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

Palangat, M., Hittinger, C. T., & Landick, R. (2004). Downstream DNA Selectively Affects a Paused Conformation of Human RNA Polymerase II. Journal of Molecular Biology, 341(2), 429–442.

Authors 3
  1. Murali Palangat (first)
  2. Christopher T. Hittinger (additional)
  3. Robert Landick (additional)
References 54 Referenced 39
  1. 10.1016/S0092-8674(01)00381-6 / Cell / RNA polymerase clamps down by Landick (2001)
  2. 10.1016/S0167-4781(02)00454-2 / Biochim. Biophys. Acta / The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription by Erie (2002)
  3. 10.1016/j.tig.2003.08.008 / Trends Genet. / Running with RNA polymerase: eukaryotic transcript elongation by Arndt (2003)
  4. 10.1146/annurev.biochem.72.121801.161551 / Annu. Rev. Biochem. / The RNA polymerase II elongation complex by Shilatifard (2003)
  5. 10.1006/jmbi.1993.1482 / J. Mol. Biol. / Dissection of the his leader pause site by base substitution reveals a multipartite signal that includes a pause RNA hairpin by Chan (1993)
  6. 10.1093/nar/13.23.8425 / Nucl. Acids Res. / Comparison of pausing during transcription and replication by LaFlamme (1985)
  7. 10.1021/bi00438a044 / Biochemistry / Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7 by Telesnitsky (1989)
  8. 10.1016/S0021-9258(18)77234-7 / J. Biol. Chem. / Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences by Lee (1990)
  9. 10.1016/0022-2836(92)90575-5 / J. Mol. Biol. / Parameters affecting transcription termination by Escherichia coli RNA polymerase. II. Construction and analysis of hybrid terminators by Reynolds (1992)
  10. 10.1128/MCB.8.10.4389 / Mol. Cell. Biol. / Intrinsic sites of transcription termination and pausing in the c-myc gene by Kerppola (1988)
  11. 10.1021/bi00453a037 / Biochemistry / Analysis of the signals for transcription termination by purified RNA polymerase II by Kerppola (1990)
  12. 10.1126/science.284.5414.611 / Science / Mechanism of instrinsic termination and antitermination by Yarnell (1999)
  13. 10.1074/jbc.M301103200 / J. Biol. Chem. / NTP-driven translocation by human RNA polymerase II by Nedialkov (2003)
  14. 10.1074/jbc.M304496200 / J. Biol. Chem. / Downstream DNA sequence effects on transcription elongation: allosteric binding of nucleoside triphosphate faciliates translocation via a ratchet mechanism by Holmes (2003)
  15. 10.1126/science.1059493 / Science / Structural basis of transcription: RNA polymerase II at 2.8Å resolution by Cramer (2001)
  16. 10.1126/science.1059495 / Science / Structural basis of transcription: an RNA polymerase II elongation complex at 3.3Å resolution by Gnatt (2001)
  17. 10.1073/pnas.052054099 / Proc. Natl Acad Sci. USA / Conformational flexibility of bacterial RNA polymerase by Darst (2002)
  18. 10.1074/jbc.M207038200 / J. Biol. Chem. / The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing by Ederth (2002)
  19. 10.1126/science.288.5466.640 / Science / Architecture of RNA polymerase II and implications for the transcription mechanism by Cramer (2000)
  20. 10.1126/science.273.5272.211 / Science / Transcription processivity: RNA polymerase–DNA interactions holding together the elongation complex by Nudler (1996)
  21. 10.1101/sqb.1998.63.337 / Cold Spring Harb. Symp. Quant. Biol. / Mechanistic model of the elongation complex of Escherichia coli RNA polymerase by Korzheva (1998)
  22. 10.1074/jbc.275.9.6530 / J. Biol. Chem. / The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex by Kireeva (2000)
  23. 10.1016/S1097-2765(00)80103-3 / Mol. Cell / Transcriptional pausing at +62 of the HIV-1 nascent RNA modulates formation of the TAR RNA structure by Palangat (1998)
  24. 10.1006/jmbi.2001.4842 / J. Mol. Biol. / Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II by Palangat (2001)
  25. 10.1074/jbc.270.5.2290 / J. Biol. Chem. / RNA polymerase II ternary complexes may become arrested after transcribing to within 10 bases of the end of linear templates by Izban (1995)
  26. 10.1021/bi0014249 / Biochemistry / Topology of yeast RNA polymerase II subunits in transcription elongation complexes studied by photoaffinity cross-linking by Wooddell (2000)
  27. 10.1093/nar/27.15.3173 / Nucl. Acids Res. / Transcriptional pause, arrest and termination sites for RNA polymerase II in mammalian N- and c-myc genes by Keene (1999)
  28. {'key': '10.1016/j.jmb.2004.06.009_BIB28', 'first-page': '501', 'article-title': 'DNA bending at adenine.thymine tracts', 'volume': '320', 'author': 'Koo', 'year': '1986', 'journal-title': 'Science'} / Science / DNA bending at adenine.thymine tracts by Koo (1986)
  29. 10.1073/pnas.85.6.1763 / Proc. Natl Acad. Sci. USA / Calibration of DNA curvature and a unified description of sequence-directed bending by Koo (1988)
  30. 10.1038/330221a0 / Nature / The structure of an oligo(dA)·(dT) tract and its biological implications by Nelson (1987)
  31. 10.1073/pnas.86.6.1816 / Proc. Natl Acad. Sci. USA / Crystal lattice packing is important in determining the bend of a DNA dodecamer containing adenine tract by DiGabrielle (1989)
  32. 10.1006/jmbi.1996.0878 / J. Mol. Biol. / X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature by Shatzky-Schwartz (1997)
  33. 10.1101/gad.870001 / Genes Dev. / Fine structure of E.coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove by Ross (2001)
  34. 10.1126/science.1076376 / Science / Structural basis of transcription activation: the CAP–alpha CTD–DNA complex by Benoff (2002)
  35. 10.1016/0092-8674(91)90299-E / Cell / TFIID binds in the minor groove of the TATA box by Starr (1991)
  36. 10.1126/science.289.5479.619 / Science / A structural model of transcription elongation by Korzheva (2000)
  37. 10.1016/S0092-8674(00)80872-7 / Cell / Structural organization of the RNA polymerase-promoter open complex by Naryshkin (2000)
  38. 10.1016/S0092-8674(03)00598-1 / Cell / Architecture of the RNA polymerase II–TFIIS complex and implications for mRNA cleavage by Kettenberger (2003)
  39. 10.1038/nature752 / Nature / Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6Å resolution by Vassylyev (2002)
  40. 10.1016/0968-0004(89)90066-2 / Trends Biochem. Sci. / Structural basis of DNA–protein recognition by Brennan (1989)
  41. 10.1006/jmbi.2001.5089 / J. Mol. Biol. / Indirect readout of DNA sequence at the primary-kink site in the CAP–DNA complex: DNA binding specificity based on energetics of DNA kinking by Chen (2001)
  42. 10.1146/annurev.bi.61.070192.005201 / Annu. Rev. Biochem. / Transcription factors: structural families and principles of DNA recognition by Pabo (1992)
  43. 10.1074/jbc.M212667200 / J. Biol. Chem. / The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor by Mauro (2003)
  44. 10.1146/annurev.bi.59.070190.003543 / Annu. Rev. Biochem. / Sequence-directed curvature of DNA by Hagerman (1990)
  45. 10.1146/annurev.biophys.29.1.497 / Annu. Rev. Biophys. Biomol. Struct. / Electrostatic mechanisms of DNA deformation by Williams (2000)
  46. 10.1016/S0959-440X(02)00326-3 / Curr. Opin. Struct. Biol. / Protein surface salt bridges and paths for DNA wrapping by Saecker (2002)
  47. 10.1016/S1367-5931(98)80104-X / Curr. Opin. Chem. Biol. / Mechanisms of DNA bending by Maher (1998)
  48. 10.1126/science.1057738 / Science / Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins by Toulokhonov (2001)
  49. 10.1016/S1097-2765(03)00439-8 / Mol. Cell / The flap domain is required for pause RNA hairpin inhibition of catalysis by RNA polymerase and can modulate intrinsic termination by Toulokhonov (2003)
  50. 10.1016/S0092-8674(03)00845-6 / Cell / Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking by Neuman (2003)
  51. 10.1016/S1097-2765(02)00640-8 / Mol. Cell / Swing-gate model of nucleotide entry into the RNA polymerase active center by Epshtein (2002)
  52. 10.1126/science.286.5448.2337 / Science / Binding of transcription termination protein nun to nascent RNA and template DNA by Watnick (1999)
  53. 10.1089/dna.1988.7.47 / DNA / A high-efficiency HeLa cell nuclear transcription extract by Shapiro (1988)
  54. 10.1006/jmbi.1996.0707 / J. Mol. Biol. / A model for the mechanism of polymerase translocation by Guajardo (1997)
Dates
Type When
Created 21 years, 2 months ago (June 24, 2004, 1:47 p.m.)
Deposited 4 years, 2 months ago (June 23, 2021, 2:50 p.m.)
Indexed 2 months, 3 weeks ago (June 4, 2025, 10:27 a.m.)
Issued 21 years, 1 month ago (Aug. 1, 2004)
Published 21 years, 1 month ago (Aug. 1, 2004)
Published Print 21 years, 1 month ago (Aug. 1, 2004)
Funders 0

None

@article{Palangat_2004, title={Downstream DNA Selectively Affects a Paused Conformation of Human RNA Polymerase II}, volume={341}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/j.jmb.2004.06.009}, DOI={10.1016/j.jmb.2004.06.009}, number={2}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Palangat, Murali and Hittinger, Christopher T. and Landick, Robert}, year={2004}, month=aug, pages={429–442} }