNA in oligonucleotide single crystals and in oriented polycrystalline fibers of polyoligonucleotides, and therefore provides a basis for evaluating the variations that may be due to sequence effects in polyoligonucleotides in fibers and oligonucleotides in single crystals.

Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase

RNA polymerases pause conspicuously at certain positions on a DNA template. At the well-studied pause sites in the attenuation control regions that precede the trp and his operons, both formation of secondary structure in the nascent transcript and the DNA sequence immediately downstream contribute to pausing. The mechanisms of these effects are unknown. We report here studies on the structure of the RNA and DNA strands in purified trp and his paused transcription complexes in comparison to ten elongation complexes halted by nucleoside triphosphate deprivation. A 14 to 22 nucleotide region of the DNA strands was accessible to modification by KMnO4 or diethylpyrocarbonate in both the paused and halted transcription complexes. However, the region in front of the nucleotide-addition site was reactive only in some halted complexes. In both types of complexes, approximately eight nucleotides on the template strand immediately preceding the 3' end were protected from modification. We also examined the sensitivity of the nascent transcript to RNase A and found that the 3'-proximal eight nucleotide region could be cleaved without complete loss of the potential for elongation. However, a model RNA:DNA hybrid designed to mimic a hybrid in the transcription complex could also be cleaved under similar conditions. Together, the results suggest that the 3'-proximal eight nucleotides of transcript may pair with the DNA template and that this structure is not disrupted by hairpin formation at a pause site. Rather, pausing may result from distinct interactions between RNA polymerase and both the pause RNA hairpin and the downstream DNA sequence.

DNA gyrase: structure and function

DNA gyrase is an essential bacterial enzyme that catalyzes the ATP-dependent negative super-coiling of double-stranded closed-circular DNA. Gyrase belongs to a class of enzymes known as topoisomerases that are involved in the control of topological transitions of DNA. The mechanism by which gyrase is able to influence the topological state of DNA molecules is of inherent interest from an enzymological standpoint. In addition, much attention has been focused on DNA gyrase as the intracellular target of a number of antibacterial agents as a paradigm for other DNA topoisomerases. In this review we summarize the current knowledge concerning DNA gyrase by addressing a wide range of aspects of the study of this enzyme.

Paranemic structures of DNA and their role in DNA unwinding

A DNA structure is defined as paranemic if the participating strands can be separated without mutual rotation of the opposite strands. The experimental methods employed to detect paranemic, unwound, DNA regions is described, including probing by single-strand specific nucleases (SNN), conformation-specific chemical probes, topoisomer analysis, NMR, and other physical methods. The available evidence for the following paranemic structures is surveyed: single-stranded DNA, slippage structures, cruciforms, alternating B-Z regions, triplexes (H-DNA), paranemic duplexes and RNA, protein-stabilized paranemic DNA. The problem of DNA unwinding during gene copying processes is analyzed; the possibility that extended paranemic DNA regions are transiently formed during replication, transcription, and recombination is considered, and the evidence supporting the participation of paranemic DNA forms in genes committed to or undergoing copying processes is summarized.

The new model of DNA structures

The new model of the DNA dynamic state is proposed in terms of Watson-Crick (WC) and Corey-Pauling-Kortum (CPK) models by the modification of the cis ladder conformation. The model may rationally explain the DNA replication, transcription, renaturation, hybridization, premelting and breach etc.

Modeling DNA supercoils and knots with B-spline functions

A method is offered to model the complex trajectories of closed circular DNA supercoils and knots. The trajectories are approximated by polygons and analytical expressions of the curves are generated from the polygons with B-spline functions. The resulting curves are used to evaluate the writhe and elastic energy of a series of interrelated supercoils, and to generate detailed atomic models of the deformed double helix.

Reason in the Zeitgeist

The pages of the history of science record thousands of instances of similar discoveries having been made by scientists working independently of one another. Sometimes the discoveries are simultaneous or almost so; sometimes a scientist will make anew a discovery which, unknown to him, somebody else had made years before.

Determination of the absolute handedness of knots and catenanes of DNA

DNA winds about itself in a right-handed or left-handed fashion at several structural levels. The double helix is generally right-handed and is given a (+) sign by convention, whereas supercoiling of the helix axis is always (-) in the cell. The winding in higher -order forms such as knots and catenanes is unknown, and this has impeded elucidation of the mechanisms of their formation and resolution by replication, recombination and topoisomerase action. We introduce here a procedure for determining the handedness of DNA winding by inspection of electron micrographs of DNA molecules coated with Escherichia coli RecA protein. We demonstrate the validity of the method and show that DNA topoisomerase I of E. coli generates an equal mixture of (+) and (-) duplex DNA knots, and that one product of recombination by resolvase of transposon Tn3 (refs 8, 9) is a catenane of uniquely (+) sign.

Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes

A method based on the differential rate of cytosine methylation in single- and double-stranded nucleic acids by dimethyl sulfate [Peattie, D.A. & Gilbert, W. (1980) Proc. Natl. Acad. Sci. USA 77, 4679-4682] has been developed for probing unpaired cytosines in DNA and DNA-protein complexes at the sequence level. Application of the method to the complexes between Escherichia coli RNA polymerase (EC 2.7.7.6) and three related promoters, lac UV5, trp, and a hybrid promoter tac resulting from the fusion of the two, reveals distinct differences in the way RNA polymerase unpairs DNA in these promoters. No single-stranded region is detectable in the complex with the trp promoter. For the lac UV5 promoter, the cytosines at positions -6, -4, -2, and -1 are in an unpaired region. The same cytosines in the tac promoter, which is homologous in sequence to lac UV5 in this region, are also found to be single stranded. For the pair of promoters lac UV5 and tac, the cytosine methylation reaction has also been used to demonstrate the steep temperature dependence of opening of base pairs by RNA polymerase. One striking feature is that the midpoint of this transition for the tac promoter is 3 degrees C lower than the corresponding value for lac UV5, even though the sequence of the unpaired region in the two promoters is identical.

A critical analysis of a left-handed double helix model for B-DNA fibers

A search for a left-handed double helix model for B-DNA fibers has been undertaken. The model has to present good stereochemistry and also to be in agreement with X-ray and infrared data. Dihedral angles as well as atomic coordinates and calculated intensities curves are given for the best model obtained. Comparison with experimental results shows that this model must be rejected as a candidate for the representation of B-DNA fibers.

Proteins that shape DNA

During the last five years, considerable accumulation of data on nucleic acids metabolism leads to the discovery of a number of proteins designed to change the conformation of DNA and to "shape" it. Experimental results emphasize the importance of the conformation and the flexibility of DNA itself in such interactions. The mutual recognition of nucleic acids by proteins may be or not dependent on the nnucleotide sequence and in most cases is accompanied by conformational changes in the proteins involved. Among these are proteins that bind in stoichiometric amounts to DNA, proteins that promote the separation of the two strands in a duplex, and finally proteins that change the topology of DNA.

Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution

Helical periodicity of DNA, poly(dA) . poly(dT) and poly(dA-dT) . poly(dA-dT) has been measured in solution by using the band shift method fo Wang [Wang, J. (1979) Proc. Natl Acad. Sci. USA, 76, 200-203]. The method makes use of the effect, on the superhelicity of closed circular DNA molecules, of the insertion of specific nucleotide sequences of known length. The method was applied to a variety of recombinant plasmid DNAs which were constructed by inserting DNA, poly(dA) . poly(dT) or poly(dA-dT) . poly(dA-dT) into pBR322 DNA. When compared to DNA, poly(dA) . poly (dT) was found to have a smaller pitch (by about 0.5 base pair/turn), whereas poly(dA-dT) . poly(dA-dT) has a slightly larger pitch (by 0.1 base pair/turn). These features correlate well with the known ability of the alternating copolymer to reconstitute nucleosomes upon incubation with histones, in contrast to the non-alternating one which fails to do so. Finally, a detailed analysis of the principles underlying the methods developed by Wang [reference quoted above and Wang, J. (1978) Cold Spring Harb. Symp. Quant. Biol. 42, 29-33] leads to an increase in the estimate of the helical periodicity of DNA of 0.15 base pair/turn, over the reported value of 10.4 base pairs/turn (references quoted above). This essentially accounts for the discrepancy observed with the value of 10.6 base pairs/turn obtained by nuclease digestion of DNA immobilized on a surface [Rhodes, D & Klug, A. (1980) Nature (Lond.) 286, 573-578].

The early melting of closed duplex DNA: analysis by banding in buoyant neutral rubidium trichloroacetate

Aqueous RbTCA permits the buoyant banding of both native and denatured DNA at room temperature and neutral pH. A unique property of this solvent is the bouyant resolution of closed circular, underwound DNA (I) from the corresponding nicked (II) species. Conditions are reported here in which PM-2 DNA I is physically resolved from native PM-2 DNA II, the buoyant separation being 1.27 mq/ml in 3.3 M RbTCA at 25 degrees C. The separation between nicked and closed DNAs increases with temperature up to 35.5 degrees C, at which PM-2 DNA II cooperatively melts and subsequently pellets. The isothermal buoyant density of a cloed DNA increases linearly as the linking number (Lk) of the closed DNA decreases. The early melting of closed DNA may be monitored with high precision by buoyant banding in RbTCA, it being possible to detect the disruption of as few as 40 base pairs in PM-2 DNA (10,000 base pairs). The constraint that the linking number be conserved in closed DNA requires that a change in duplex winding be accompanied by a compensating change in supercoiling. We estimate the linking number deficiency of PM-2 DNA I to be 0.094 turns per decibase pair. This result permits the estimation of the EtdBr unwinding angle, phi, by comparison with alternative determinations of the linking number deficiency which depend upom the value of phi. The result obtained here is that phi = 27.7 degrees +/- 0.5 degrees and is approximately independent of temperature over the range 15 degrees-35 degrees.

Unlinked strands as a topological constraint on chromosomal DNA, plasmid integration, and DNA repair

It is proposed that circular chromosomal DNA must be constrained such that the two strands are topologically unlinked. This structure can be replicated without strand breakage (nicking) by locally acting enzymes. The recently discovered form V DNA satisfies this topological constraint. The structure is likely to consist of left-handed and right-handed segments of double helix. The constraint of zero linkage has to be preserved by DNA repair, plasmid insertion and by crossing over. The argument presented in this paper is a topological one, following W.F. Pohl, that linkage is a global property that cannot be measured by locally acting enzymes. In contrast to Pohl no argument in favor of a side-by-side structure is presented. A zero linkage constraint would be hereditary and compatible with a multitude of local structures.