Crossref journal-article
Elsevier BV
Journal of Molecular Biology (78)
Bibliography

Šponer, J., Mokdad, A., Šponer, J. E., Špačková, N., Leszczynski, J., & Leontis, N. B. (2003). Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of Cis Watson–Crick A/G Base-pairs. Journal of Molecular Biology, 330(5), 967–978.

Authors 6
  1. Jiřı́ Šponer (first)
  2. Ali Mokdad (additional)
  3. Judit E. Šponer (additional)
  4. Nad'a Špačková (additional)
  5. Jerzy Leszczynski (additional)
  6. Neocles B. Leontis (additional)
References 47 Referenced 65
  1. 10.1021/cr9800255 / Chem. Rev. / Structure, energetics, and dynamics of the nucleic acid base-pairs: non-empirical ab initio calculations by Hobza (1999)
  2. 10.1002/1097-0282(2001)61:1<3::AID-BIP10048>3.0.CO;2-4 / Biopolymers / Electronic properties, hydrogen bonding, stacking, and cation-binding of DNA and RNA bases by Šponer (2001)
  3. 10.1080/07391102.1996.10508895 / J. Biomol. Struct. Dynam. / Non-planar DNA base-pairs by Šponer (1996)
  4. 10.1017/S1355838201002515 / RNA / Geometric nomenclature and classification of RNA base-pairs by Leontis (2001)
  5. 10.1006/jmbi.1997.0914 / J. Mol. Biol. / Sheared purine·purine pairing in biology by Chou (1997)
  6. 10.1073/pnas.88.1.26 / Proc. Natl Acad. Sci. USA / NMR and molecular modeling evidence for a G·A mismatch base-pair in a purine-rich DNA duplex by Li (1991)
  7. 10.1016/S0969-2126(00)00049-6 / Structure / Crystal and molecular structure of r(CGCGAAUUAGCG)—an RNA duplex containing 2 G(anti)·A(anti) base-pairs by Leonard (1994)
  8. 10.1073/pnas.83.8.2402 / Proc. Natl Acad. Sci. USA / Molecular structure of the G·A base-pair in DNA and its implications for the mechanism of transversion mutations by Brown (1986)
  9. 10.1126/science.3310237 / Science / Helix geometry, hydration, and G·A mismatch in a B-DNA decamer by Prive (1987)
  10. 10.1016/S0969-2126(00)80033-7 / Struct. Fold. Des. / The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges by Ennifar (1999)
  11. 10.1038/13277 / Nature Struct. Biol. / Crystal structure of a DNA Holliday junction by Ortiz-Lombardia (1999)
  12. 10.1021/bi960133q / Biochemistry / Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach by Wu (1996)
  13. 10.1021/bi00210a009 / Biochemistry / Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics by SantaLucia (1993)
  14. 10.1021/bi9724873 / Biochemistry / Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA by Allawi (1998)
  15. 10.1093/nar/gkf481 / Nucl. Acids Res. / The non-Watson–Crick base-pairs and their associated isostericity matrices by Leontis (2002)
  16. 10.1021/j100063a019 / J. Phys. Chem. / Non-planar geometries of DNA bases—ab initio 2nd-order Moller–Plesset study by Šponer (1994)
  17. 10.1063/1.472904 / J. Chem. Phys. / Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are non-planar: results of correlated ab initio quantum chemical calculations and anharmonic analysis of the aniline inversion motion by Bludský (1996)
  18. 10.1021/ja00081a036 / J. Am. Chem. Soc. / Bifurcated hydrogen bonds in DNA crystal structures—ab initio quantum chemical study by Šponer (1994)
  19. 10.1006/jmbi.1998.1833 / J. Mol. Biol. / On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules by Luisi (1998)
  20. 10.1021/bi9907882 / Biochemistry / Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode by Vlieghe (1999)
  21. 10.1126/science.1076947 / Science / Vibrational transition moment angles in isolated biomolecules: a structural tool by Dong (2002)
  22. 10.1016/S0006-3495(97)78049-4 / Biophys. J. / Base–base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study by Šponer (1997)
  23. 10.1006/jmbi.2001.5131 / J. Mol. Biol. / Quadruple intercalated G-6 stack: a possible motif in the fold-back structure of the Drosophila centromeric dodeca-satellite? by Chou (2001)
  24. 10.1017/S0033583599003479 / Quart. Rev. Biophys. / Conserved geometrical base-pairing patterns in RNA by Leontis (1998)
  25. 10.1093/nar/26.1.148 / Nucl. Acids Res. / Compilation of tRNA sequences and sequences of tRNA genes by Sprinzl (1998)
  26. 10.1093/emboj/18.22.6532 / EMBO J. / Synthesis of aspartyl-tRNA(Asp) in Escherichia coli—a snapshot of the second step by Eiler (1999)
  27. 10.1038/84927 / Nature Struct. Biol. / Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase by Sekine (2001)
  28. 10.1017/S1355838200000364 / RNA / The crystal structure of yeast phenylalanine tRNA at 1.93 angstrom resolution: a classic structure revisited by Shi (2000)
  29. 10.1038/26912 / Nature / Crystal structure of a hepatitis delta virus ribozyme by Ferre-D'Amare (1998)
  30. 10.1007/s00018-002-8409-7 / Cell. Mol. Life Sci. / Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus by Wadkins (2002)
  31. 10.1006/jmbi.2000.4368 / J. Mol. Biol. / A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion by Wadkins (2001)
  32. 10.1006/jmbi.2000.4454 / J. Mol. Biol. / Structural and energetic analysis of RNA recognition by a universally conserved protein from the signal recognition particle by Batey (2001)
  33. 10.1093/nar/29.1.169 / Nucl. Acids Res. / SRPDB (Signal Recognition Particle Database) by Gorodkin (2001)
  34. 10.1017/S1355838298980566 / RNA / The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure by Leontis (1998)
  35. 10.1038/35071009 / Nature / Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis by Rupert (2001)
  36. 10.1093/nar/22.6.1096 / Nucl. Acids Res. / Mutagenesis of the hairpin ribozyme by Anderson (1994)
  37. {'key': '10.1016/S0022-2836(03)00667-3_BIB37', 'first-page': '357', 'article-title': 'Mutagenesis and modeling of the hairpin ribozyme family', 'volume': '74', 'author': 'Siwkowski', 'year': '1997', 'journal-title': 'Methods Mol. Biol.'} / Methods Mol. Biol. / Mutagenesis and modeling of the hairpin ribozyme family by Siwkowski (1997)
  38. 10.1021/bi9628735 / Biochemistry / Analysis of hairpin ribozyme base mutations in loops 2 and 4 and their effects on cis-cleavage in vitro by Siwkowski (1997)
  39. 10.1021/bi00048a024 / Biochemistry / Catalytic properties of hairpin ribozymes derived from Chicory yellow mottle virus and arabis mosaic virus satellite RNAs by De Young (1995)
  40. 10.1038/35030006 / Nature / Structure of the 30S ribosomal subunit by Wimberly (2000)
  41. 10.1093/nar/29.1.175 / Nucl. Acids Res. / The European large subunit ribosomal RNA database by Wuyts (2001)
  42. 10.1093/nar/30.1.183 / Nucl. Acids Res. / The European database on small subunit ribosomal RNA by Wuyts (2002)
  43. 10.1126/science.289.5481.905 / Science / The complete atomic structure of the large ribosomal subunit at 2.4Å resolution by Ban (2000)
  44. 10.1016/S0092-8674(01)00546-3 / Cell / High resolution structure of the large ribosomal subunit from a mesophilic Eubacterium by Harms (2001)
  45. 10.1093/nar/28.24.4893 / Nucl. Acids Res. / Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)2 B↔A intermediate crystal structure by Šponer (2000)
  46. 10.1016/0166-1280(85)80058-0 / J. Mol. Struct. Theochem. / The use of a moment-optimized DZP basis set for describing the interaction in the water dimer by Kroon-Batenburg (1985)
  47. 10.1021/ja026759n / J. Am. Chem. Soc. / Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations by Hobza (2002)
Dates
Type When
Created 22 years, 1 month ago (July 16, 2003, 8:18 a.m.)
Deposited 6 years, 5 months ago (March 17, 2019, 5:21 a.m.)
Indexed 1 year ago (Aug. 3, 2024, 5:43 p.m.)
Issued 22 years, 2 months ago (July 1, 2003)
Published 22 years, 2 months ago (July 1, 2003)
Published Print 22 years, 2 months ago (July 1, 2003)
Funders 0

None

@article{_poner_2003, title={Unique Tertiary and Neighbor Interactions Determine Conservation Patterns of Cis Watson–Crick A/G Base-pairs}, volume={330}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/s0022-2836(03)00667-3}, DOI={10.1016/s0022-2836(03)00667-3}, number={5}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Šponer, Jiřı́ and Mokdad, Ali and Šponer, Judit E. and Špačková, Nad’a and Leszczynski, Jerzy and Leontis, Neocles B.}, year={2003}, month=jul, pages={967–978} }