Rigorous conformational analysis of right and left DNA helices and junction between them

On the basis of complete scanning through conformational space of dihedral angles, twelve structural genera were obtained. Subsequent energy minimization within these genera yielded a limited set of duplexes with stacking: right-handed B-form (Wilkins type), B2-form (Watson and Crick type) and left-handed Ll-form (Sasisekharan type) and the new L2-form. In the polymeric DNA only right-handed double-helices are possible, the left-handed helices are forbidden due to poor 1–5 interchain contacts. In contrast, for short fragments the left- and right-handed helicek have practically the same energies providing some physical ground for side-by-side form, which biologically is possible as recombination form and may be as replication form.     

DNA models for A, B, C and D conformations related to fiber X-ray, infrared and NMR measurements

A conformational analysis of the A, B, C and D DNA forms was made in order to establish molecular models presenting a good agreement with experimental data obtained from fiber X-ray, infrared linear dichroism and 31P NMR. The proposed models have been refined and do present good stereochemistry and optimized H-bond distances between bases associated with the Watson-Crick pairing. The DNA conformations proposed are a left handed double helix for the C form and right handed helices for A, B and D. Relations to conformational transitions between these forms are discussed.     

No braiding of Holliday junctions in positively supercoiled DNA molecules

The Holliday junction is a prominent intermediate in genetic recombination that consists of four double helical arms of DNA flanking a branch point. Under many conditions, the Holliday junction arranges its arms into two stacked domains that can be oriented so that genetic markers are parallel or antiparallel. In this arrangement, two strands retain a helical conformation, and the other two strands effect the crossover between helical domains. The products of recombination are altered by a crossover isomerization event, which switches the strands fulfilling these two roles. It appears that effecting this switch from the parallel conformation by the simplest mechanism results in braiding the crossover strands at the branch point. In previous work we showed by topological means that a short, parallel, DNA double crossover molecule with closed ends did not braid its branch point; however, that molecule was too short to adopt the necessary positively supercoiled topology. Here, we have addressed the same problem using a larger molecule of the same type. We have constructed a parallel DNA double crossover molecule with closed ends, containing 14 double helical turns in each helix between its crossover points. We have prepared this molecule in a relaxed form by simple ligation and in a positively supercoiled form by ligation in the presence of netropsin. The positively supercoiled molecule is of the right topology to accommodate braiding. We have compared the relaxed and supercoiled versions for their responses to probes that include hydroxyl radicals, KMnO4, the junction resolvases endonuclease VII and RuvC, and RuvC activation of KMNO4 sensitivity. In no case did we find evidence for a braid at the crossover point. We conclude that Holliday junctions do not braid at their branch points, and that the topological problem created by crossover isomerization in the parallel conformation is likely to be solved by distributing the stress over the helices that flank the branch point.     

Conformations of A-DNA and B-DNA in agreement with fiber X-ray and infrared dichroism

Two right handed double helices are proposed as models for DNA fibers in respectively the A and the B form. The present conformations have geometrical parameters which agree very well with fiber X-ray and the orientation of their phosphate groups is in good accordance with infrared dichroïsm measurements. Dihedral angles and complete sets of atomic coordinates are given together with stereo-views and curves of the calculated diffracted intensities. Results are compared with experimental data and with preceding DNA models.     

Macroscopic DNA helices

Presently there is great interest in the construction of nanostructures from DNA fragments. Here we report the preparation of much larger helical textures with different shapes from pure DNA fragments. We have observed them while preparing crystals of the dodecamer d(AAAAAATTTTTT), which only contains adenine and thymine. Noncoding regions of the genome are always rich in these two bases. We have found a strong influence of ions either monovalent or divalent, with which different crystalline structures are found. All of them contain long helical stacks of duplexes in the unit cell. The most remarkable structures are macroscopic helices with diameters and pitch in the range of 20-40 microm. Thus, pure DNA oligonucleotides may form a hierarchy of helical structures, going from the B-form double helix (pitch, p = 33 A) to helical stacks of duplexes (p approximately 900 A), and to macroscopic helices (p approximately 300,000 A). These different levels of organization are reminiscent of the different levels of organization of DNA in eukaryotic chromosomes.     

DNA Models for A,B, C and D Conformations Related to Fiber X-ray,Infrared and NMR Measurements

Abstract

A conformational analysis of the A, B, C and D DNA forms was made in order to establish molecular models presenting a good agreement with experimental data obtained from fiber X-ray, infrared linear dichroism and ³¹P NMR. The proposed models have been refined and do present good stereochemistry and optimized H-bond distances between bases associated with the Watson-Crick pairing. The DNA conformations proposed are a left handed double helix for the C form and right handed helices for A, B and D. Relations to conformational transitions between these forms are discussed.     

A proposal for a specific double-helical structure in which the polynucleotide strands intercalate instead of forming base-pairs

Double helices, since the discovery of the DNA structure by Watson and Crick, represent the single most important secondary structural form of nucleic acids. The secondary structures of a variety of polynucleotide helices have now been well characterised with hydrogen-bonded base-pairs as building blocks. We wish to propose here the possibility, in a specific case, of a double stranded helical structure without any base-pair, but having a repeat unit of two nucleotides with their bases stacked through intercalation. The proposal comes from the initial models we have built for poly(dC) using the stacking patterns found in the crystal structures of 5'-dCMPNa2 which crystallises in two forms depending on the degree of hydration. These structures have pairs of nucleotides with the cytosine rings partially overlapping and separated by 3.3A. Using these as repeat units one could generate a model for poly(dC) with parallel strands, having a turn angle of 30 degrees and a base separation of 6.6A along each strand. Both right and left handed models with these parameters can be built in a smooth fashion without any obviously unreasonable stereochemical contacts. The helix diameter is about 13.5A, much smaller than that of normal helices with base-pair repeats. The changes in the sugar-phosphate backbone conformation in the present models compared to normal duplexes only reflect the torsional flexibility available for extension of polynucleotide chains as manifested by the crystal structures of drug-inserted oligonucleotide complexes. Intercalation proposed here could have some structural relevance elsewhere, for instance to the base-mismatched regions on the double helix and the packing of noncomplementary single strands as found in the filamentous bacteriophage Pf1.     

Conformations of C-DNA in agreement with fiber X-ray and infrared dichroism

Different left handed double helices are proposed as models for DNA fibers in the C form. These conformations have geometrical parameters which agree well with fiber X-ray data and the orientations of their phosphate groups are in good agreement with infrared dichroism results. A complete set of atomic coordinates and dihedral angles are given together with curves of calculated diffracted intensities. The present results are compared with experimental values and with the other C-DNA models.     

NMR studies of conformational states and dynamics of DNA

The application of high resolution NMR techniques to the investigation of DNA double helices in solution is currently in a rapid state of change as a result of advances in three different fields. First, new methods (cloning, enzymatic degradation, sonication, and chemical synthesis) have been developed for producing large quantities of short DNA suitable for NMR studies. Second, there have been major advances in the field of NMR in terms of the introduction of new pulse techniques and improvements in instrumentation. Finally, as a result of recent X-ray diffraction studies on short DNA helices and the discovery of left-handed Z-DNA there is heightened interest in the study of DNA structures in solution and the effect of sequence on structure. In the present review, we discuss the way in which NMR techniques have been used to probe various aspects of the DNA properties, including base pairing structure, dynamics of breathing, effect of sequence on DNA structure, internal molecular motions, the effect of environment on the DNA, and the interaction of DNA with small ligands.     

TRANSFORMATION OF NONPOLAR FILAMENTS OF THE BLUE-GREEN ALGA GLOEOTRICHIA ECHINULATA U. WISC. 1052 INTO DOUBLE HELICES12

Normally straight filaments of Gloeotrichia echinulata U. Wisc. 1052 transform into double helices when a critical culture density has been attained. In inorganic Zehnder-Gorham's medium No. 11, the alga initially is morphologically uniform and forms single, lightly curved, polar filaments. When a stage of close proximity of the filaments is reached, excessively long filaments are observed that are nonpolar. Some of these nonpolar filaments form helices. Two independent single helices may entwine to form a double helix. Double helices also form when both ends of an excessively long filament meet and start entwining until a loop is left at about the original middle of the filament. In another manner of double-helix formation, a straight filament makes a hairpin bend at about its middle; then 2 helices form starting at the bend and they entwine into a double helix, leaving a loop at the location of the original bend. Under proper culture conditions, the structures of double helices show an amazing regularity. Once double-helix formation has started, some strong force brings the process to completion. In a mature culture, helices disintegrate into apparently healthy, short pieces of filaments or single cells, while the straight or slightly curved polar filaments still persist. Helical transformation of nonpolar filaments does not appear to be a sign of nutritional or other stress but rather appears to serve a specific purpose. One might speculate that a genetic exchange between opposite cells takes place.     

RNA double helices generated from crystal structures of double helical dinucleoside phosphates.

The dinucleoside phosphates ApU and GpC form right-handed anti-parallel double helical fragments within their crystal lattices. Using a least squares procedure, we have generated the extended double helices which these fragments represent. ApU corresponds to a double helix with 11.9 residues per turn and a pitch of 28. 1Å. The GpC double helix has 10.4 residues per turn and a pitch of 26. 9Å.     

Multiple topological labeling for imaging single plasmids

Sequence-specific labeling methods for double-stranded DNA are required for mapping protein binding sites or specific DNA structures on circular DNA molecules by high-resolution imaging techniques such as electron and atomic force microscopies. Site-specific labeling can be achieved by ligating a DNA fragment to a stem-loop-triplex-forming oligonucleotide, thereby forming a topologically linked complex. The superhelicity of the plasmid is not altered and the process can be applied to two different target sites simultaneously, using DNA fragments of different sizes. Observation of the labeled plasmids by electron microscopy revealed that, under conditions where the triple helices were stable, the two labels were located at 339+/-34 bp from one another, in agreement with the distance between the two target sequences for triple helix formation (350 bp). Under conditions where the triple helices were not stable, the short DNA fragments could slide away from their target site. The concomitant attachment of two different stable labels makes it possible, for the first time to our knowledge, to label a circular DNA molecule and obtain information on its direction. In addition to its potential applications as a tool for structural investigations of single DNA molecules and their interactions with proteins, this DNA labeling method may also prove useful in biotechnology and gene therapy.     

Conformations of C-DNA in Agreement with Fiber X-ray and Infrared Dichroísm

Abstract

Different left handed double helices are proposed as models for DNA fibers in the C form. These conformations have geometrical parameters which agree well with fiber X-ray data and the orientations of their phosphate groups are in good agreement with infrared dichroísm results. A complete set of atomic coordinates and dihedral angles are given together with curves of calculated diffracted intensities. The present results are compared with experimental values and with the other C-DNA models.     

A Proposal For A Specific Double-Helical Structure In Which The Polynucleotide Strands Intercalate Instead of Forming Base-pairs

Abstract

Double helices, since the discovery of the DNA structure by Watson and Crick, represent the single most important secondary structural form of nucleic acids. The secondary structures of a variety of polynucleotide helices have now been well characterised with hydrogen- bonded base-pairs as building blocks. We wish to propose here the possibility, in a specific case, of a double stranded helical structure without any base-pair, but having a repeat unit of two nucleotides with their bases stacked through intercalation. The proposal comes from the initial models we have built for poly(dC) using the stacking patterns found in the crystal structures of 5′-dCMPNa₂ which crystallises in two forms depending on the degree of hydration. These structures have pairs of nucleotides with the cytosine rings partially overlapping and separated by 3.3Å. Using these as repeat units one could generate a model for poly(dC) with parallel strands, having a turn angle of 30° and a base separation of 6.6Å along each strand. Both right and left handed models with these parameters can be built in a smooth fashion without any obviously unreasonable stereochemical contacts. The helix diameter is about 13.5Å, much smaller than that of normal helices with base-pair repeats. The changes in the sugar-phosphate backbone conformation in the present models compared to normal duplexes only reflect the torsional flexibility available for extension of polynucleotide chains as manifested by the crystal structures of drug-inserted oligonucleotide complexes. Intercalation proposed here could have some structural relevance elsewhere, for instance to the base-mismatched regions on the double helix and the packing of noncomplementary single strands as found in the filamentous bacteriophage Pf1.     

A Stochastic Model of DNA Fragments Rejoining

When cells are exposed to ionizing radiation, DNA damages in the form of single strand breaks (SSBs), double strand breaks (DSBs), base damage or their combinations are frequent events. It is known that the complexity and severity of DNA damage depends on the quality of radiation, and the microscopic dose deposited in small segments of DNA, which is often related to the linear transfer energy (LET) of the radiation. Experimental studies have suggested that under the same dose, high LET radiation induces more small DNA fragments than low-LET radiation, which affects Ku efficiently binding with DNA end and might be a main reason for high-LET radiation induced RBE [1] since DNA DSB is a major cause for radiation-induced cell death. In this work, we proposed a mathematical model of DNA fragments rejoining according to non-homologous end joining (NHEJ) mechanism. By conducting Gillespie''s stochastic simulation, we found several factors that impact the efficiency of DNA fragments rejoining. Our results demonstrated that aberrant DNA damage repair can result predominantly from the occurrence of a spatial distribution of DSBs leading to short DNA fragments. Because of the low efficiency that short DNA fragments recruit repair protein and release the protein residue after fragments rejoining, Ku-dependent NHEJ is significantly interfered with short fragments. Overall, our work suggests that inhibiting the Ku-dependent NHEJ may significantly contribute to the increased efficiency for cell death and mutation observed for high LET radiation.     

Structural studies of DNA fragments: the G.T wobble base pair in A, B and Z DNA; the G.A base pair in B-DNA

The crystal structures of five double helical DNA fragments containing non-Watson-Crick complementary base pairs are reviewed. They comprise four fragments containing G.T base pairs: two deoxyoctamers d(GGGGCTCC) and d(GGGGTCCC) which crystallise as A type helices; a deoxydodecamer d(CGCGAATTTGCG) which crystallises in the B-DNA conformation; and the deoxyhexamer d(TGCGCG), which crystallises as a Z-DNA helix. In all four duplexes the G and T bases form wobble base pairs, with bases in the major tautomer forms and hydrogen bonds linking N1 of G with O2 of T and O6 of G with N3 of T. The X-ray analyses establish that the G.T wobble base pair can be accommodated in the A, B or Z double helix with minimal distortion of the global conformation. There are, however, changes in base stacking in the neighbourhood of the mismatched bases. The fifth structure, d(CGCGAATTAGCG), contains the purine purine mismatch G.A where G is in the anti and A in the syn conformation. The results represent the first direct structure determinations of base pair mismatches in DNA fragments and are discussed in relation to the fidelity of replication and mismatch recognition.     

HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments.

Using the gel retardation technique we have studied the protein-DNA complexes formed between HU--the major histone-like protein of Escherichia coli--and short DNA fragments. We show that several HU heterodimers bind DNA in a regularly spaced fashion with each heterodimer occupying about 9 base pairs. The alpha 2 and beta 2 HU homodimers form the same structure as the alpha beta heterodimer on double stranded DNA. However when compared to the heterodimer, they bind single stranded DNA with higher affinity. We also show that HU and the Integration Host Factor of E. coli (IHF) form different structures with the same DNA fragments. Moreover, HU seems to enhance the DNA-binding capacity of IHF to a DNA fragment which does not contain its consensus sequence.