ABSTRACT
We report the coiled-coil structure of DNA, which is generated by the dodecanucleotide d(ATATATATATAT). The structure has been determined by single-crystal x-ray crystallography. The molecules form duplexes with single-stranded overhangs, which associate with neighbor molecules and give rise to infinite double helices in a coiled-coil conformation, with staggered nicks in both strands. The coiled coils have six dodecamer duplexes per turn. Despite the presence of nicks, the structure is very rigid. Statistical disorder is present, which gives rise to continuous scattering along the layer lines. This observation can be interpreted by the classical theory of coiled coils developed for proteins, which we apply here to a DNA structure. A clear splitting of the original layer lines of the DNA double helix is detected. The structure we have found adds a previously unrecognized element to the architectures that can be built from DNA oligonucleotides. Any duplex with complementary single-strand overhangs should be expected to give rise to regular coiled-coil structures.
Subject(s)
DNA, Superhelical/chemistry , DNA/chemistry , Nucleic Acid Conformation , Crystallography, X-RayABSTRACT
The title compound, dimethyl 2,2'-(oxalyldiimino)diethanoate, C(8)H(12)N(2)O(6), exhibits a network of hydrogen bonds between amide and ester groups. Molecules lie on inversion centres and show a planar conformation for both the oxalamide and ester groups. The glycine residues adopt a conformation close to the polyglycine II structure.
Subject(s)
Amides/chemistry , Oxalates/chemistry , Crystallography, X-Ray , Hydrogen Bonding , Models, Molecular , Molecular Conformation , SolutionsABSTRACT
We have determined by X-ray crystallography the structure of the hexamer duplex d(GGCGCC)2 in the A-form using ethanol as a precipitant. The same sequence had previously been crystallized in the B-form, but with 2-methyl-2,4-pentanediol as a precipitant. It appears that ethanol precipitation is a useful method to induce the formation of A-form crystals of DNA. Packing of the molecules in the crystal has unique features: the known interaction of A-DNA duplexes between terminal base-pairs and the minor groove of neighbor molecules is combined with a superstructure consisting in an alternation of DNA layers and solvent layers (water/ions). This organization in layers has been observed before, also with hexamers in the A conformation which crystallize in the same space group (C2221). The solvent layer has a precise thickness, although very few ordered water molecules can be detected. Another feature of this crystal is its large unit cell, which gives rise to an asymmetric unit with three hexamer duplexes. One of the three duplexes is quite different from the other two in several aspects: the number of base pairs per turn, the twist pattern, the mean value of the twist angle and the fact that one terminal base-pair is not stacked as part of the duplex and appears to be disordered. So the variability in conformation of this sequence is remarkable.
Subject(s)
DNA/chemistry , Nucleic Acid Conformation , Oligodeoxyribonucleotides/chemistry , Base Sequence , Crystallization , Crystallography, X-Ray , DNA/isolation & purification , Ethanol , Models, Molecular , Oligodeoxyribonucleotides/isolation & purification , SolventsABSTRACT
We present the structure of the dodecamer CGCTCTAGAGCG and the related octamer CGCTAGCG, both in the B form, determined by single crystal X-ray diffraction. Two different crystal forms of the octamer have been obtained, with either three or four duplexes in the asymmetric unit. The dodecamer crystallizes in the P2(1) space group with two duplexes in the asymmetric unit. Very few such structures have been previously reported, while the octamer structure is the first one determined with three duplexes in the asymmetric unit. It is also the first octamer with standard Watson-Crick base pairs to be crystallized in the B form. The crystal structure is stabilized in both cases by interactions between the guanines in the two terminal base pairs of each duplex. This interaction is similar to that found in most dodecamers which have been previously studied, but here it is found in a new unit cell (for the dodecamer) and in one octamer. In the dodecamer cytosine-stacking interactions between neighbor duplexes are also present. The two dodecamer duplexes in the asymmetric unit show different patterns of bending, while the octamer molecule has a rather straight helical axis. The results presented confirm the strong conformational variability of the TA pyrimidine-purine step and demonstrate a clear alternating structure for the (CT/GA)n sequence.
Subject(s)
DNA/chemistry , Nucleic Acid Conformation , Oligodeoxyribonucleotides/chemistry , Base Composition , Base Sequence , Calcium/metabolism , Crystallization , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , SoftwareABSTRACT
We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.
Subject(s)
Models, Molecular , Nucleic Acid Conformation , Oligodeoxyribonucleotides/chemistry , Crystallization , Crystallography, X-Ray , DNA/chemistry , Dinucleoside Phosphates/chemistry , Molecular Structure , Oligodeoxyribonucleotides/chemical synthesis , Recombination, GeneticABSTRACT
Two crystals d(C2GCG2) and d(C5GCG5) have been studied under microscope by Fourier transform ir spectroscopy and Raman spectroscopy. The x-ray diffraction study of the latter crystal had shown that the d(C5GCG5) sequence is the first DNA dodecamer known to adopt a canonical A conformation [N. Verdaguer, J. Aymami, D. Fernandez-Forner, I. Fita, M. Coll, T. Huynh-Dinh, J. Igolen, and J. A. Subirana (1991) Journal of Molecular Biology, Vol. 221, pp. 623-635]. Characteristic ir marker bands and Raman marker peaks of the A conformation have thus been obtained and are compared with previously proposed assignments correlated to fiber diffraction x-ray results obtained on polymers. The d(C2GCG2) sequence crystal had previously been studied in an intermediate form between B and Z [L. Urpi, J. P. Ridoux, J. Liquier, N. Verdagner, I. Fita, J. A. Subirana, F. Iglesias, T. Huynh-Dinh, J. Igolen, and E. Taillandier (1989) Nucleic Acids Research, Vol. 17, pp. 6669-6679]. In this paper we present results obtained from a crystal with this oligonucleotide in Z conformation. The effect of the crystallization conditions on the geometry of the obtained oligomer helix is discussed. The influence of the addition, to the central tetramer CGCG, of dCn stretches (at the 5' end) and dGn stretches (at the 3' end) of different lengths, on the conformational flexibility of the nucleic acid, is considered.
Subject(s)
Oligonucleotides/chemistry , Base Sequence , Chemical Phenomena , Chemistry, Physical , Molecular Sequence Data , Nucleic Acid Conformation , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, RamanABSTRACT
Crystals of self complementary DNA hexamers d(CACGTG), d(CCGCGG) and d(GGCGCC) were grown by vapour diffusion technique and studied by microRaman and microIR spectroscopies. The oligonucleotides were studied in parallel in solution by vibrational spectroscopy. A B- greater than Z transition was detected by Raman spectroscopy during the crystallization process for d(CACGTG). Vibrational spectroscopy shows that the d(GGCGCC) crystals adopt a B geometry. On the contrary the d(CCGCGG) sequence which is shown to be able to undergo in solution or in films quite easily the B- greater than Z transition, remains trapped in crystals in a geometry which may correspond to an intermediate conformation often proposed in models of the B- greater than Z transition. The crystals used in this study were characterized by X-ray diffraction. The unit cell and space group have been determined.
Subject(s)
Oligodeoxyribonucleotides , Base Sequence , Crystallization , Nucleic Acid Conformation , Solutions , Spectrophotometry, Infrared , Spectrum Analysis, Raman/methodsABSTRACT
The crystal structure of the nucleoside 2',3'-dideoxyformycin A has been determined. The structure shows a syn conformation about the glycosidic bond, stabilised by an intramolecular hydrogen bond between the 05' and N3 atoms. HIV activity was examined in a syncytium inhibition assay. In contrast to the marked decrease in viral titre observed with 2',3'-dideoxycytidine, the formycin analogue produced no effect. It may be concluded that the syn conformation for a dideoxy nucleoside is probably deleterious to HIV inhibition of HIV replication.
