Primary Citation PubMed: 11856858
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DNA conformations and their sequence preferences.
(2008) Nucleic Acids Res 36
PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260
The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).
The Holliday junction of the ‘inverted repeat sequence’ CCGGTACCGG [e.g. 1DCW ( 81 ), 1JUC ( 82 )] is characterized by a high proportion of unclassified and BII-form residues, but only the residue joining two double-helical segments radically deviates from B-like torsion values, mainly in ζ and α + 1.
Publication Year: 2008
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