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PubMed1990

The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps?

The structure of the self-complementary octamer d(GTACGTAC) has been analyzed by a single crystal X-ray diffraction method at 2.25 A resolution. The crystallographic R factor was 0.184 for all 1233 reflections at this resolution. In spite of the alternating purine-pyrimidine sequence, d(GTACGTAC) adopts the A-form conformation rather than the left-handed Z-form. The average helix twist and the mean rise per base pair are 32.1 degrees and 3.18 A, respectively. The d(GTACGTAC) helix is characterized by a wide open major groove and small base-pair tilt (9.7 degrees). The partial unwinding of the helix is observed only at the central pyrimidine-purine C-G step, but not at the other pyrimidine-purine T-A steps. Based on this study and six other X-ray studies, we propose a hypothesis that the A-DNA's are always unwound approximately 10 degrees at the C-G steps. Significant differences in base-pair stacking modes are seen between the purine-pyrimidine step and the pyrimidine-purine step. All deoxyribose rings adopt the C3'-endo conformation. All backbone torsion angles fall into the range expected for the A-DNA form, except for the nucleotide G5, whose alpha and gamma torsion angles adopt the trans, trans conformation instead of the common gauche-, gauche+ conformation.

Base Sequence↗

PubMed1989

Scanning tunneling microscopy of nucleic acids.

The scanning tunneling microscope (STM) has been used to measure properties of poly(rA).poly(rU) and DNA, such as helical pitch, half-period oscillations that were interpreted as the alternation between the major and minor grooves, and interhelical spacing. Average pitches were measured by two-dimensional Fourier transforms and by topographic profiles along the fiber axes. Values were typically 7 percent less than standard dimensions of A-form RNA and B-form DNA fibers. This result is compatible with the mild dehydration that occurred under air-drying conditions. More extensive dehydration typically led to 19 percent shrinkage. Analysis of specific regions allowed local variations in helical pitch as small as 1 angstrom to be detected, thus demonstrating that the STM can visualize functionally significant modulations of nucleic acid structure.

DNA↗

PubMedDate not supplied

[Study of the relationship between secondary DNA strucure and base sequence by the technic of theoretical conformational analysis].

An investigation of double-stranded polynucleotide conformations using the algorithm for exclusion of redundant dihedral angles and flexible sugar unit has been performed. The fragment of DNA including three nucleotide pairs was taken into account for polynucleotides poly[d(A--T)].poly[d(T--A)], poly[d(G--C)].poly[d(C--G)], poly(dA).poly(dT) and poly(dG).poly(dC). The resulting structures being energetically optimal have helical parameters corresponding to X-ray experimental values for A- and B-forms. It was revealed that B-form is the most energetically favorable structure, therefore the earlier conception that water is of importance for B-form stabilisation may be revised. Relative stabilities of B- and A-forms depend upon base sequence because unequal contributions of the stacking and backbone energy in whole potential energy of the structrues with different sequences.

Base Sequence↗

PubMed1977

A kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues in DNA.

The kinetic study of 1H leads to 3H exchange in C(8) H-groups of purinic residues of DNAs with different G-C content as well as in corresponding dNMP mixtures have been carried out. The present results show that 1H--3H exchange in DNA is retarded (as compared to the exchange in dNMP mixtures) to a lesser extent (Kret =2.4-2.8) than in RNA (Kret=6-8). The degree of retardation in these polymers is practically independent of their nucleotide composition. Assuming the ylide mechanism of exchange reaction it is suggested that the lower rate of 1H leads to 3H exchange in C(8) H-groups of purinic residues in polynucleotides of A-form (RNA and other polyribonucleotides) as compared to those of B-form (DNA and other polydeoxyribonucleotides) might be accounted for by decreased availability of C(8) H-groups for OH-ions of the solvent due to a different microenviroment of these groups in A- and B-type helixes.

DNA↗

PubMed1989

Molecular mechanics studies on poly(purine).poly(pyrimidine) sequences in DNA: polymorphism and local variability.

Energy minimization has been carried out on three poly(purine).poly(pyrimidine) sequences--d(G)10.d(C)10, d(A)10.d(T)10, and d(AG)5.d(CT)5--using the molecular mechanics program AMBER (Assisted Model Building and Energy Refinement). In order to extensively scan the conformational space available, five different helical models were studied, three of them being right-handed helices while the other two were left helical. For all three sequences the right-handed A- and B-type helices are energetically slightly preferred over the left helices, but the energy difference between the various right-handed helices is only marginal. A detailed analysis has been carried out to characterize the local structural variability in the refined structures, both in terms of torsion angles as well as other parameters such as base-pair tilt, wedge roll, and wedge tilt, etc. All three sequences exhibit similar structural features for a particular form, but both the forms A and B show significant deviations from fiber models. In particular, the A-form structures have higher unit rise (2.7 A), and lower unit twist (31 degrees) and base-pair tilt (12 degrees), compared to the fiber model, which has corresponding values of 2.56 A, 32.7 degrees, and 20 degrees, respectively. All these changes indicate that the refined models are closer to the A-form structure observed in crystals of oligonucleotides. In the refined B-for models, the helical parameters are close to the fiber B-form, although the torsion angles show considerable variations. None of the three sequences examined, including the d(A)n.d(T)n sequence, show any pronounced curvature for the B-form structure.

Base Sequence↗

PubMed1990

Z-RNA: the solution NMR structure of r(CGCGCG).

Left-handed double-helical Z-RNA has been studied using the ribohexanucleotide pentaphosphate r(CpGpCpGpCpG). One-dimensional and two-dimensional proton nmr experiments were used to probe the structural details of the left-handed helix in concentrated sodium perchlorate solution. In 1M NaClO4 the RNA adopts the normal A-form double helix, and in 6M NaClO4 it is nearly all in the Z form. In 4M NaClO4 it exists as nearly equal parts of A form and Z form. Resonances corresponding to both A and Z form appear in the nmr spectrum, indicating that the duplex exchanges slowly between forms. Spin-spin coupling constants between protons in the ribose rings were used to determine the sugar-pucker conformations of the individual nucleotides. Quantitative nuclear Overhauser experiments were used to determine proton-proton distances within the nucleoside, and from these distances values for the glycosidic torsion angle were determined. The results show that the cytidines adopt C2'-endo sugar puckers (S type) with pseudo-rotation phase values (P) of approximately 165 degrees. The bases are in the anti conformation, with chi values of approximately -140 degrees. The internal guanosines adopt C3'-endo sugar puckers (N type) with P approximately 18 degrees, while the 3'-terminal guanosine ribose exists in an equilibrium between S- and N-type conformations. All three guanosine bases adopt the syn conformation, with chi approximately 70 degrees. The results indicate that the solution structure of Z-RNA is very similar to that of Z-DNA.

Base Sequence↗

PubMed1989

The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure.

On the basis of nuclease digestion studies we proposed that the DNA binding site of transcription factor IIIA (TFIIIA) may have an overall structure with A-type rather than B-type characteristics. This proposal was substantiated by the crystal structure of a part of the TFIIIA binding site. Recently, however, it has been reported that the binding site for TFIIIA is B-form in solution, thus implying that the conformation present in crystals is not the structure in solution. We have carried out a study using comparative circular dichroism (CD) spectroscopy of a number of double stranded deoxyoligonucleotides of different sequence, and known crystal structure. The correlation we have found between CD characteristics and certain structural parameters indicates that the solution and crystal structures of the TFIIIA binding site are closely related. This structure may be classed as an intermediate type, between A-form and B-form DNA.

Animals↗

PubMed1987

Molecular mechanics calculations of dA12.dT12 and of the curved molecule d(GCTCGAAAAA)4.d(TTTTTCGAGC)4.

Using the AMBER software package (Weiner and Kollman 1981) substantially modified for electrostatic contributions, the structural energies of the double-stranded oligonucleotides dA12.dT12 and d(GCTCGAAAAA)4.d(TTTTTCGAGC)4 were minimized. Using various starting structures for the molecule dA12.dT12, one final structure is obtained which possesses the experimentally determined properties of poly(dA).poly(dT). This structure is an A-form-B-form-hybrid structure similar to that of Arnott et al. (1983). The dA-strand is similar to an A-form while the dT-strand is similar to normal B-form. This structure and separately optimized B-form sequence stretches were used to construct the double-stranded fragment d(GCTCGAAAAA)4 which again was optimized. This sequence, when imbedded in a DNA fragment as contiguous repeats, shows a gel migration anomaly which has been interpreted as stable curvature of the DNA (Diekmann 1986). The calculated structure of this sequence indeed has a curved helix axis and is discussed as a model for curved DNA. A theoretical formalism is presented which allows one to calculate the structural parameters of any nucleic acid double helix in two different geometrical representations. This formalism is used to determine the parameters of the base-pair orientations of the curved structure in terms of wedge as well as cylindrical parameters. In the structural model presented here, the curvature of the helix axis results from an alternation of two different DNA structures in which the base-pairs possess different angles with the helix axis ('cylinder tilt'). Resulting from geometric restraints, a negative cylinder tilt angle correlates strongly with the closing of the minor groove ('wedge roll'). The blocks with different structure are not exactly coincident with the dA5-blocks and the B-DNA stretches. Within the dA5 block, base-pair tilt and wedge roll adopt large values which proceed into the 3' flanking B-DNA sequence by about one base-pair. These properties of the structure calculated here are discussed in terms of different models explaining DNA curvature.

DNA↗

PubMed1985

Poly(d2NH2A-dT): two-dimensional NMR shows a B to A conversion in high salt.

Poly(d2NH2A-dT) forms a structure in high salt that is clearly distinct from the B form present in low salt. Two-dimensional nuclear Overhauser effect (2D NOE) NMR spectra establish that the conformation of the high-salt form is not Z. Correlations of observed cross peaks in the 2D NOE spectra and estimated interproton distances of the common DNA conformations are consistent only with an A form or closely related structure. This interpretation is also consistent with the negative circular dichroic band observed in the high-salt form of poly(d2NH2A-dT) and in A-form ribohomopolymer helices containing 2NH2A.

Kinetics↗

PubMed1988

Binding of ethidium ion to left-handed Z-RNA induces a cooperative transition to right-handed RNA at the intercalation site.

The equilibrium binding of the ethidium cation (Etd+) to the right-handed A-form of poly-[r(C-G)], the B-form of poly[d(C-G)], and the left-handed Z-forms of Br-poly[r(C-G)] and Br-poly[d(C-G)] was investigated in 0.22 M NaCl by optical methods. Scatchard analysis indicates that Etd+ intercalates into right-handed forms of poly[r(C-G)] and poly[d(C-G)] in a noncooperative manner. Correlation of Etd+ absorbance binding isotherms and polynucleotide circular dichroism data indicates that drug binding to Br-poly[r(C-G) and Br-poly[d(C-G)] results in cooperative conversion from left-handed Z-forms to right-handed intercalated conformations. Approximate stoichiometries necessary to induce the left- to right-handed transitions are 1 Etd+/9 base pairs (bp) for Z-RNA and 1 Etd+/6 bp for Z-DNA. The apparent limiting binding stoichiometries are approximately 1 Etd+/3 bp for RNA and 1 Etd+/2 bp for DNA. The equilibrium binding constants for binding to the right-handed forms decrease in the order Br-poly[d(C-G)], Br-poly[r(C-G)], poly[d(C-G)], and poly[r(C-G)]. Thermodynamic parameters are obtained by van't Hoff analysis of Etd+ absorbance thermal dissociation data. Enthalpy values for all four polynucleotides are negative and of similar magnitude. Negative entropy values indicate that the binding processes are primarily enthalpically driven.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1991

Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs.

The crystal structure of the RNA dodecamer duplex (r-GGACUUCGGUCC)2 has been determined. The dodecamers stack end-to-end in the crystal, simulating infinite A-form helices with only a break in the phosphodiester chain. These infinite helices are held together in the crystal by hydrogen bonding between ribose hydroxyl groups and a variety of donors and acceptors. The four noncomplementary nucleotides in the middle of the sequence did not form an internal loop, but rather a highly regular double-helix incorporating the non-Watson-Crick base pairs, G.U and U.C. This is the first direct observation of a U.C (or T.C) base pair in a crystal structure. The U.C pairs each form only a single base-base hydrogen bond, but are stabilized by a water molecule which bridges between the ring nitrogens and by four waters in the major groove which link the bases and phosphates. The lack of distortion introduced in the double helix by the U.C mismatch may explain its low efficiency of repair in DNA. The G.U wobble pair is also stabilized by a minor-groove water which bridges between the unpaired guanine amino and the ribose hydroxyl of the uracil. This structure emphasizes the importance of specific hydrogen bonding between not only the nucleotide bases, but also the ribose hydroxyls, phosphate oxygens and tightly bound waters in stabilization of the intramolecular and intermolecular structures of double helical RNA.

Base Sequence↗

PubMed1990

The infrared and Raman spectra of the duplex of d(GGTATACC) in the crystal show bands due to both the A-form and the B-form of DNA.

The deoxyoligonucleotide, d(GGTATACC), forms a duplex structure that crystallizes in the DNA A form. This has been shown by both X-ray diffraction studies and Raman spectroscopy (1,2). The presence of the DNA B form has been reported using diffuse X-ray scattering from a crystal of the closely related sequence d(GGBrUABrUACC)(3). In this paper the infrared spectrum of the d(GGTATACC) crystal is presented and curve resolution of both the Raman and IR spectra have been carried out. The percentage of A and B forms have been estimated. The %B form in the crystal has been estimated from the IR spectra to be about 15% and from Raman to be about 20%. Moreover the IR spectrum of the A conformation in the crystal is slightly different from the IR spectrum of the A conformation in polynucleotide fibers in particular in the region of the phosphate stretching vibrations and of the in-plane double bond vibrations of the bases. We show that it is feasible to obtain IR as well as Raman spectra of small crystals of oligonucleotides and that this is a good method of identifying all of the different conformations that may be in the crystal.

Base Sequence↗

PubMed1984

Conformations of poly(dG-dC).poly(dG-dC) modified by the O-acetyl derivative of the carcinogen 4-hydroxyaminoquinoline 1-oxide.

Poly(dG-dC).poly(dG-dC) has been modified by reaction with 4-acetoxyaminoquinoline 1-oxide (Ac-4 HAQO), the ultimate carcinogen of 4-nitroquinoline 1-oxide. The circular dichroism (CD) spectra of the modified and unmodified polymers have been compared under various experimental conditions. The CD spectra were recorded in 1 mM phosphate, 50% (v/v) ethanol, 3.8 M LiCl and 95% (v/v) ethanol, conditions in which poly(dG-dC).poly(dG-dC) adopts the B-, Z-, C- and A-form respectively. In 1 mM phosphate buffer, poly(dG-dC).poly(dG-dC) modified by Ac-4 HAQO seems not to contain regions in the Z-form. Z-form induction could be progressively obtained by the addition of ethanol as follows: in the buffer with about 30% ethanol the modified polymer started to adopt the Z structure, while 40% of ethanol in the buffer was necessary for the unmodified polymer. In the 50% ethanol-1 mM phosphate buffer mixture (v/v), poly(dG-dC).poly(dG-dC) was entirely in the Z-form while poly(dG-dC).poly(dG-dC) modified by Ac-4 HAQO remained partially in the B-form. Enzymatic digestions with the nuclease S1 which is specific of the single-stranded DNA were carried out in order to support the modified poly(dG-dC).poly(dG-dC) CD study conclusions. The role played by the two major adducts on the conformational characteristics of modified polymer is discussed.

Aminoquinolines↗

PubMed1986

Does 5S RNA from E. coli have a pseudoknotted structure?

Chemical modification and limited enzymatic hydrolysis on isolated E. coli 5S RNA have provided informations on the secondary- and tertiary structure compatible with pseudoknotted structures for the A- and B-conformers of the molecule. Changes in the accessibility and reactivity of nucleotides in loop C and at the stem of helix IV in two different 5S RNA conformers are highly suggestive for interactions between bases C35 to C37 with G105 to G107 for the A-form and C38 to U40 and A94 to G96 with additional interactions of C35, C37 with G98 and G100 for the B-form. In both cases the molecules are folded forming pseudoknots and two quasi--continuous double stranded helices with coaxial stacking. The two structures are in perfect agreement with the biochemical data concerning the stability of the molecule and the chemical reactivities of individual nucleotides of the 5S RNA A- and B-conformers.

Base Sequence↗

PubMed1991

A sequence dimorphism in a conserved domain of human 28S rRNA. Uneven distribution of variant genes among individuals. Differential expression in HeLa cells.

In humans, cellular 28S rRNA displays a sequence dimorphism within an evolutionarily conserved motif, with the presence, at position +60, of either a A (like the metazoan consensus) or a G. The relative abundance of the two forms of variant genes in the genome exhibit large differences among individuals. The two variant forms are generally represented in cellular 28S rRNA in proportion of their relative abundance in the genome, at least for leucocytes. However, in some cases, one form of variant may be markedly underexpressed as compared to the other. Thus, in HeLa cells, A-form genes contribute to only 1% of the cellular content in mature 28S rRNA although amounting to 15% of the ribosomal genes. The differential expression seems to result from different transcriptional activities rather than from differences in pre-rRNA processing efficiency or in stabilities of mature rRNAs. G-form ribosomal genes were not detected in other mammals, including chimpanzee, which suggests that the fixation of this variant type is a rather recent event in primate evolution.

Base Sequence↗

PubMed1978

On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule.

The degree of orientation of DNA in a flow has been studied within the interval of the B - A transition induced by ethanol. The orientation of the B DNA (60-65% ethanol, v/v) and that of the A DNA (80-82% ethanol) are nearly identical. This means that both conformations have similar persistence lengths and that there is no aggregation in the course of formation of the A form. Within the transition range (65-78% ethanol) the orientation attains a sharp minimum which coincides with the half-transition point (73% ethanol). The cooperative character of the B - A transition presupposes the existence of boundaries between the alternating sections of the A and B conformations that may entail an increased flexibility of the DNA molecule and a corresponding drop of orientation. Theory predicts an elliptical dependence of the number of boundaries on the proportion of the A form. The experimental degree of orientation follows the same pattern. Quantitative evaluation shows that the flexibility of a boundary is small, so that several dozen of boundaries are required to simulate free rotation.

Chemical Phenomena↗

PubMed1984

Escherichia coli 5S RNA A and B conformers. Characterisation by enzymatic and chemical methods.

The structures of the two stable conformers of Escherichia coli 5 S RNA, the and B form, were compared. Information about the structures were obtained using the methods of limited enzymatic hydrolysis and chemical modification of accessible nucleotides. Base-specific modifications were performed for adenosines and cytidines using diethylpyrocarbonate and dimethylsulfate in combination with a strand-scission reaction at the modified site. Base-specific (RNase T1) as well as conformation-specific (nuclease S1, cobra venom nuclease) enzymes were employed for the limited enzymatic hydrolysis. Clear differences in the accessibility of the two 5 S RNA conformers to the enzymes and the chemical reagents were established and the regions with altered reactivities were localized in the 5 S RNA structure. The results are consistent with the disruption of the secondary structural interactions in helix II and partly in helices III and IV during the transition from the A to the B form. (The numbering of the helices is according to the generally accepted Fox and Woese model.) In addition some regions presumably involved in the tertiary structure are distorted. There is evidence, however, for the new formation of structural regions between two distant sites in the 5 S RNA B form. The results enable us to refine the existing 5 S RNA A-form model and provide insight into the structural dynamics that lead to the formation of the 5 S RNA B form.

Adenosine↗

PubMed1985

Salt induced conformational transition between A and Z forms of r(CGCGCG) as revealed by a Raman spectroscopic study.

Solution conformation in different conditions of r(CGCGCG) has been studied by a Raman spectroscopic method. In NaCl solution, r (CGCGCG) takes only an A-form duplex in which guanosine and cytidine have C3'endo-anti conformation even at 5M salt concentration. In much higher ionic strength condition (5M NaCl plus 1M MgCl2 or 6M NaClO4), it undergoes a transition to a left-handed Z-form. The Raman spectrum of the Z-form RNA was found to be very similar to that of Z-form DNA, suggesting that Z-RNA involves a C3'endo-syn guanosine and an in between form of C2'endo-Cl'exo-anti cytidine.

Kinetics↗