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At least 811 records · Page 45Linked to original sources
PubMed2000

Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage.

The protein encoded by gene 45 of T4 bacteriophage (gene 45 protein or gp45), is responsible for tethering the catalytic subunit of T4 DNA Polymerase to DNA during high-speed replication. Also referred to as a sliding DNA clamp, gp45 is similar in its function to the processivity factors of bacterial and eukaryotic DNA polymerases, the beta-clamp and PCNA, respectively. Crystallographic analysis has shown that the beta-clamp and PCNA form highly symmetrical ring-shaped structures through which duplex DNA can be threaded. Gp45 shares no sequence similarity with beta-clamp or PCNA, and sequence comparisons have not been able to establish whether it adopts a similar structure. We have determined the crystal structure of gp45 from T4 bacteriophage at 2.4 A resolution, using multiple isomorphous replacement. The protein forms a trimeric ring-shaped assembly with overall dimensions that are similar to those of the bacterial and eukaryotic processivity factors. Each monomer of gp45 contains two domains that are very similar in chain fold to those of beta-clamp and PCNA. Despite an overall negative charge, the inner surface of the ring is in a region of positive electrostatic potential, consistent with a mechanism in which DNA is threaded through the ring.

Amino Acid Sequence↗
PubMed2001

Crystal structure of rabbit phosphoglucose isomerase complexed with its substrate D-fructose 6-phosphate.

Phosphoglucose isomerase (PGI, EC 5.3.1.9) catalyzes the interconversion of D-glucose 6-phosphate (G6P) and D-fructose 6-phosphate (F6P) and plays important roles in glycolysis and gluconeogenesis. Biochemical characterization of the enzyme has led to a proposed multistep catalytic mechanism. First, the enzyme catalyzes ring opening to yield the open chain form of the substrate. Then isomerization proceeds via proton transfer between C2 and C1 of a cis-enediol(ate) intermediate to yield the open chain form of the product. Catalysis proceeds in both the G6P to F6P and F6P to G6P directions, so both G6P and F6P are substrates. X-ray crystal structure analysis of rabbit and bacterial PGI has previously identified the location of the enzyme active site, and a recent crystal structure of rabbit PGI identified Glu357 as a candidate functional group for transferring the proton. However, it was not clear which active site amino acid residues catalyze the ring opening step. In this paper, we report the X-ray crystal structure of rabbit PGI complexed with the cyclic form of its substrate, D-fructose 6-phosphate, at 2.1 A resolution. The location of the substrate relative to the side chains of His388 suggest that His388 promotes ring opening by protonating the ring oxygen. Glu216 helps to position His388, and a water molecule that is held in position by Lys518 and Thr214 accepts a proton from the hydroxyl group at C2. Comparison to a structure of rabbit PGI with 5PAA bound indicates that ring opening is followed by loss of the protonated water molecule and conformational changes in the substrate and the protein so that a helix containing amino acids 513-520 moves in toward the substrate to form additional hydrogen bonds with the substrate.

Amino Acids↗
PubMed1996

Structural transitions during activation and ligand binding in hexadecameric Rubisco inferred from the crystal structure of the activated unliganded spinach enzyme.

Activation of ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco; EC 4.1.1.39) by CO2 involves carbamylation of Lys 201 and the subsequent binding of a magnesium ion to complete the active site. The refined crystal structure of activated Rubisco shows that the magnesium ligands are Asp 203, Glu 204, the carbamate of Lys 201, and three water molecules. Structural differences between the unactivated and activated forms are minimal. Substrate binding replaces water ligands around the metal and triggers substantial structural changes in loops covering the active site. This leads to a contraction and tightening of the structure of the large subunits with the movements transmitted to and modulated by the small subunits.

Crystallography, X-Ray↗
PubMed2003

Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms.

The crystal structure of a small, basic DNA binding protein, Sso10b2, from the thermoacidophilic archaeon Sulfolobus solfataricus was determined by the Zn multiwavelength anomalous diffraction method and refined to 1.85 A resolution. The 89-amino-acid protein adopts a betaalphabetaalphabetabeta topology. The structure is similar to that of Sso10b1 (also called Alba) from the same organism. However, Sso10b2 contains an arginine-rich loop RDRRR motif, which may play an important role in nucleic acid binding. There are two independent Sso10b2 proteins in the asymmetric unit, and a plausible stable dimer could be deduced from the crystal structure. Topology comparison revealed that Sso10b2 is similar to several RNA-binding proteins, including IF3-C, YhhP, and DNase I. Models of the Sso10b2 dimer bound to either B-DNA or A-DNA have been constructed.

Amino Acid Sequence↗
PubMed2001

Trimerization of alkali dicyanamides M[N(CN)2] and formation of tricyanomelaminates M3[C6N9] (M = K, Rb) in the melt: crystal structure determination of three polymorphs of K[N(CN)2], two of Rb[N(CN)2], and one of K3[C6N9] and Rb3[C6N9] from X-ray powder diffractometry.

The alkali dicyanamides M[N(CN)2] (M=K, Rb) were synthesized through ion exchange, and the corresponding tricyanomelaminates M3[C6N9] were obtained by heating the respective dicyanamides. The thermal behavior of the dicyanamides and their reaction to form the tricyanomelaminates were investigated by temperature-dependent X-ray powder diffractometry and thermoanalytical measurements. Potassium dicyanamide K[N(CN)2] was found to undergo four phase transitions: At 136 degrees C the low-temperature modification alpha-K[N(CN)2] transforms to beta-K[N(CN)2], and at 187degrees C the latter transforms to the high-temperature modification gamma-K[N(CN)2], which melts at 232 degrees C. Above 310 degrees C the dicyanamide ions [N(CN)2]- trimerize and the resulting tricyanomelaminate K3[C6N9] solidifies. Two modifications of rubidium dicyanamide have been identified: Even at -25 degrees C, the a form slowly transforms to beta-Rb[N(CN)2] within weeks. Rb[N(CN)2] has a melting point of 190 degrees C. Above 260 degrees C the dicyanamide ions [N(CN)2]- of the rubidium salt trimerize in the melt and the tricyanomelaminate Rb3[C6N9] solidifies. The crystal structures of all phases were determined by powder diffraction methods and were refined by the Rietveld method. alpha-K[N(CN)2] (Pbcm, a = 836.52(1), b = 46.90(1), c =7 21.27(1) pm, Z = 4), gamma-K[N(CN)2] (Pnma, a = 855.40(3), b = 387.80(1), 1252.73(4) pm, Z = 4), and Rb[N(CN)2] (C2/c, a = 1381.56(2), b = 1000.02(1), c = 1443.28(2) pm, 116.8963(6) degrees, Z = 16) represent new structure types. The crystal structure of beta-K[N(CN)2] (P2(1/n), a = -726.92(1), b 1596.34(2), c = 387.037(5) pm, 111.8782(6) degrees, Z = 4) is similar but not isotypic to the structure of alpha Na[N(CN)2]. alpha-Rb[N(CN)2] (Pbcm, a = 856.09(1), b = 661.711(7), c = 765.067(9) pm, Z = 4) is isotypic with alpha-K[N(CN)2]. The alkali dicyanamides contain the bent planar anion [N(CN)2]- of approximate symmetry C2, (average bond lengths: C-N(bridge) 133, C-N(term) 113 pm; average angles N-C-N 170 degrees, C-N-C 120 degrees). K3[C6N9] (P2(1/c), a = 373.82(1), b = 1192.48(5), c = 2500.4(1) pm, beta = 101.406(3) degrees, Z = 4) and Rb,[C6N9] (P2(1/c), a = 389.93(2), b = 1226.06(6), c = 2547.5(1) pm, 98.741(5) degrees, Z=4) are isotypic and they contain the planar cyclic anion [C6N9]3-. Although structurally related, Na3[C6N9] is not isotypic with the tricyanomelaminates M3[C6N9] (M = K, Rb).

Journal Article↗
PubMed1999

Crystal structure of cyanovirin-N, a potent HIV-inactivating protein, shows unexpected domain swapping.

The crystal structure of cyanovirin-N (CV-N), a protein with potent antiviral activity, was solved at 1.5 A resolution by molecular replacement using as the search model the solution structure previously determined by NMR. The crystals belong to the space group P3221 with one monomer of CV-N in each asymmetric unit. The primary structure of CV-N contains 101 residues organized in two domains, A (residues 1 to 50) and B (residues 51 to 101), with a high degree of internal sequence and structural similarity. We found that under the conditions of the crystallographic experiments (low pH and 26 % isopropanol), two symmetrically related monomers form a dimer by domain swapping, such that domain A of one monomer interacts with domain B' of its crystallographic symmetry mate and vice versa. Because the two swapped domains are distant from each other, domain swapping does not result in additional intramolecular interactions. Even though one of the protein sample solutions that was used for crystallization clearly contained 100 % monomeric CV-N molecules, as judged by various methods, we were only able to obtain crystals containing domain-swapped dimers. With the exception of the unexpected phenomenon of domain swapping, the crystal structure of CV-N is very similar to the NMR structure, with a root-mean-square deviation of 0.55 A for the main-chain atoms, the best agreement reported to date for structures solved using both techniques.

Antiviral Agents↗
PubMed2007

Crystal structure of an FIV/HIV chimeric protease complexed with the broad-based inhibitor, TL-3.

We have obtained the 1.7 A crystal structure of FIV protease (PR) in which 12 critical residues around the active site have been substituted with the structurally equivalent residues of HIV PR (12X FIV PR). The chimeric PR was crystallized in complex with the broad-based inhibitor TL-3, which inhibits wild type FIV and HIV PRs, as well as 12X FIV PR and several drug-resistant HIV mutants 1234. Biochemical analyses have demonstrated that TL-3 inhibits these PRs in the order HIV PR > 12X FIV PR > FIV PR, with Ki values of 1.5 nM, 10 nM, and 41 nM, respectively 234. Comparison of the crystal structures of the TL-3 complexes of 12X FIV and wild-typeFIV PR revealed theformation of additinal van der Waals interactions between the enzyme inhibitor in the mutant PR. The 12X FIV PR retained the hydrogen bonding interactions between residues in the flap regions and active site involving the enzyme and the TL-3 inhibitor in comparison to both FIV PR and HIV PR. However, the flap regions of the 12X FIV PR more closely resemble those of HIV PR, having gained several stabilizing intra-flap interactions not present in wild type FIV PR. These findings offer a structural explanation for the observed inhibitor/substrate binding properties of the chimeric PR.

Animals↗
PubMed2006

Cu4Mo6Se8: synthesis, crystal structure, and electronic structure of a new Chevrel phase structure type.

Cu4Mo6Se8 has been synthesized by intercalation of Cu into Cu2Mo6Se8 at room temperature, and its crystal structure has been determined. This compound crystallizes in the triclinic space group P, with a = 6.7609(8) A, b = 6.8122(7) A, c = 7.9355(10) A, alpha = 70.739(4) degrees , beta = 72.669(4) degrees , gamma = 84.555(5) degrees , and Z = 1. Instead of residing in the voids between corners or edges of Mo6Se8 clusters as in the classic R Chevrel structure, the Cu atoms in Cu4Mo6Se8 fully occupy four sites between faces of two adjacent Mo6Se8 clusters. Thus, two of the six Mo atoms in each cluster do not have capping Se atoms from neighboring clusters. This represents a new triclinic structure type for Chevrel phases. In addition to the synthesis and crystal structure, we present and discuss results from electronic structure calculations using both extended Hückel and density functional theory. These calculations predict Cu4Mo6Se8 to be metallic. We also report results from Cu intercalation into Chevrel phase sulfides and tellurides. Preliminary experiments suggest that a telluride analogue of Cu4Mo6Se8 exists.

Journal Article↗
PubMed1996

The crystal structure of horse deoxyhaemoglobin trapped in the high-affinity (R) state.

Co-operative oxygen binding by the vertebrate haemoglobins arises from an equilibrium between a quaternary structure with low affinity (T), favoured in the absence of ligand, and a high affinity form (R) adopted by the fully ligated protein. While R state haemoglobin has an oxygen affinity close to that of isolated subunits, the affinity of the T state is roughly 300-fold lower. The mechanism by which the T state restrains ligand binding, and the pathway of the quaternary transition, have been largely revealed by detailed crystallographic analyses of a number of haemoglobin molecules in the equilibrium states, as well as intermediate forms of the T state including partially ligated species. The ligation intermediates of the R state, however, have not been as well characterized structurally. We report here the crystal structure of one such intermediate species, namely, horse deoxyhaemoglobin in the R state, at 1.8 A resolution. While ligand binding in the T state may result in unfavourable stereochemistry in and around the haem-ligand complex, the more plastic R structure appears to accommodate equally well both liganded and ligand-free haem. Loss of ligand at the R state haem results in movements of the haem and shifts of the FG corners, which form characteristic intersubunit contacts that distinguish the quaternary states. The shifts are comparable in magnitude to the corresponding movements associated with de-ligation in the T state, although they differ in direction. These and other differences illustrate how the structural changes in the haem pocket are communicated to the subunit interfaces and how the movements that can occur in the R state may be impeded in the T state.

Animals↗
PubMed1989

Molecular mechanics and X-ray crystal structure investigations on conformations of 11 beta substituted 4,9-dien-3-one steroids.

The influence of 11 beta-phenyl substitution upon 4,9-dien-3-one steroid-backbone conformations is calculated by means of the MM2p molecular mechanics scheme. In the case of steroids having a 13 beta configuration, the lowest strain energy is always evaluated for the conformational combination of rings A(inverted) B(normal) while, moreover, the 11 beta substitution increases the relative stability of the conformation A(normal) B(normal) compared to the nonsubstituted compound. Introduction of the 11 beta substituent causes some bowing of the energy-minimum structures in the A-ring region toward the beta side. For 13 alpha configurated steroids, the ring conformations A(inverted) B(normal) C(boat) and A(normal) B(inverted) C(twist/boat) are found to be energetically preferred. Quantitative description of different ring conformations using asymmetry and pseudorotational parameters as well as the comparison of molecular mechanics and available X-ray structure data give an impression of the conformational mobility. Whereas the effect of 11 beta substitution within a given ring conformation is limited, contributions to molecular flexibility can be found in the ability to adopt different basic conformations and in the occupation of near-minimum structures. An X-ray crystal structure analysis of a potential antiprogestational steroid has been performed, and the results are in good agreement with the calculated structure.

Crystallography↗
PubMed2006

The crystal structure of ORF-9b, a lipid binding protein from the SARS coronavirus.

To achieve the greatest output from their limited genomes, viruses frequently make use of alternative open reading frames, in which translation is initiated from a start codon within an existing gene and, being out of frame, gives rise to a distinct protein product. These alternative protein products are, as yet, poorly characterized structurally. Here we report the crystal structure of ORF-9b, an alternative open reading frame within the nucleocapsid (N) gene from the SARS coronavirus. The protein has a novel fold, a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules. This cavity is likely to be involved in membrane attachment and, in mammalian cells, ORF-9b associates with intracellular vesicles, consistent with a role in the assembly of the virion. Analysis of ORF-9b and other overlapping genes suggests that they provide snapshots of the early evolution of novel protein folds.

Amino Acid Sequence↗
PubMed2003

Crystal structure and site-directed mutagenesis of enzymatic components from Clostridium perfringens iota-toxin.

Iota-toxin from Clostridium perfringens type E is an ADP-ribosylating toxin (ADPRT) that ADP-ribosylates actin, which is lethal and dermonecrotic in mammals. It is a binary toxin composed of an enzymatic component (Ia) and a binding component (Ib). Ia ADP-ribosylates G-actin at arginine 177, resulting in the depolymerization of the actin cytoskeleton. Here, we report on studies of the structure-function relationship by the crystal structures of Ia complexed with NADH and NADPH (at 1.8 A and 2.1 A resolution, respectively) and mutagenesis that map the active residues. The catalytic C-domain structure was similar to that of Bacillus cereus vegetative insecticidal protein (VIP2), which is an insect-targeted toxin, except for the EXE loop region. However, a significant structural difference could be seen in the N-domain, which interacts with Ib, suggesting an evolutionary difference between mammalian-targeted and insect-targeted ADPRT. The high resolution structure analysis revealed specific NAD conformation (a ring-like conformation of nicotinamide mononucleotide (NMN)) supported by Arg295, Arg296, Asn335, Arg352 and Glu380. Additionally, the mutagenesis study showed that the residues Tyr251, Arg295, Glu301, Ser338, Phe349, Arg352 and Glu380, including a newly identified one, are essential for NAD(+)-glycohydrolase (NADase) activity. At least one residue, Glu378, is an essential residue for ADP-ribosyltransferase (ARTase), but not for NADase. Consequently, the structural feature and these mutagenesis findings suggest that the catalytic mechanism of Ia proceeds via an Sn1-type reaction.

ADP Ribose Transferases↗
PubMed2003

Crystal structure of the collagen alpha1(VIII) NC1 trimer.

Collagen VIII is a major component of Descemet's membrane and is also found in vascular subendothelial matrices. The C-terminal non-collagenous domain (NC1) domain of collagen VIII, which is a member of the C1q-like protein family, forms a stable trimer and is thought to direct the assembly of the collagen triple helix, as well as polygonal supramolecular structures. We have solved the crystal structure of the mouse alpha1(VIII)(3) NC1 domain trimer at 1.9 A resolution. Each subunit of the intimate NC1 trimer consists of a ten-stranded beta-sandwich. The surface of the collagen VIII NC1 trimer presents three strips of partially exposed aromatic residues shown to interact with the non-ionic detergent CHAPS, which are likely to be involved in supramolecular assemblies. Equivalent strips exist in the NC1 domain of the closely related collagen X, suggesting a conserved assembly mechanism. Surprisingly, the collagen VIII NC1 trimer lacks the buried calcium cluster of the collagen X NC1 trimer. The mouse alpha1(VIII) and alpha2(VIII) NC1 domains are 71.5% identical in sequence, with the differences being concentrated on the NC1 trimer surface. A few non-conservative substitutions map to the subunit interfaces near the surface, but it is not obvious from the structure to what extent they determine the preferred assembly of collagen VIII alpha1 and alpha2 chains into homotrimers.

Amino Acid Sequence↗
PubMed2003

Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum.

A novel, 68 amino acid long flavoprotein called dodecin has been discovered in the proteome of Halobacterium salinarum by inverse structural genomics. The 1.7 A crystal structure of this protein shows a dodecameric, hollow sphere-like arrangement of the protein subunits. Unlike other known flavoproteins, which bind only monomeric flavin cofactors, the structure of the dodecin oligomer comprises six riboflavin dimers. The dimerization of these riboflavins along the re-faces is mediated by aromatic, antiparallel pi staggering of their isoalloxazine moieties. A unique aromatic tetrade is formed by further sandwiching of the riboflavin dimers between the indole groups of two symmetry-related Trp36s. So far, the dodecins represent the smallest known flavoproteins. Based on the structure and the wide spread occurrences in pathogenic and soil eubacteria, a function in flavin storage or protection against radical or oxygenic stress is suggested for the dodecins.

Amino Acid Sequence↗
PubMed1996

A pancreatic lipase with a phospholipase A1 activity: crystal structure of a chimeric pancreatic lipase-related protein 2 from guinea pig.

BACKGROUND: The guinea pig pancreatic lipase-related protein 2 (GPLRP2) differs from classical pancreatic lipases in that it displays both lipase and phospholipase A1 activities; classical pancreatic lipases have no phospholipase activity. The sequence of GPLRP2 is 63 % identical to that of human pancreatic lipase (HPL), but the so-called lid domain, is much reduced in GPLRP2. A phospholipase A1 from hornet venom (Dolml PLA1) is very similar to HPL and GPLRP2 but is devoid of lipase activity; Dolml PLA1 also contains a reduced lid domain and lacks a region termed the beta9 loop, which is located in the vicinity of the HPL and GPLRP2 active sites. The structure determination of a chimera of GPLRP2 and HPL and domain building of Dolml PLA1 were undertaken to gain a better understanding of the structural parameters responsible for the differences in lipase versus phospholipase activity among these structurally related enzymes. RESULTS: The crystal structure of a chimeric mutant of GPLRP2, consisting of the catalytic domain of GPLRP2 and the C-terminal domain of HPL, has been solved and refined to 2.1 A resolution. This enzyme belongs to the alpha/beta hydrolase fold family and shows high structural homology with classical pancreatic lipases. The active site is closely related to those of serine esterases, except for an unusual geometry of the catalytic triad. Due to the reduced size of the lid domain, the catalytic serine is fully accessible to solvent. Part of the beta9 loop, which stabilizes the lid domain in the closed conformation of the classical HPL, is totally exposed to the solvent and is not visible in the electron-density map. CONCLUSIONS: The structures of the related enzymes, GPLRP2 and HPL and the model of Dolml PLA1, provide insights into the role played by the loops located above the active site in controlling substrate selectivity towards triglycerides or phospholipids. In GPLRP2, the lid domain is reduced in size compared to HPL, and hydrophilic residues are exposed to solvent. GPLRP2 is thus able to accommodate the polar head of phospholipids. The beta9 loop is still present in GPLRP2, making it possible for this enzyme to still accommodate triglycerides. In Dolml PLA1, the beta9 loop is absent, and this enzyme is unable to process triglycerides retaining only the phospholipase A1 activity.

Amino Acid Sequence↗
PubMedDate not supplied

The crystal structure of d(GGATGGGAG): an essential part of the binding site for transcription factor IIIA.

Most genes in higher organisms are activated by the binding of proteins called transcription factors. One such protein, transcription factor IIIA (TFIIIA) from the frog, activates the gene for 5S RNA by binding to the region of the gene between nucleotides 45 and 97. This binding site has been defined by a variety of biochemical studies, including base-deletion experiments and DNase I footprinting. The protein also binds to the gene product: in immature frogs it is stored as a complex with 5S RNA. From the observation that TFIIIA can bind to either double-helical DNA or RNA, and from their own measurements, Rhodes and Klug have proposed that the DNA-binding site for TFIIIA has an RNA-like structure. Here we present the crystal structure analysis of a part of the DNA-binding site (nucleotides 81-89 of the gene) which forms a particularly strong interaction with the protein, and show that it has a conformation similar to the A' form of double-helical RNA.

Base Sequence↗
PubMed2002

HLA-E allelic variants. Correlating differential expression, peptide affinities, crystal structures, and thermal stabilities.

Previous studies of HLA-E allelic polymorphism have indicated that balancing selection may be acting to maintain two major alleles in most populations, indicating that a functional difference may exist between the alleles. The alleles differ at only one amino acid position, where an arginine at position 107 in HLA-E*0101 (E(R)) is replaced by a glycine in HLA-E*0103 (E(G)). To investigate possible functional differences, we have undertaken a study of the physical and biochemical properties of these two proteins. By comparing expression levels, we found that whereas steady-state protein levels were similar, the two alleles did in fact differ with respect to cell surface levels. To help explain this difference, we undertook studies of the relative differences in peptide affinity, complex stability, and three-dimensional structure between the alleles. The crystal structures for HLA-E(G) complexed with two distinct peptides were determined, and both were compared with the HLA-E(R) structure. No significant differences in the structure of HLA-E were induced as a result of binding different peptides or by the allelic substitution at position 107. However, there were clear differences in the relative affinity for peptide of each heavy chain, which correlated with and may be explained by differences between their thermal stabilities. These differences were completely consistent with the relative levels of the HLA-E alleles on the cell surface and may indeed correlate with functional differences. This in turn may help explain the apparent balancing selection acting on this locus.

Alleles↗
PubMed1999

Crystal structure of a 14 bp RNA duplex with non-symmetrical tandem GxU wobble base pairs.

Adjacent GxU wobble base pairs are frequently found in rRNA. Atomic structures of small RNA motifs help to provide a better understanding of the effects of various tandem mismatches on duplex structure and stability, thereby providing better rules for RNA structure prediction and validation. The crystal structure of an RNA duplex containing the sequence r(GGUAUUGC-GGUACC)2 has been solved at 2.1 A resolution using experimental phases. Novel refinement strategies were needed for building the correct solvent model. At present, this is the only short RNA duplex structure containing 5'-U-U-3'/3'-G-G-5' non-symmetric tandem GxU wobble base pairs. In the 14mer duplex, the six central base pairs are all displaced away from the helix axis, yielding significant changes in local backbone conformation, helix parameters and charge distribution that may provide specific recognition sites for biologically relevant ligand binding. The greatest deviations from A-form helix occur where the guanine of a wobble base pair stacks over a purine from the opposite strand. In this vicinity, the intra-strand phosphate distances increase significantly, and the major groove width increases up to 3 A. Structural comparisons with other short duplexes containing symmetrical tandem GxU or GxT wobble base pairs show that nearest-neighbor sequence dependencies govern helical twist and the occurrence of cross-strand purine stacks.

Base Pairing↗