The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

Berman, Helen M.; Olson, Wilma K.; Beveridge, D. L.; Westbrook, John D.; Gelbin, Anke; Demeny, T.; Hsieh, Shu Hsin; Srinivasan, A. R.; Schneider, Bohdan

doi:10.1016/s0006-3495(92)81649-1

Cited by 942 publications

(745 citation statements)

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“…The list of pdb files deposited in Nucleic Acid Database [33,34] that were used in this study as the source of structural parameters of dinucleotide steps. First two columns comprise B-DNA codes according to NDB and PDB identification styles.…”

Section: Table S1mentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Selected conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of 162 analyzed tetramers both threeand four-body contributions are negligible except of d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal/mol. This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of the total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.Response to Reviewers: 1) I recommend to do a careful proofreading, there are many typos and some sentences are difficult to understand. Thank you. Careful proofreading was applied and text was modified accordingly.2) Page 3, Results and discussion Alltogether 162 dinucleotide steps were analyzed. The number of individual steps is variable, why is it so? Why there was 48 d(GpG) steps, but only 10 d(GpC) steps? What were the PDB codes of structures from which steps were chosen, and which steps (chain ID, res ID) were chosen? What was the resolution of these structures? This information could go to the Supplementary material.In supplementary material details related to analyzed structures are provided now. The differences in dinucleotide populations have strictly technical reason. Since in my previous work accepted for publication in Int.J.Quantum Chem. (DOI:10.1002/qua.22435) detailed analysis of d(GpG) steps were presented I have just included these data in this work. Consequently this dinucleotide is overrepresented. Since it constitutes its own class I do not think that such overrepresentation changes papers conclusions. On the other hand it is not necessary extending the number of other dinucleotide steps since the non-additivity is quite small and they were selected from broad range of data according to IIE and structural parameters diversities.3) Page 3, Results and discussion The numbers of steps are large enough to perform some statistical analysis of resulting energies. E.g. ANOVA could be performed to test whether the mean energies in dinucleotide steps differ significantly each from other. Also, is the distribution of energies for individual steps Gaussian or not? If not, some non-parametric ...

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Section: Table S1mentioning

confidence: 99%

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Cysewski

2010

J Mol Model

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“…This process has helped us to refine and improve the software and has prompted us to add new functionality. As a result, 3DNA has found widespread use and the 3DNA homepage is linked from the websites of various bioinformatics databases and computer-graphics tools, such as the Nucleic Acid Database (NDB) 31 , the RNA World website at Jena 32 , and the Raster3D graphics toolset 33 .…”

Section: Introductionmentioning

confidence: 99%

“…While it is not practical to summarize the literature on all of the applications of the suite of programs, we draw attention here to several projects where 3DNA has played a particularly significant role: (1) the NDB 31 reports 3DNA base-pair and base-pair-step parameters for the double-helical fragments of each structure in the database; (2) both the NDB 31 and the PDB (Protein Data Bank) 34 report the simple and informative molecular images generated with the blocview component of 3DNA; (3) the nucleic-acid Solvation Web Service 35 (SwS) uses 3DNA to find base pairs, collect conformational patterns, and set the orientation of molecular images; (4) the DNA structural bioinformatics server 36 (MDDNA) uses the 3DNA rebuild routine to construct models of arbitrary DNA sequences based on predictions obtained from molecular-dynamics simulations; (5) the ARTS 37 (Alignment of RNA Tertiary Structures) software uses 3DNA to identify both canonical and non-canonical base pairs for its seed-match construction; (6) the information-driven protein-DNA docking method HADDOCK 38 uses 3DNA to build canonical B-DNA models, generate custom DNA libraries, calculate various base-pair and base-pair-step parameters, determine the torsion angles of the sugar-phosphate backbone, and evaluate the puckering of the sugar ring; (7) the base-pair server (BPS) from this laboratory uses find_pair and other utility programs from 3DNA to build a comprehensive database and to generate illustrative molecular images of the base pairs in RNA structures; (8) our recent identification of a roll-slide-induced DNA folding mechanism in chromatin 1 takes advantage of the rigorous matrix-based analysis and rebuilding functions of 3DNA, and (9) our generalization of the 3DNA code to treat the rigid-body parameters of planar molecular fragments 39 facilitates the classification of small, flexible drug molecules and identification of representative structures for three-dimensional quantitative structure-activity relationship analyses.…”

Section: Introductionmentioning

confidence: 99%

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

2008

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We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild, and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases, etc. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.

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“…Secondary structure of tRNA anticodon hairpins for which coordinates are deposited in the Nucleic Acid Database (NDB) (Berman et al+, 1992) Brown et al+, 1985;trna04: Sussman et al+, 1978;trna05: Comarmond et al+, 1986;trna06: Westhof & Sundaralingam, 1986;trna07, trna08, trna09: Westhof et al+, 1988;trna10: Hingerty et al+, 1978;pr0004: Nissen et al+, 1999;pr0024: Goldgur et al+, 1997;ptr012: Nissen et al+, 1995+ b In tRNAs, purines represent roughly a little more than 50% of the nucleotides present at position 35 (Auffinger & Westhof, 1998b) as expected from the genetic code and deduced from the 550 tRNAs and 3,704 tDNA gene sequences itemized in the tRNA database (Sprinzl et al+, 1998)+ From the nine available crystallographic structures of yeast tRNA Phe (including the structures extracted from the yeast tRNA Phe /EF-TU and the Thermus thermophilus tRNA Phe /RS complexes where the anticodon loop structure is not altered, ptr012 and pr0024, respectively, see Table 1), it has been inferred that the 29-hydroxyl group of U33 forms a hydrogen bond with the N7 atom of A35 (Fig+ 2)+ This assumes that the hydroxyl (U33)O29-H group points toward the (A35)N7…”

Section: Introductionmentioning

confidence: 99%

An extended structural signature for the tRNA anticodon loop

Auffinger

Westhof

2001

RNA

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Anticodon hairpins are structural motifs with contradictory functions. The recognition by aminoacyl synthetases implies extended interactions with the anticodon base triplet and thus, usually, an unfolding of the anticodon loop. The recognition by the ribosome and cognate interaction with a mRNA codon implies, on the other hand, the formation of a mini-helix with a canonical anticodon hairpin structure as observed by crystallography and NMR. To be able to understand the various properties of this motif, a precise description of its structural conservation is required. Here, on the basis of phylogenetic, structural, and molecular dynamics data, we discuss a conserved interaction established between the ribose of the U33 and the base at position 35, either a purine or a pyrimidine. This interaction involves the hydrogen bonding donor or acceptor potential of the hydroxyl group of U33 and has to be integrated in an extended definition of the anticodon hairpin. The extended structural signature provides also an explanation for the role played by pseudouridines at position 35.

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The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

Cited by 942 publications

References 16 publications

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

An extended structural signature for the tRNA anticodon loop

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