- M.R. Singleton and D.B. Wigley, Multiple roles for ATP hydrolysis in nucleic acid modifying
enzymes. EMBO J., 2003, 22 , 4579–4583. - K.J. Polach and J. Widom, A model for the cooperative binding of eukaryotic regulatory proteins to
nucleosomal target sites. J. Mol. Biol., 1996, 258 , 800–812. - J.D. Anderson and J. Widom, Sequence and position-dependence of the equilibrium accessibility of
nucleosomal DNA target sites. J. Mol. Biol., 2000, 296 , 979–987. - T.A. Steitz, A mechanism for all polymerases. Nature, 1998, 391 , 231–232.
- J.C. Delaney, P.T. Henderson, S.A. Helquist, J.C. Morales, J.M. Essigmann and E.T. Kool, High-
fidelity in vivoreplication of DNA base shape mimics without Watson–Crick hydrogen bonds. Proc.
Natl. Acad. Sci. USA, 2003, 100 , 4469–4473. - T.H. Tahirov, D. Temiakov, M. Anikin, V. Patlan, W.T. McAllister, D.G. Vassylyev and S. Yokoyama,
Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature, 2002, 420 , 43–50. - Y.W. Yin and T.A. Steitz, Structural basis for the transition from initiation to elongation transcription
in T7 RNA polymerase. Science, 2002, 298 , 1387–1395. - P.D. Morris and K.D. Raney, DNA helicases displace streptavidin from biotin-labeled oligonucleotides.
Biochemistry, 1999, 38 , 5164–5171. - S.S. Velankar, P. Soultanas, M.S. Dillingham, H.S. Subramanya and D.B. Wigley, Crystal structures
of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell,
1999, 97 , 75–84. - D.E. Smith, S.J. Tans, S.B. Smith, S. Grimes, D.L. Anderson and C. Bustamante, The bacteriophage
straight phi29 portal motor can package DNA against a large internal force. Nature, 2001, 413 , 748–752. - A. Guasch, J. Pous, B. Ibarra, F.X. Gomis-Ruth, J.M. Valpuesta, N. Sousa, J.L. Carrascosa and
M. Coll, Detailed architecture of a DNA translocating machine: the high-resolution structure of the
bacteriophage phi29 connector particle. J. Mol. Biol., 2002, 315 , 663–676. - A.A. Simpson, Y. Tao, P.G. Leiman, M.O. Badasso, Y. He, P.J. Jardine, N.H. Olson, M.C. Morais,
S. Grimes, D.L. Anderson, T.S. Baker and M.G. Rossmann, Structure of the bacteriophage phi29
DNA packaging motor. Nature, 2000, 408 , 745–750. - S.N. Savvides, H.J. Yeo, M.R. Beck, F. Blaesing, R. Lurz, E. Lanka, R. Buhrdorf, W. Fischer,
R. Haas and G. Waksman, VirB11 ATPases are dynamic hexameric assemblies: new insights into bac-
terial type IV secretion. EMBO J., 2003, 22 , 1969–1980. - F.X. Gomis-Ruth, G. Moncalian, R. Perez-Luque, A. Gonzalez, E. Cabezon, F. de la Cruz and
M. Coll, The bacterial conjugation protein TrwB resembles ring helicases and F1-ATPase. Nature,
2001, 409 , 637–641. - R.M. Story and T.A. Steitz, Structure of the recA protein–ADP complex. Nature, 1992, 355 , 374–376.
- K. Nagai, RNA–protein complexes. Curr. Opin. Struct. Biol., 1996, 6 , 53–61.
- D.E. Draper, Themes in RNA–protein recognition. J. Mol. Biol., 1999, 293 , 255–270.
- S. Jones, D.T. Daley, N.M. Luscombe, H.M. Berman and J.M. Thornton, Protein–RNA interactions:
a structural analysis. Nucleic Acids Res., 2001, 29 , 943–954. - J.R. Williamson, Induced fit in RNA–protein recognition. Nat. Struct. Biol., 2000, 7 , 834–837.
- N.H. Hopcroft, A. Manfredo, A.L. Wendt, A.M. Brzozowski, P. Gollnick and A.A. Antson, The inter-
action of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides. J. Mol. Biol.,
2004, 338 , 43–53. - K. Valegard, J.B. Murray, N.J. Stonehouse, S. van den Worm, P.G. Stockley and L. Liljas, The three-
dimensional structures of two complexes between recombinant MS2 capsids and RNA operator frag-
ments reveal sequence-specific protein–RNA interactions. J. Mol. Biol., 1997, 270 , 724–738. - C. Kambach, S. Walke, R. Young, J.M. Avis, E. de la Fortelle, V.A. Raker, R. Luhrmann, J. Li and
K. Nagai, Crystal structures of two Sm protein complexes and their implications for the assembly of
the spliceosomal snRNPs. Cell, 1999, 96 , 375–387.
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