Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Marathe, Arvind ^a   Karandur, Deepti ^a   Bansal, Manju ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; TRINUCLEOTIDE; DNA; DNA A;

ARTICLE; CRYSTAL STRUCTURE; DNA STRUCTURE; GENETIC VARIABILITY; GEOMETRY; HUMAN; PARAMETER; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN MOTIF; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; DINUCLEOTIDE REPEAT; METABOLISM;

NON-A, NON-B HEPATITIS VIRUS;

AMINO ACID MOTIFS; COMPUTER SIMULATION; DINUCLEOTIDE REPEATS; DNA; DNA, A-FORM; DNA-BINDING PROTEINS; NUCLEIC ACID CONFORMATION;

EID: 66349114339     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-24     Document Type: Article

References (105)

1. W Saenger, Principles of nucleic acid structure New York: Springer 1984
2. A glossary of DNA structures from A to Z. A Ghosh M Bansal, Acta Cryst 2003 59 620 626 10.1107/S0108270103019577 (Pubitemid 36453631)
3. Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G. BN Conner C Yun JL Dickerson RE Dickerson, J Mol Biol 1984 174 663 695 10.1016/0022-2836(84) 90089-5 6726797
4. Base sequence and helix structure variation in B and A DNA. RE Dickerson, J Mol Biol 1983 166 419 441 10.1016/S0022-2836(83)80093-X 6854650
5. RE Dickerson ML Kopka P Pjura, J Mol Biol Wiley, NewYork 1984 2
6. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. B Schneider S Neidle HM Berman, Biopolymers 1997 42 113 124 10.1002/(SICI)1097-0282(199707)42:1<113::AID-BIP10>3.0.CO;2-O 19350745
7. Groove width and depth of B-DNA structures depend on local variation in slide. D Bhattacharyya M Bansal, J Biomol Struct Dyn 1992 10 213 226 1418742
8. Structure of a B-DNA dodecamer. III. Geometry of hydration. HR Drew RE Dickerson, J Mol Biol 1981 151 535 556 10.1016/0022-2836(81)90009-7 7338904 (Pubitemid 12252694)
9. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. AV Fratini ML Kopka HR Drew RE Dickerson, J Biol Chem 1982 257 14686 14707 7174662 (Pubitemid 13159563)
10. Local variability and base sequence effects in DNA crystal structures. D Bhattacharyya M Bansal, J Biomol Struct Dyn 1990 8 539 572 2100518
11. B-DNA twisting correlates with base-pair morphology. A Gorin VB Zhurkin WK Olson, J Mol Biol 1995 247 34 48 10.1006/jmbi.1994.0120 7897660
12. A standard reference frame for the description of nucleic acid base-pair geometry. WK Olson M Bansal SK Burley RE Dickerson M Gerstein SC Harvey U Heinemann XJ Lu S Neidle Z Shakked H Sklenar M Suzuki CS Tung E Westhof C Wolberger HM Berman, J Mol Biol 2001 313 229 237 10.1006/jmbi.2001.4987 11601858
13. The crystal structure of d(G-G-G-G-C-C-C-C). a model for poly(dG).poly(dC). M McCall T Brown O Kennard, J Mol Biol 1985 183 385 396 10.1016/0022-2836(85)90009-9 4020865
14. A-form conformational motifs in ligand-bound DNA structures. X Lu Z Shakked WK Olson, J Mol Biol 2000 300 819 840 10.1006/jmbi.2000.3690 10891271
15. Conformational characteristics of DNA: empirical classifcations and a hypothesis for the conformational behaviour of dinucleotide steps. MA El Hassan CR Calladine, Phil Trans R Soc Lond A 1997 355 43 100 10.1098/rsta.1997.0002
16. How sequence defines structure: a crystallographic map of DNA structure and conformation. F Hays A Teegarden ZJ Jones M Harms D Raup J Watson E Cavaliere P Ho, Proc Natl Acad Sci 2005 102 7157 7162 15870206 10.1073/pnas.0409455102
17. DNA structure from A to B. RE Dickerson HL Ng, Proc Natl Acad Sci 2001 98 6986 6988 11416174 10.1073/pnas.141238898
18. Mildly eccentric 'E-DNA'. HL Ng RE Dickerson, Nat Struct Biol 2001 8 107 108 10.1038/84078 11175893
19. RNA double-helical fragments at atomic resolution. I. the crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate. NC Seeman JM Rosenberg FL Suddath JJ Kim A Rich, J Mol Biol 1976 104 109 144 10.1016/0022-2836(76)90005-X 957429
20. RNA double-helical fragments at atomic resolution. II. the crystal structure of sodium guanylyl-3',5'-cytidine nonahydrate. JM Rosenberg NC Seeman RO Day A Rich, J Mol Biol 1976 104 145 167 10.1016/0022-2836(76)90006-1 957430
21. The crystal and molecular structure of a calcium salt of guanylyl-3',5'-cytidine (GpC). B Hingerty E Subramanian SD Stellman T Sato SB Broyde R Langridge, Acta Cryst 1976 B32 2998 3013
22. The structure of the ribodinucleoside monophosphate guanylyl-3',5'- cytidine as its ammonium octahydrate salt. A Aggarwal SA Islam R Kuroda MR Sanderson S Neidle HM Berman, Acta Cryst 1983 B39 98 104
23. High resolution structure of the RNA duplex [U(U-A) 6 A] 2. AC Dock-Bregeon B Chevrier A Podjarnyl J Johnson JS de Bear GR Gough PT Gilham D Moras, Nature 1988 335 375 378 10.1038/335375a0 2458530
24. Crystallographic structure of an RNA helix: [U(UA) 6 A] 2. AC Dock-Bregeon B Chevrier A Podjarnyl J Johnson JS de Bear GR Gough PT Gilham D Moras, J Mol Biol 1989 209 459 474 10.1016/0022-2836(89)90010-7 2479753
25. DNA sequence-dependent deformabilty deduced from protein-DNA crystal complexes. WK Olson AA Gorin X Lu LM Hock VB Zhurkin, Proc Natl Acad Sci 1998 95 11163 11168 9736707 10.1073/pnas.95.19.11163
26. Protein-DNA interactions: a structural analysis. S Jones P van Heyningen HM Berman JM Thornton, J Mol Biol 1999 287 877 896 10.1006/jmbi.1999.2659 10222198
27. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. X Lu WK Olson, Nucleic Acids Res 2003 31 5108 5121 12930962 10.1093/nar/gkg680
28. The B to A transition of DNA in solution. VI Ivanov LE Minchenkova EE Minyat MD Frank-Kamenetskii AK Schyolkina, J Mol Biol 1974 87 817 833 10.1016/0022-2836(74)90086-2 4427376
29. On the flexibility of the boundaries between the A-form and B-form sections in DNA molecule. SK Zavriev LE Minchenkova MD Frank-Kamenetskii VI Ivanov, Nucleic Acids Res 1978 5 2657 2663 673864 10.1093/nar/5.7.2657 (Pubitemid 8369759)
30. CC/CG contacts facilitate the B to A transition of DNA in solution. LE Minchenkova AK Schyolkina BK Chernov VI Ivanov, J Biomol Struct Dyn 1986 4 463 476 2908426 (Pubitemid 17231777)
31. Some rules for predicting the base-sequence dependence of DNA conformation. WL Peticolas Y Y Wang GA Thomas, Proc Natl Acad Sci 1988 85 2579 2583 3357884 10.1073/pnas.85.8.2579
32. Sequence-dependent BA transition in DNA evaluated with dimeric and trimeric scales. MY Tolstorukov VI Ivanov GG Malenkov RL Jernigan VB Zhurkin, Biophys J 2001 81 3409 3421 11721003 10.1016/S0006-3495(01)75973-5 (Pubitemid 33111486)
33. Crystalline A-DNA: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C). Z Shakked D Rabinovich WB Cruse E Egert O Kennard G Sala SA Salisbury MA Viswamitra, Proc R Soc Lond 1981 B213 479 487 10.1098/rspb.1981.0076 (Pubitemid 12196760)
34. Structures of the DNA-binding site of Runt-domain transcription regulators. M Kitayner R H D Rabinovich Z Shakked, Acta Crystallogr D Biol Crystallogr 2005 61 236 246 10.1107/S0907444904032378 15735333
35. H Berman W Olson, Molecular biology in the new era Faircount, LLC, London 2003
36. Pyrimidine 5-methyl groups influence the magnitude of DNA curvature. PJ Hagerman, Biochemistry 1990 29 1980 1983 10.1021/bi00460a003 2328230 (Pubitemid 20085420)
37. Stereochemical basis of DNA bending by transcription factors. M Suzuki N Yagi, Nucleic Acids Res 1995 23 2083 2091 7610037 10.1093/nar/23.12.2083
38. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. MA Young G Ravishanker DL Beveridge HM Berman, Biophys J 1995 68 2454 2468 7647248 10.1016/S0006-3495(95)80427-3
39. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. G Guzikevich-Guerstein Z Shakked, Nat Struct Biol 1996 3 32 37 10.1038/nsb0196-32 8548452
40. Helix bending as a factor in protein/DNA recognition. RE Dickerson TK Chiu, Biopolymers 1997 44 361 403 10.1002/(SICI)1097-0282(1997)44:4<361::AID- BIP4>3.0.CO;2-X 9782776
41. DNA bending: the prevalence of kinkiness and the virtues of normality. RE Dickerson, Nucleic Acids Res 1998 26 1906 1926 9518483 10.1093/nar/26.8.1906
42. Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles. Y Mandel-Gutfreund O Schueler H Margalit, J Mol Biol 1995 253 370 382 10.1006/jmbi.1995.0559 7563096
43. Crystal structure of trp repressor/operator complex at atomic resolution. Z Otwinowski RW Schevitz RG Zhang CL Lawson A Joachimiak RQ Marmorstein BF Luisi PB Sigler, Nature 1988 335 321 329 10.1038/335321a0 3419502
44. Refined 1.8 crystal structure of the lambda repressor-operator complex. LJ Beamer CO Pabo, J Mol Biol 1992 227 177 196 10.1016/0022-2836(92)90690-L 1387915
45. Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV. H Thorogood TR Waters AW Parker CW Wharton BA Connolly, Biochemistry 1996 35 8723 8733 10.1021/bi960230j 8679635
46. Probing the indirect readout of the restriction enzyme EcoRV. mutational analysis of contacts to the DNA backbone. C Wenz A Jeltsch A Pingoud, J Biol Chem 1996 271 5565 5573 10.1074/jbc.271.10.5565 8621416
47. Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites. B Hartmann MR Sullivan LF Harris, Biopolymers 2003 68 250 264 10.1002/bip.10243 12548627
48. Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA. W Flader B Wellenzohn RH Winger A Hallbrucker E Mayer KR Liedl, Biopolymers 2003 68 139 149 10.1002/bip.10242 12548619
49. Predicting indirect readout effects in protein-DNA interactions. Y Zhang X Zhiqun RS Hegde Z Shakked DM Crothers, Proc Natl Acad Sci 2004 101 8337 8341 15148366 10.1073/pnas.0402319101
50. Sequence-dependent conformation of an A-DNA double helix: the crystal structure of the octamer d(G-G-T-A-T-A-C-C). Z Shakked D Rabinovich, J Mol Biol 1983 6854642
51. Crystallographic refinement of yeast aspartic acid transfer RNA. E Westhof P Dumas D Moras, J Mol Biol 1985 184 119 145 10.1016/0022-2836(85)90048- 8 3897553
52. - transitions in the B-DNA backbone. P Varnai D Djuranovic R Lavery B Hartmann, Nucleic Acids Res 2002 30 5398 5406 12490708 10.1093/nar/gkf680
53. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps. SB Dixit DL Beveridge DA Case TE Cheatham III E Giudice F Lankas R Lavery JH Maddocks R Osman H Sklenar KM Thayer P Varnai, Biophys J 2005 89 3721 3740 16169978 10.1529/biophysj.105. 067397
54. Sequence preference for BI/BII Conformations in DNA: MD and crystal structure data analysis. A Madhumalar M Bansal, J Biomol Struct Dyn 2005 23 13 27 15918673 (Pubitemid 40868935)
55. Sequence-dependent DNA structure: a database of octamer structural parameters. EJ Gardiner CA Hunter MJ Packer DS Palmer P Willett, J Mol Biol 2003 332 1025 1035 10.1016/j.jmb.2003.08.006 14499606
56. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps. DL Beveridge G Barreiro KS Byun DA Case TEI Cheatham SB Dixit E Giudice F Lankas R Lavery JH Maddocks R Osman E Seibert H Sklenar G Stoll KM Thayer P Varnai MA Young, J Biomol Struct Dyn 2004 10 213 226
57. Bent helical structure in kinetoplast DNA. JC Marini SD Levene DM Crothers PT Englund, Proc Natl Acad Sci 1982 79 7664 7668 16593261 10.1073/pnas.79.24.7664
58. Physical characterization of a kinetoplast DNA fragment with unusual properties. JC Marini PN Effron TC Goodman CK Singleton RD Wells MR Wartell PT Englund, J Biol Chem 1984 259 8974 8979 6086618 (Pubitemid 14098872)
59. The pitch of chromatin DNA is reflected in its nucleotide sequence. EN Trifonov JL Sussman, Proc Natl Acad Sci 1980 77 3816 3820 6933438 10.1073/pnas.77.7.3816
60. A computer graphics study of sequence directed bending in DNA. SD Levene DM Crothers, J Biomol Struct Dyn 1983 1 429 435 6400882 (Pubitemid 14082474)
61. Curved DNA without AA/TT dinucleotide step. I Brukner V Jurukovski M Konstantinovic A Savic, Nucleic Acids Res 1991 19 3549 3551 1852605 10.1093/nar/19.13.3549 (Pubitemid 21912715)
62. Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. A Bolshoy P McNamara RE Harrington EN Trifonov, Proc Natl Acad Sci 1991 88 2312 2316 2006170 10.1073/pnas.88.6.2312 (Pubitemid 21916406)
63. Structural variations observed in DNA crystalstructures and their implications for protein-DNA interaction. M Bansal, Proceedings of the Ninth Conversation: Biological Structure and Dynamics New York: Adenine press 1996 121 134
64. A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data. Y Liu DL Beveridge, J Biomol Struct Dyn 2001 18 505 526 11245247 (Pubitemid 32164727)
65. M Bansal D Bhattacharyya D Mohanty, Molecular Conformation and Biological Interactions Bangalore: Indian Academy of Sciences 1991 chap. DNA bending: a natural consequence of base sequence dependent variability 347 362
66. Base sequence effects in double helical DNA. I. Potential energy estimates of local base morphology. AR Srinivasan R Torres W Clark WK Olson, J Biomol Struct Dyn 1987 5 459 496 3271482
67. Measures of DNA curvature. C Tung AE Garcia TG Marr SK Mishra C Burks, DNA Bending and Curvature 1988 3 265 277
68. Unconventional helical phasing of repetitive DNA motifs reveals their relative bending contributions. M Dlakic RE Harrington, Nucleic Acids Res 1998 26 4274 4279 9722649 10.1093/nar/26.18.4274
69. An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data. A Kanhere M Bansal, Nucleic Acids Res 2003 31 2647 2658 12736315 10.1093/nar/gkg362
70. Relationship between curved DNA conformation and slow gel migration. RL Jernigan A Sarai B Shapiro R Nussinov, J Biomol Struct Dyn 1987 4 561 567 3271455 (Pubitemid 17039405)
71. Influence of flutuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. WK Olson NL Marky RL Jernigan VB Zhurkin, J Mol Biol 1993 232 530 554 10.1006/jmbi.1993.1409 8345522
72. Bending and curvature calculations in B-DNA. DS Goodsell RE Dickerson, Nucleic Acids Res 1994 22 5497 5503 7816643 10.1093/nar/22.24.5497
73. DNA recognition by proteins with the helix-turn-helix motif. SC Harrison AK Aggarwal, Annu Rev Biochem 1990 59 933 969 10.1146/annurev.bi.59.070190. 004441 2197994
74. Protein-DNA recognition. CO Pabo RT Sauer, Annu Rev Biochem 1984 53 293 321 10.1146/annurev.bi.53.070184.001453 6236744 (Pubitemid 14059145)
75. Transcription factors: structural families and principles of DNA recognition. CO Pabo RT Sauer, Annu Rev Biochem 1992 61 1053 1095 10.1146/annurev.bi.61.070192.005201 1497306
76. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. R Wintjens M Rooman, J Mol Biol 1996 262 294 313 10.1006/jmbi.1996.0514 8831795
77. The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. HM Berman WK Olson DL Beveridge J Westbrook A Gelbin T Demeny SH Hsieh AR Srinivasan B Schneider, Biophys J 1992 63 751 759 1384741 10.1016/S0006-3495(92)81649-1
78. SCOP: a structural classification of proteins database for the investigation of sequences and structures. AG Murzin SE Brenner T Hubbard C Chothia, J Mol Biol 1995 247 536 540 7723011
79. CA/TG sequence at the 5' end of oligo(A)-tracts strongly modulates DNA curvature. AK Nagaich D Bhattacharyya SK Brahmachari M Bansal, J Biol Chem 1994 269 7824 7833 8126009
80. Optimised parameters for A-DNA and B-DNA. S Arnott DW Hukins, Biochem Biophys Res Commun 1972 47 1504 1509 10.1016/0006-291X(72)90243-4 5040245
81. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. K Grzeskowiak K Yanagi GG Prive RE Dickerson, J Biol Chem 1991 266 8861 8883 2026600 (Pubitemid 21906593)
82. Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. K Yanagi GG Prive R Dickerson, J Mol Biol 1991 217 201 214 10.1016/0022-2836(91)90620-L 1988678 (Pubitemid 121003285)
83. Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. GG Prive K Yanagi RE Dickerson, J Mol Biol 1991 217 177 199 10.1016/0022-2836(91)90619-H 1988677 (Pubitemid 121003284)
84. Conformational flexibility of B-DNA at 0.74 resolution: d(CCAGTACTGG) 2. CL Kielkopf S Ding P Kuhn DC Rees, J Mol Biol 2000 296 787 801 10.1006/jmbi.1999.3478 10677281
85. 1 crystal structure of B-DNA reveal sequence specific binding and groove specific bending of DNA by magnesium and calcium. TK Chiu R Dickerson, J Mol Biol 2000 301 915 945 10.1006/jmbi.2000.4012 10966796
86. Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 Resolution. CA Davey DF Sargent K Luger AW Maeder TJ Richmond, J Mol Biol 2002 319 1097 1113 10.1016/S0022-2836(02)00386-8 12079350
87. The structure of a stable intermediate in the A B DNA helix transition. HL Ng ML Kopka RE Dickerson, Proc Natl Acad Sci 2000 97 2035 2039 10688897 10.1073/pnas.040571197
88. Hydration and recognition of methylated CpG steps in DNA. C Mayer-Jung D Moras Y Timsit, EMBO J 1998 17 2709 2718 9564052 10.1093/emboj/17.9.2709
89. Crystal structure of the nucleosome core particle at 2.8 resolution. K Luger AW Mader RK Richmond DF Sargent TJ Richmond, Nature 1997 389 251 260 10.1038/38444 9305837
90. Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure. D Lejeune N Delsaux B Charloteaux A Thomas R Brasseur, Proteins: Str Func Bioinf 2005 61 258 271 10.1002/prot.20607
91. Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA. S Watkins G van Pouderoyen TK Sixma, Nucleic Acids Res 2004 32 4306 4312 15304566 10.1093/nar/gkh770
92. Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. L Nekludova CO Pabo, Proc Natl Acad Sci 1994 91 6948 6952 8041727 10.1073/pnas.91.15.6948
93. DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending. D Bartfeld L Shimon GC Couture D Rabinovich F Frolow D Levanon Y Groner Z Shakked, Structure 2002 10 1395 1407 10.1016/S0969-2126(02)00853-5 12377125
94. Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. DR Mack TK Chiu RE Dickerson, J Mol Biol 2001 312 1037 1049 10.1006/jmbi.2001.4994 11580248
95. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. O Littlefield Y Korkhin PB Sigler, Proc Natl Acad Sci 1999 96 13668 13673 10570130 10.1073/pnas.96.24.13668
96. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. G Patikoglou JL Kim L Sun SH Yang T Kodadek SK Burley, Genes Dev 1999 13 3217 3230 10617571 10.1101/gad.13.24.3217
97. An A-DNA structure with two independent duplexes in the asymmetric unit. G Savitha MA Viswamitra, Acta Crystallogr D Biol Crystallogr 1999 55 1136 1143 10.1107/S0907444999003182 10329775
98. Structural basis of preinitiation complex assembly on human pol II promoters. FTF Tsai PB Sigler, EMBO J 2000 19 25 36 10619841 10.1093/emboj/19.1.25 (Pubitemid 30009222)
99. Protein-DNA recognition in the minor groove is facilitated by sugar switching. MY Tolstorukov RL Jernigan VB Zhurkin, J Mol Biol 2004 337 65 76 10.1016/j.jmb.2004.01.011 15001352
100. Kinking occurs during molecular dynamics simulations of small DNA minicircles. F Lankas R Lavery JH Maddocks, Structure 2006 14 1527 1534 10.1016/j.str.2006.08.004 17027501
101. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic Acids Res 2000 28 235 242 10592235 10.1093/nar/28.1.235 (Pubitemid 30047768)
102. Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif. WA McLaughlin H Berman, J Mol Biol 2003 330 43 55 10.1016/S0022-2836(03)00532-1 12818201
103. A self-consistent formulation for the analysis and generation of non-uniform DNA structures. D Bhattacharyya M Bansal, J Biomol Struct Dyn 1989 6 635 653 2619932 (Pubitemid 19079751)
104. NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. M Bansal D Bhattacharyya B Ravi, Comput Appl Biosci 1995 11 281 287 7583696
105. Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. S Mukherjee M Bansal D Bhattacharyya, J Comput Aided Mol Des 2006 20 629 645 10.1007/s10822-006-9083-x 17124630