@Article{Dickerson1998, author = {Dickerson, R. E.}, journal = {Nucleic acids research}, title = {{DNA} bending: the prevalence of kinkiness and the virtues of normality.}, year = {1998}, pages = {1906--1926}, volume = {26}, abstract = {DNA bending in 86 complexes with sequence-specific proteins has been examined using normal vector plots, matrices of normal vector angles between all base pairs in the helix, and one-digit roll/slide/twist tables. FREEHELIX, a new program especially designed to analyze severely bent and kinked duplexes, generates the foregoing quantities plus local roll, tilt, twist, slide, shift and rise parameters that are completely free of any assumptions about an overall helix axis. In nearly every case, bending results from positive roll at pyrimidine-purine base pair steps: C-A (= T-G), T-A, or less frequently C-G, in a direction that compresses the major groove. Normal vector plots reveal three well-defined types of bending among the 86 examples: (i) localized kinks produced by positive roll at one or two discrete base pairs steps, (ii) three-dimensional writhe resulting from positive roll at a series of adjacent base pairs steps, or (iii) continuous curvature produced by alternations of positive and negative roll every 5 bp, with side-to-side zig-zag roll at intermediate position. In no case is tilt a significant component of the bending process. In sequences with two localized kinks, such as CAP and IHF, the dihedral angle formed by the three helix segments is a linear function of the number of base pair steps between kinks: dihedral angle = 36 degrees x kink separation. Twenty-eight of the 86 examples can be described as major bends, and significant elements in the recognition of a given base sequence by protein. But even the minor bends play a role in fine-tuning protein/DNA interactions. Sequence-dependent helix deformability is an important component of protein/DNA recognition, alongside the more generally recognized patterns of hydrogen bonding. The combination of FREEHELIX, normal vector plots, full vector angle matrices, and one-digit roll/slide/twist tables affords a rapid and convenient method for assessing bending in DNA.}, doi = {10.1093/nar/26.8.1906}, file = {:by-author/D/Dickerson/1998_Dickerson_1906.pdf:PDF}, keywords = {YR; bending; readout; Bacterial Proteins, chemistry, metabolism; Base Composition; Base Sequence; Binding Sites; Computer Simulation; DNA, chemistry, metabolism; DNA Restriction Enzymes, chemistry, metabolism; DNA-Binding Proteins, chemistry, metabolism; Homeodomain Proteins, chemistry, metabolism; Humans; Integration Host Factors; Models, Molecular; Nucleic Acid Conformation; Protein Structure, Secondary; RNA Cap-Binding Proteins; RNA-Binding Proteins, chemistry, metabolism; Repressor Proteins, chemistry, metabolism; Software; TATA Box; TATA-Box Binding Protein; Transcription Factors, chemistry, metabolism; Viral Proteins; Viral Regulatory and Accessory Proteins; FREEHELIX}, owner = {em}, timestamp = {2012.11.09}, } @Article{Dickerson1983a, author = {Dickerson, R. E.}, journal = {Journal of molecular biology}, title = {Base sequence and helix structure variation in B and A DNA.}, year = {1983}, pages = {419--41}, volume = {166}, abstract = {The observed propeller twist in base-pairs of crystalline double-helical DNA oligomers improves the stacking overlap along each individual helix strand. But, as proposed by Calladine, it also leads to clash or steric hindrance between purines at adjacent base-pairs on opposite strands of the helix. This clash can be relieved by: (1) decreasing the local helix twist angle between base-pairs; (2) opening up the roll angle between base-pairs on the side on which the clash occurs; (3) separating purines by sliding base-pairs along their long axes so that the purines are partially pulled out of the stack (leading to equal but opposite alterations in main-chain torsion angle delta at the two ends of the base-pair); and (4) flattening the propeller twist of the offending base-pairs. Simple sum functions, sigma 1 through sigma 4, are defined, by which the expected local variation in helix twist, base roll angle, torsion angle delta and propeller twist may be calculated from base sequence. All four functions are quite successful in predicting the behavior of B DNA. Only the helix twist and base roll functions are applicable to A DNA, and the helix twist function begins to fail for an A helical RNA/DNA hybrid. Within these limits, the sequence-derived sum functions match the observed helix parameter variation quite closely, with correlation coefficients greater than 0.900 in nearly all cases. Implications of this sequence-derived helix parameter variation for repressor-operator interactions are considered.}, file = {:by-author/D/Dickerson/1983_Dickerson_419.pdf:PDF}, keywords = {Calladine rules, readout}, owner = {em}, timestamp = {2012.11.09}, } @Article{Fratini1982, author = {Fratini, A. V. and Kopka, M. L. and Drew, H. R. and Dickerson, R. E.}, journal = {The Journal of biological chemistry}, title = {Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.}, year = {1982}, pages = {14686--707}, volume = {257}, abstract = {A double-helical B-DNA dodecamer has been analyzed by single crystal x-ray diffraction methods and refined independently in four variants: sequence CGCGAATTCGCG at 20 degrees C and at 16 K, and CGCGAATTBrCGCG in 60\% methylpentanediol at 20 and at 7 degrees C. The first three forms show a 14-19 degrees bend in overall helix axis, but the fourth is straight and unbent. Detailed comparisons of the various forms have led to a better understanding of helix geometry and bending. Structural principles can be understood best if organized under four headings: 1) intrinsic geometry of the sugar rings, 2) stacking and relative motion of base pairs, 3) geometry of the connecting phosphate backbone, and 4) mechanics of bending in B-DNA. The observed bending is neither completely localized nor smooth and continuous, but an intermediate compromise that can be termed "annealed kinking."}, file = {1982_Fratini_14686.pdf:by-author/F/Fratini/1982_Fratini_14686.pdf:PDF;3bdn.pdb:by-author/F/Fratini/1982_Fratini_14686/3bdn.pdb:PDB;4bna.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna.pdb:PDB;4bna-sym.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna-sym.pdb:PDB;4bna-sphere.pdb:by-author/F/Fratini/1982_Fratini_14686/4bna-sphere.pdb:PDB}, keywords = {RY, readout, stacking, DNA structure}, owner = {em}, timestamp = {2012.10.21}, } @Article{Goodsell1994, author = {Goodsell, D. S. and Dickerson, R. E.}, journal = {Nucleic acids research}, title = {Bending and curvature calculations in B-DNA.}, year = {1994}, pages = {5497--503}, volume = {22}, abstract = {A simple program, BEND, has been written to calculate the magnitude of local bending and macroscopic curvature at each point along an arbitrary B-DNA sequence, using any desired bending model that specifies values of twist, roll and tilt as a function of sequence. The program has been used to evaluate six different DNA bending models in three categories. Two are bent non-A-tract models: (a) A new model based on the nucleosome positioning data of Satchwell et al 1986 (J. Mol. Biol. 191, 659-675), (b) The model of Calladine et al 1988 (J. Mol. Biol. 201, 127-137). Three are bent A-tract models: (c) The wedge model of Bolshoy et al 1991 (Proc. Natl. Acad. Sci. USA 88, 2312-2316), (d) The model of Cacchione et al 1989 (Biochem. 28, 8706-8713), (e) A reversed version of model (b). The last is a junction model: (f) The model of Koo & Crothers 1988 (Proc. Natl. Acad. Sci. USA 85, 1763-1767). Although they have widely different assumptions and values for twist, roll and tilt, all six models correctly predict experimental A-tract curvature as measured by gel retardation and cyclization kinetics, but only the new nucleosome positioning model is successful in predicting curvature in regions containing phased GGGCCC sequences. This model--showing local bending at mixed sequence DNA, strong bends at the sequence GGC, and straight, rigid A-tracts--is the only model consistent with both solution data from gel retardation and cyclization kinetics and structural data from x-ray crystallography.}, file = {:by-author/G/Goodsell/1994_Goodsell_5497.pdf:PDF}, keywords = {readout}, owner = {em}, timestamp = {2012.11.09}, } @Article{Lu2003, author = {Lu, Xiang-Jun and Olson, Wilma K.}, journal = {Nucleic acids research}, title = {3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.}, year = {2003}, pages = {5108--21}, volume = {31}, abstract = {We present a comprehensive software package, 3DNA, for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. Starting from a coordinate file in Protein Data Bank (PDB) format, 3DNA can handle antiparallel and parallel double helices, single-stranded structures, triplexes, quadruplexes and other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify and categorize all base interactions and classify the double helical character of appropriate base pair steps. The program makes use of a recently recommended reference frame for the description of nucleic acid base pair geometry and a rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these parameters. The rebuilding routines produce rectangular block representations of nucleic acids as well as full atomic models with the sugar-phosphate backbone and publication quality 'standardized' base stacking diagrams. Utilities are provided to locate the base pairs and helical regions in a structure and to reorient structures for effective visualization. Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program.}, comment = {Citation 19 has incorrect volume, should be vol. 205 instead of 208 (see entry Diekmann1989).}, doi = {10.1093/nar/gkg680}, file = {:by-author/L/Lu/2003_Lu_5108.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry; Base Pairing; DNA; chemistry; Hydrogen Bonding; Models; Molecular; Nucleic Acid Conformation; Software}, owner = {saulius}, timestamp = {2008.07.28}, } @Article{Olson2001, author = {Olson, W. K. and Bansal, M. and Burley, S. K. and Dickerson, R. E. and Gerstein, M. and Harvey, S. C. and Heinemann, U. and Lu, X. J. and Neidle, S. and Shakked, Z. and Sklenar, H. and Suzuki, M. and Tung, C. S. and Westhof, E. and Wolberger, C. and Berman, H. M.}, journal = {Journal of molecular biology}, title = {A standard reference frame for the description of nucleic acid base-pair geometry.}, year = {2001}, pages = {229--237}, volume = {313}, doi = {10.1006/jmbi.2001.4987}, file = {:by-author/O/Olson/2001_Olson_229.pdf:PDF}, keywords = {readout, review; biochemistry; structural biology; nucleic acids; DNA geometry; RNA geometry}, owner = {em}, timestamp = {2012.11.09}, } @Article{Olson1998, author = {Olson, W. K. and Gorin, A. A. and Lu, X. J. and Hock, L. M. and Zhurkin, V. B.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, title = {{DNA} sequence-dependent deformability deduced from protein-{DNA} crystal complexes.}, year = {1998}, pages = {11163--11168}, volume = {95}, abstract = {The deformability of double helical DNA is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in DNA-protein crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the DNA-protein complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe DNA deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of DNA in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long DNA polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.}, doi = {10.1073/pnas.95.19.11163}, file = {1998_Olson_11163.pdf:by-author/O/Olson/1998_Olson_11163.pdf:PDF}, keywords = {readout; stacking; DNA, chemistry, Dimerization, Models, Molecular, Nucleic Acid Conformation, Protein Binding; Proteins, chemistry; Purines, chemistry; Pyrimidines}, owner = {em}, timestamp = {2008.07.28}, } @Article{Prive1987, author = {Privé, G. G. and Heinemann, U. and Chandrasegaran, S. and Kan, L. S. and Kopka, M. L. and Dickerson, R. E.}, journal = {Science (New York, N.Y.)}, title = {Helix geometry, hydration, and G.A mismatch in a B-DNA decamer.}, year = {1987}, pages = {498--504}, volume = {238}, abstract = {The DNA double helix is not a regular, featureless barberpole molecule. Different base sequences have their own special signature, in the way that they influence groove width, helical twist, bending, and mechanical rigidity or resistance to bending. These special features probably help other molecules such as repressors to read and recognize one base sequence in preference to another. Single crystal x-ray structure analysis is beginning to show us the various structures possible in the B-DNA family. The DNA decamer C-C-A-A-G-A-T-T-G-G appears to be a better model for mixed-sequence B-DNA than was the earlier C-G-C-G-A-A-T-T-C-G-C-G, which is more akin to regions of poly(dA).poly(dT). The G.A mismatch base pairs at the center of the decamer are in the anti-anti conformation about their bonds from base to sugar, in agreement with nuclear magnetic resonance evidence on this and other sequences, and in contrast to the anti-syn geometry reported for G.A pairs in C-G-C-G-A-A-T-T-A-G-C-G. The ordered spine of hydration seen earlier in the narrow-grooved dodecamer has its counterpart, in this wide-grooved decamer, in two strings of water molecules lining the walls of the minor groove, bridging from purine N3 or pyrimidine O2, to the following sugar O4'. The same strings of hydration are present in the phosphorothioate analog of G-C-G-C-G-C. Unlike the spine, which is broken up by the intrusion of amine groups at guanines, these water strings are found in general, mixed-sequence DNA because they can pass by unimpeded to either side of a guanine N2 amine. The spine and strings are perceived as two extremes of a general pattern of hydration of the minor groove, which probably is the dominant factor in making B-DNA the preferred form at high hydration.}, file = {:by-author/P/Privé/1987_Prive_498.pdf:PDF}, keywords = {conformation, readout}, owner = {em}, timestamp = {2012.11.09}, } @Article{Subirana1997, author = {Subirana, J. A. and Faria, T.}, journal = {Biophysical journal}, title = {Influence of sequence on the conformation of the B-DNA helix.}, year = {1997}, pages = {333--8}, volume = {73}, abstract = {We have tried to ascertain whether the variability found in the conformational features of the 10 base steps in B-DNA is mainly due to the flanking sequences or to interactions with the environment. From an analysis of the twist parameter of the base-pair steps available from crystals of oligonucleotides and protein/oligonucleotide complexes, we conclude that in most cases the flanking sequences show little influence: the conformation of a DNA region results from the combination of the independent intrinsic features of each base step (average conformation and intrinsic variability), modulated by their interactions with the environment. Only in some cases (YR steps, in particular CG and CA/TG) does it appear that flanking sequences have an influence on the conformation of the central base step. The values obtained allow an approximation to the parameters expected for repetitive DNA sequences. In particular, it is found that poly[d(AG/CT)] should have a strongly alternating conformation, in agreement with recently reported oligonucleotide structures.}, file = {:by-author/S/Subirana/1997_Subirana_333.pdf:PDF}, keywords = {RY, readout}, owner = {em}, timestamp = {2012.11.09}, } @Article{Wynveen2008, author = {Wynveen, Aaron and Lee, Dominic J and Kornyshev, Alexei A and Leikin, Sergey}, journal = {Nucleic acids research}, title = {Helical coherence of DNA in crystals and solution.}, year = {2008}, pages = {5540--51}, volume = {36}, abstract = {The twist, rise, slide, shift, tilt and roll between adjoining base pairs in DNA depend on the identity of the bases. The resulting dependence of the double helix conformation on the nucleotide sequence is important for DNA recognition by proteins, packaging and maintenance of genetic material, and other interactions involving DNA. This dependence, however, is obscured by poorly understood variations in the stacking geometry of the same adjoining base pairs within different sequence contexts. In this article, we approach the problem of sequence-dependent DNA conformation by statistical analysis of X-ray and NMR structures of DNA oligomers. We evaluate the corresponding helical coherence length--a cumulative parameter quantifying sequence-dependent deviations from the ideal double helix geometry. We find, e.g. that the solution structure of synthetic oligomers is characterized by 100-200 A coherence length, which is similar to approximately 150 A coherence length of natural, salmon-sperm DNA. Packing of oligomers in crystals dramatically alters their helical coherence. The coherence length increases to 800-1200 A, consistent with its theoretically predicted role in interactions between DNA at close separations.}, file = {2008_Wynveen_5540.pdf:by-author/W/Wynveen/2008_Wynveen_5540.pdf:PDF}, keywords = {stacking}, owner = {saulius}, timestamp = {2008.07.28}, } @Article{Dickerson1989, author = {Richard E. Dickerson}, journal = {Journal of Biomolecular Structure and Dynamics}, title = {Definitions and nomenclature of nucleic acid structure parameters}, year = {1989}, month = {feb}, number = {4}, pages = {627--634}, volume = {6}, comment = {The same information was repeatedly published in EMBO J. and JMB?}, doi = {10.1080/07391102.1989.10507726}, file = {:by-author/D/Dickerson/1989_Dickerson_627.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry}, owner = {saulius}, publisher = {Informa {UK} Limited}, timestamp = {2022.04.16}, } @Article{Gabb1996, author = {H.A. Gabb and S.R. Sanghani and C.H. Robert and C. Pr{\'{e}}vost}, journal = {Journal of Molecular Graphics}, title = {Finding and visualizing nucleic acid base stacking}, year = {1996}, month = {feb}, number = {1}, pages = {6--11}, volume = {14}, doi = {10.1016/0263-7855(95)00086-0}, file = {:by-author/G/Gabb/1996_Gabb_6.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry}, owner = {saulius}, publisher = {Elsevier {BV}}, timestamp = {2022.04.16}, } @Article{McLachlan1979, author = {A.D. McLachlan}, journal = {Journal of Molecular Biology}, title = {Gene duplications in the structural evolution of chymotrypsin}, year = {1979}, month = {feb}, number = {1}, pages = {49--79}, volume = {128}, comment = {Cited by 1989_Lavrey_655.}, doi = {10.1016/0022-2836(79)90308-5}, file = {:by-author/M/McLachlan/1979_McLachlan_49.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry; base planes}, owner = {saulius}, publisher = {Elsevier {BV}}, timestamp = {2022.04.16}, } @Article{1989a, journal = {The {EMBO} Journal}, title = {Definitions and nomenclature of nucleic acid structure parameters.}, year = {1989}, month = {jan}, number = {1}, pages = {1--4}, volume = {8}, comment = {Same information as in Dickerson1989 ???}, doi = {10.1002/j.1460-2075.1989.tb03339.x}, file = {:by-author/u/unknown/1989__1.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry}, owner = {saulius}, publisher = {Wiley}, timestamp = {2022.04.16}, url = {https://www.embopress.org/doi/pdf/10.1002/j.1460-2075.1989.tb03339.x}, } @Article{Diekmann1989, author = {Stephan Diekmann}, journal = {Journal of Molecular Biology}, title = {Definitions and nomenclature of nucleic acid structure parameters}, year = {1989}, month = {feb}, number = {4}, pages = {787--791}, volume = {205}, comment = {Same information as in Dickerson1989 ???}, doi = {10.1016/0022-2836(89)90324-0}, file = {:by-author/D/Diekmann/1989_Diekmann_787.pdf:PDF}, keywords = {nucleic acids; biochemistry; roll; twist; definitions; structural biology; nucleic acids; DNA geometry; RNA geometry}, owner = {saulius}, publisher = {Elsevier {BV}}, timestamp = {2022.04.17}, } @Article{Lu1997, author = {Lu, X. J. and El Hassan, M. A. and Hunter, C. A.}, journal = {Journal of molecular biology}, title = {Structure and conformation of helical nucleic acids: analysis program ({SCHNAaP}).}, year = {1997}, issn = {0022-2836}, month = oct, pages = {668--680}, volume = {273}, abstract = {We present a new versatile program, SCHNAaP, for the analysis of double-helical nucleic acid structures. The program uses mathematically rigorous and fully reversible procedures for calculating the structural parameters: the Cambridge University Engineering Department Helix computation Scheme (CEHS) is used to determine the local helical parameters and an analogous procedure is used to determine the global helical parameters. These parameters form a complete set that conforms to the "Cambridge Accord" on definitions and nomenclature of nucleic acid structure parameters. In addition to the two standard Watson-Crick base-pairs, the program handles mismatched base-pairs and chemically modified bases. An analysis of the sugar-phosphate backbone conformation is included. Standardized base-stacking diagrams of each dinucleotide step with reference to the mid-step triad are generated. Structures are classified as one of the four polymorphic families, A/B, Z, W or R, although W- and R-DNA (two types of hypothetical structure) have yet to be observed experimentally.}, chemicals = {DNA}, citation-subset = {IM}, comment = {Cited by Lu2003 (2003_Lu_5108.pdf, "3DNA ...").}, completed = {1998-01-20}, country = {England}, doi = {10.1006/jmbi.1997.1346}, file = {:by-author/L/Lu/1997_Lu_668.pdf:PDF}, issn-linking = {0022-2836}, issue = {3}, keywords = {Base Composition; DNA, chemistry, classification; Mathematical Computing; Molecular Structure; Nucleic Acid Conformation; Software}, nlm-id = {2985088R}, owner = {saulius}, pii = {S0022-2836(97)91346-2}, pmid = {9356255}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2006-11-15}, timestamp = {2022.04.17}, } @Article{Hassan1995, author = {el Hassan, M. A. and Calladine, C. R.}, journal = {Journal of molecular biology}, title = {The assessment of the geometry of dinucleotide steps in double-helical {DNA}; a new local calculation scheme.}, year = {1995}, issn = {0022-2836}, month = sep, pages = {648--664}, volume = {251}, abstract = {In this paper, we develop a new local Euler-angle-based scheme for assessing the internal kinematics or geometry of a general dinucleotide step in double-helical DNA. The geometry of a dinucleotide step is completely defined by: (1) the base-pair parameters that describe the relative position and orientation of one base with respect to the other in a standard Watson-Crick base-pair, and (2) the step parameters that describe the relative position and orientation of the two base-pairs. The key feature of our scheme is that it makes use of the concept of a mid-step reference frame. In addition to ensuring that identical values of step parameters are obtained irrespective of the direction of reckoning of a dinucleotide step (in the 5'-->3' direction along either strand), this mid-step-triad concept leads to local definitions of the step parameters that render them independent of the overall global conformation of the oligomer in question. In addition to presenting our own calculation scheme we also examine critically the most widely used package for the calculation of some of the step and base-pair parameters, viz, the NEWHELIX suite of programmes by R.E. Dickerson. Finally, a dodecamer, a decamer and an octamer are arbitrarily selected from a public data-base (N.D.B at Rutgers), and their step parameters are calculated by using both NEWHELIX and the proposed scheme. A comparison of the results is given whereby it is shown that for the step parameters: Helical Twist and Slide, and the base-pair parameters Propeller and Buckle, NEWHELIX and our proposed scheme give rather similar values. Substantial differences are seen, however, in the case of Rise. Two alternative definitions are given by NEWHELIX for the calculation of Roll and Tilt. Whereas one definition agrees well with our proposed scheme, the other is substantially different.}, chemicals = {Oligodeoxyribonucleotides, DNA}, citation-subset = {IM}, comment = {Cited by Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1995-10-06}, country = {England}, doi = {10.1006/jmbi.1995.0462}, file = {:by-author/H/Hassan/1995_Hassan_648.pdf:PDF}, issn-linking = {0022-2836}, issue = {5}, keywords = {Base Composition; Base Sequence; DNA, chemistry; Mathematics; Molecular Sequence Data; Nucleic Acid Conformation; Oligodeoxyribonucleotides, chemistry; Software}, nlm-id = {2985088R}, owner = {saulius}, pii = {S0022-2836(85)70462-7}, pmid = {7666417}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2006-11-15}, timestamp = {2022.04.17}, } @Article{Drew1981, author = {Drew, H. R. and Wing, R. M. and Takano, T. and Broka, C. and Tanaka, S. and Itakura, K. and Dickerson, R. E.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, title = {Structure of a B-DNA dodecamer: conformation and dynamics.}, year = {1981}, issn = {0027-8424}, month = apr, pages = {2179--2183}, volume = {78}, abstract = {The crystal structure of the synthetic DNA dodecamer d(CpGpCpGpApApTpTpCpGpCpG) has been refined to a residual error of R = 17.8% at 1.9-A resolution (two-sigma data). The molecule forms slightly more than one complete turn of right-handed double-stranded B helix. The two ends of the helix overlap and interlock minor grooves with neighboring molecules up and down a 2(1) screw axis, producing a 19 degrees bend in helix axis over the 11-base-pair steps of the dodecamer. In the center of the molecule, where perturbation is least, the helix has a mean rotation of 36.9 degrees per step, or 9.8 base pairs per turn. The mean propeller twist (total dihedral angle between base planes) between A . T base pairs in the center of the molecule is 17.3 degrees, and that between C . G pairs on the two ends averages 11.5 degrees. Individual deoxyribose ring conformations as measured by the C5'-C4'-C3'-O3' torsion angle delta, exhibit an approximately Gaussian distribution centered around the C1'-exo position with delta avg = 123 degrees and a range of 79 degrees to 157 degrees. Purine sugars cluster at high delta values, and pyrimidine sugars cluster at lower delta. A tendency toward 2-fold symmetry in sugar conformation about the center of the molecule is detectable in spite of the destruction of ideal 2-fold symmetry by the molecular bending. More strikingly, sugar conformations of paired based appear to follow a "principle of anticorrelation," with delta values lying approximately the same distance to either side of the center value, delta = 123 degrees. This same anticorrelation is also observed in other DNA and DNA . RNA structures.}, chemicals = {Oligodeoxyribonucleotides, Oligonucleotides, Deoxyribose}, citation-subset = {IM}, completed = {1981-08-20}, country = {United States}, doi = {10.1073/pnas.78.4.2179}, file = {:by-author/D/Drew/1981_Drew_2179.pdf:PDF}, issn-linking = {0027-8424}, issue = {4}, keywords = {X-ray crystallography; Crystal structure; Deoxyribose; Models, Molecular; Motion; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Oligonucleotides}, nlm-id = {7505876}, owner = {saulius}, pmc = {PMC319307}, pmid = {6941276}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2019-05-01}, timestamp = {2022.04.17}, } @Article{Srinivasan1990, author = {Srinivasan, J. and Withka, J. M. and Beveridge, D. L.}, journal = {Biophysical journal}, title = {Molecular dynamics of an in vacuo model of duplex d({CGCGAATTCGCG}) in the {B}-form based on the amber 3.0 force field.}, year = {1990}, issn = {0006-3495}, month = aug, pages = {533--547}, volume = {58}, abstract = {The characteristics of 100 ps of molecular dynamics (MD) on the DNA dodecamer d(CGCGAATTCGCG) at 300 K are described and investigated. The simulation is based on an in vacuo model of the oligomer and the AMBER 3.0 force field configured in the manner of Singh, U. C., S. J. Weiner, and P. A. Kollman, (1985, Proc. Natl. Acad. Sci. USA. 82:755-759). The analysis of the results was carried out using the "curves, dials, and windows" procedure (Ravishanker, G., S. Swaminathan, D. L. Beveridge, R. Lavery, and H. Sklenar. 1989. J. Biomol. Struct. Dyn. 6:669-699). The results indicate this dynamical model to be a provisionally stable double helix which lies at approximately 3.2 A rms deviation from the canonical B-form. There is, however, a persistent nonplanarity in the base pair orientations which resemble that observed in canonical A-DNA. The major groove width is seen to narrow during the course of the simulation and the minor groove expands, contravariant to the alterations in groove width seen in the crystal structure of the native dodecamer (Drew, H. R., R. M. Wing, T. Takano, C. Broka, S. Tanaka, I. Itakura, and R. E. Dickerson, 1981. Proc. Natl. Acad. Sci. USA. 78:2179-2183). The propeller twist in the bases, the sequence dependence of the base pair roll and aspects of bending in the helix axis are in some degree of agreement with the crystal structure. The patterns in DNA bending are observed to follow Zhurkin theory (Zhurkin, V. B. 1985. J. Biomol. Struct. Dyn. 2:785-804.). The relationship between the dynamical model and structure in solution is discussed.}, chemicals = {Oligodeoxyribonucleotides, DNA}, citation-subset = {IM}, completed = {1990-10-31}, country = {United States}, doi = {10.1016/S0006-3495(90)82397-3}, file = {:by-author/S/Srinivasan/1990_Srinivasan_533.pdf:PDF}, issn-linking = {0006-3495}, issue = {2}, keywords = {Base Composition; Base Sequence; DNA; Hydrogen Bonding; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Oligodeoxyribonucleotides}, nlm-id = {0370626}, owner = {saulius}, pii = {S0006-3495(90)82397-3}, pmc = {PMC1280992}, pmid = {2207251}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2018-11-13}, timestamp = {2022.04.17}, } @Article{Babcock1994, author = {Babcock, M. S. and Olson, W. K.}, journal = {Journal of molecular biology}, title = {The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters.}, year = {1994}, issn = {0022-2836}, month = mar, pages = {98--124}, volume = {237}, abstract = {This paper critically examines the methodologies used to analyze nucleic acid three-dimensional structure based on guidelines set at a 1988 EMBO workshop. The implications of these analyses cannot be fully understood without a thorough knowledge of how the numbers are calculated. This paper addresses one aspect of the calculations, namely the observed correlations between various parameters. These correlations are addressed in the mathematics by explicitly incorporating the concept of a pivot point, which is the point about which a base rotates as it buckles, propeller twists and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters found in other approaches. The correlations that are reduced or eliminated are actually artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. The mathematics we have developed, including the mathematics of pivot points, are presented in the companion paper. Here, we explain how some of the observed correlations occur as a by-product of the method of calculation, while others are truly structural, and we show how optimum pivot points can be determined to minimize artifactual correlations. The observation that experimental bases often rotate about the long axis in a "propeller" motion as well as rotate about the Z-axis of each base, "opening" into the major groove, is evident in the location of the optimum region for the pivot point as determined in this study. We consider locating a pivot point as a calibration step to increase the agreement between physical intuition and the mathematics of our program.}, chemicals = {DNA}, citation-subset = {IM}, comment = {Critically cited by Hassan1995. Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1994-04-18}, country = {England}, doi = {10.1006/jmbi.1994.1212}, file = {:by-author/B/Babcock/1994_Babcock_98.pdf:PDF}, issn-linking = {0022-2836}, issue = {1}, keywords = {Base Sequence; DNA, chemistry; Mathematical Computing; Mathematics; Models, Chemical; Molecular Sequence Data; Nucleic Acid Conformation; Rotation; Software}, nlm-id = {2985088R}, owner = {saulius}, pii = {S0022-2836(84)71212-5}, pmid = {8133524}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2007-11-14}, timestamp = {2022.04.17}, } @Article{Babcock1994a, author = {Babcock, M. S. and Pednault, E. P. and Olson, W. K.}, journal = {Journal of molecular biology}, title = {Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.}, year = {1994}, issn = {0022-2836}, month = mar, pages = {125--156}, volume = {237}, abstract = {Analyzing nucleic acid structures in a comparable manner has become increasingly important as the number of solved structures has increased. This paper presents the concepts, mathematics, theorems, and proofs that form the basis of a new program to analyze three-dimensional DNA and RNA structures. The approach taken here provides numerical data in accordance with guidelines set at a 1988 EMBO workshop. Mathematical definitions are provided for all local structural parameters described in the guidelines. The definitions satisfy the guideline requirements while preserving the original physical intuition of the parameters. In particular, the rotational parameters are true rotations based on a simple physical model (net rotation at constant angular velocity), not Euler angles or angles between vectors and planes as is the case with other approaches. As a result, the mathematical definitions are symmetrical with the property that a 5 degrees tilt is the same as a 5 degrees roll and a 5 degrees twist, except that the rotations take place about different axes. In other approaches, a 5 degrees tilt can mean a different amount of net rotation than a 5 degrees roll or a 5 degrees twist. A second unique feature of the mathematics is that it explicitly incorporates the concept of a pivot point, which is the point about which a base in a base-pair rotates as it buckles, propeller twists, and opens. Pivot points enable one to model the physical motion of bases more accurately. As a result, they greatly reduce and/or eliminate the statistical correlations between rotational and translational parameters that arise as mathematically induced artifacts in other approaches. This paper, together with the statistical analysis in the companion paper for determining the locations of the pivot points, provides everything needed to understand the output of the program as it relates to individual structures.}, chemicals = {DNA}, citation-subset = {IM}, comment = {Critically cited by Hassan1995. Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1994-04-18}, country = {England}, doi = {10.1006/jmbi.1994.1213}, file = {:by-author/B/Babcock/1994_Babcock_125.pdf:PDF}, issn-linking = {0022-2836}, issue = {1}, keywords = {Base Composition; Base Sequence; DNA, chemistry; Mathematics; Models, Chemical; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Rotation}, nlm-id = {2985088R}, owner = {saulius}, pii = {S0022-2836(84)71213-7}, pmid = {8133513}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2007-11-14}, timestamp = {2022.04.17}, } @Article{Mazur1995, author = {Mazur, J. and Jernigan, R. L.}, journal = {Biophysical journal}, title = {Comparison of rotation models for describing DNA conformations: application to static and polymorphic forms.}, year = {1995}, issn = {0006-3495}, month = apr, pages = {1472--1489}, volume = {68}, abstract = {A new method, based on a space-fixed rotation axis, or local helix axis, is proposed for the calculation of the relative orientation variables for a sequence of base pairs. With this method, orientation variables are determined through the rotation of a base pair about this axis. These variables uniquely determine a set of helical variables, similar to the roll, tilt, and twist, commonly used for a description of spatial orientations of internally rigid base pairs. The proposed identification of roll and tilt with the direction cosines of the space-fixed rotation axis agrees well with their customary definitions as the openings of the angles between adjoining base pairs toward the minor groove and toward the ascending (5' to 3') backbone strand, respectively. These new variables permit a more direct physical comprehension of DNA conformations and also the behavior of self-complementary sequences. These direction cosines, together with the rotation angle about the space-fixed axis, form a set of three independent orientation variables of the bases that afford some advantages over the variously defined twist, roll, and tilt angles, either for static or average forms. An example for the static form of these variables is shown through their use to interpret crystal coordinates. An example for the average of orientation variables is based on statistical calculations. In this example, the orientation variables, together with the translational variables that describe the relative displacements of a pair of adjacent base pairs, form a canonically distributed ensemble in phase space spanned by these variables. Two sets of conformational variables are generated by using two different methods for performing rotation operations on the sequences of base pairs. The first method is based on the new single rotation about a space-fixed axis of rotation. This space-fixed axis of rotation is, in fact, the local helical axis as constructed previously by others. The second method is based on three consecutive rotations by Euler angles. Because of large flexibilities and anisotropies along various conformational variables of DNA base pairs, the two sets of generated conformational variables, based on these two different methods of performing rotation operations, lead to slightly different sets of structurally different, but energetically equivalent, spatial arrangements of the base pairs.}, chemicals = {DNA}, citation-subset = {IM}, comment = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1995-07-24}, country = {United States}, doi = {10.1016/S0006-3495(95)80320-6}, file = {:by-author/M/Mazur/1995_Mazur_1472.pdf:PDF}, issn-linking = {0006-3495}, issue = {4}, keywords = {Base Composition; Base Sequence; Biophysical Phenomena; Biophysics; DNA, chemistry; Mathematics; Models, Chemical; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Rotation; Thermodynamics}, nlm-id = {0370626}, owner = {saulius}, pii = {S0006-3495(95)80320-6}, pmc = {PMC1282042}, pmid = {7787033}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2018-11-13}, timestamp = {2022.04.17}, } @Article{Bansal1995, author = {Bansal, M. and Bhattacharyya, D. and Ravi, B.}, journal = {Computer applications in the biosciences : CABIOS}, title = {{NUPARM} and {NUCGEN}: software for analysis and generation of sequence dependent nucleic acid structures.}, year = {1995}, issn = {0266-7061}, month = jun, pages = {281--287}, volume = {11}, abstract = {Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation in each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA and RNA duplex structures.}, chemicals = {RNA, DNA}, citation-subset = {IM}, comment = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1995-12-15}, country = {England}, doi = {10.1093/bioinformatics/11.3.281}, file = {:by-author/B/Bansal/1995_Bansal_281.pdf:PDF}, issn-linking = {0266-7061}, issue = {3}, keywords = {Base Composition; Base Sequence; DNA, chemistry, genetics; Models, Molecular; Molecular Sequence Data; Molecular Structure; Nucleic Acid Conformation; RNA, chemistry, genetics; Software}, nlm-id = {8511758}, owner = {saulius}, pmid = {7583696}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2019-10-23}, timestamp = {2022.04.17}, } @Article{Jursa1994, author = {Jursa, J.}, journal = {Computer applications in the biosciences : CABIOS}, title = {DNA modeller: an interactive program for modelling stacks of DNA base pairs on a microcomputer.}, year = {1994}, issn = {0266-7061}, month = feb, pages = {61--65}, volume = {10}, abstract = {DNA Modeller is a microcomputer program for interactively manipulating up to 20 bp in a DNA double helical arrangement. It calculates the van der Waals and electrostatic energies of base-base interactions using the AMBER potential, minimizes the energy with respect to the pair (buckle, propeller, opening, shear, stretch, stagger) and step (tilt, roll, twist, shift, slide, rise) parameters, calculates lengths of the canonical hydrogen bonds between the complementary bases, and calculates interatomic distances between the successive base pairs. Input/output files are simple lists of the step and pair parameters or lists of the atom specifications (N1, C2, etc.) and their Cartesian coordinates (compatible with the Desktop Molecular Modeller*.mol files). The program is supplied with a readbrk utility which transforms PDB/NDB to the *.mol format readable by DNA Modeller. The DNA crystal structures deposited in the PDB or NDB databases can thus be analyzed, and their bases visualized and interactively manipulated. In addition, DNA Modeller can calculate the base pair and step geometrical parameters and interaction energies. A plotter utility creates wire mono or stereo pictures of the bases. This program is designed for IBM-compatible computers working under DOS or can run as a DOS application under MS Windows 3.x or Merge (SCO Unix DOS emulator).}, chemicals = {DNA}, citation-subset = {IM}, comment = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)").}, completed = {1994-06-30}, country = {England}, doi = {10.1093/bioinformatics/10.1.61}, file = {:by-author/J/Jursa/1994_Jursa_61.pdf:PDF}, issn-linking = {0266-7061}, issue = {1}, keywords = {Base Composition; DNA, chemistry, genetics; Evaluation Studies as Topic; Models, Molecular; Molecular Structure; Nucleic Acid Conformation; Software}, nlm-id = {8511758}, owner = {saulius}, pmid = {8193957}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2019-10-23}, timestamp = {2022.04.17}, } @Article{Tung1994, author = {Tung, C. S. and Soumpasis, D. M. and Hummer, G.}, journal = {Journal of biomolecular structure & dynamics}, title = {An extension of the rigorous base-unit oriented description of nucleic acid structures.}, year = {1994}, issn = {0739-1102}, month = jun, pages = {1327--1344}, volume = {11}, abstract = {Our proposed description for DNA base/base-pair structures (1), though rigorous, does not satisfy some of the requirements as established at the Cambridge Workshop (2). Here, we propose a revised description for base/base-unit structures of nucleic acids. This new description is as rigorous and satisfies all the requirements (2). Following the original approach, the moment-of-inertia frame is still the choice of the internal coordinate system for a base/base-unit. The revised description has the minimum number of parameters (i.e., six parameters per rigid body) in the set. Besides regular Watson-Crick type of helices (e.g., A-DNA, A-RNA, B-DNA, Z-DNA, etc.), the revised description also works for non-Watson-Crick, multiple stranded molecules (e.g., triplex, quadruplex, etc.) as well as parallel stranded molecules.}, chemicals = {Polydeoxyribonucleotides, triplex DNA, DNA}, citation-subset = {IM}, comment = {Cited in Lu1997 (1997_Lu_668.pdf, "... (SCHNAaP)"). Suggests to use moments of inertia to define local base axes.}, completed = {1994-12-22}, country = {England}, doi = {10.1080/07391102.1994.10508071}, file = {:by-author/T/Tung/1994_Tung_1327.pdf:PDF}, issn-linking = {0739-1102}, issue = {6}, keywords = {Base Composition; Base Sequence; Computer Simulation; DNA, chemistry; Models, Molecular; Molecular Sequence Data; Nucleic Acid Conformation; Polydeoxyribonucleotides, chemistry}, nlm-id = {8404176}, owner = {saulius}, pmid = {7946077}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2006-11-15}, timestamp = {2022.04.17}, } @Article{Soumpasis1988, author = {Soumpasis, D. M. and Tung, C. S.}, journal = {Journal of biomolecular structure & dynamics}, title = {A rigorous basepair oriented description of DNA structures.}, year = {1988}, issn = {0739-1102}, month = dec, pages = {397--420}, volume = {6}, abstract = {We propose new, rigorous definitions for (i) basepair fixed coordinate systems and (ii) the twist, tilt, and roll angles (called tau, t, rho) describing the relative orientation of adjacent basepairs and bases in a pair, in arbitrary DNA structures obtained from x-ray diffraction, 2D NMR, or energy calculations. In contrast to the corresponding angular parameters (tg, theta T, theta R) and coordinate systems introduced by Dickerson and co-workers and currently in use, our angular parameters and coordinate systems, together with a set of three displacement parameters, dx, dy, dz, provide a mathematically correct and general description of DNA conformations at the basepairs and/or base level. For instance, our description is applicable when the DNA structure considered is inherently curved, irregular, and/or does not possess dyad (or pseudodyad) axes. We develop a computationally convenient algorithm for rigorous DNA conformational analysis and apply it to some of the known crystal structures. We establish the connection to the currently used parameters and test the consistency and efficiency of our methodology by reconstructing the Dickerson B dodecamer using only the sequence and the set of parameters obtained from the atomic coordinates. The six parameter (tau, t, rho, dx, dy, dz) basepair level reconstruction is good but not perfect. Perfect reconstruction is obtained when one also considers each base in a basepair (consideration of propeller twist alone is not sufficient). The variation of the rigorous parameters proposed along the sequence is much larger, but their average values agree with fiber and solution data much better than in the case of the currently used set. The results of our analysis do not support Trifonov's AA.TT wedge model for DNA curvature but provide some evidence in favor of the Crothers junction-bend model. We point out some of the limitations of basepair level approaches when applied to DNA structure prediction and quantitative understanding of sequence-dependent variations in structure.}, chemicals = {DNA}, citation-subset = {IM}, comment = {Cited in Tung1994 (1994_Tung_1327.pdf); uses settings different from the "Cambridge Workshop" definitions (Diekmann1989, Dickerson1989).}, completed = {1990-03-21}, country = {England}, doi = {10.1080/07391102.1988.10506497}, file = {:by-author/S/Soumpasis/1988_Soumpasis_397.pdf:PDF}, issn-linking = {0739-1102}, issue = {3}, keywords = {Base Composition; Computer Simulation; DNA; Models, Molecular; Nucleic Acid Conformation}, nlm-id = {8404176}, owner = {saulius}, pmid = {3271529}, pubmodel = {Print}, pubstate = {ppublish}, revised = {2007-11-14}, timestamp = {2022.04.17}, }