Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor - PubMed (original) (raw)

. 1995 Feb 23;373(6516):724-7.

doi: 10.1038/373724a0.

Affiliations

• PMID: 7854460
• DOI: 10.1038/373724a0

Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor

J D Parvin et al. Nature. 1995.

Abstract

TATA-binding protein (TBP) binds the minor groove of the TATA element with the DNA bent 80 degrees towards the major groove. A constrained minicircle strategy has been used to test the effect of DNA topology on the affinity of TBP for the TATA element. We report here that TBP bound to DNA which was slightly pre-bent towards the major groove with 100-fold higher affinity than unbent (linear) DNA of identical sequence and 300-fold higher affinity than DNA pre-bent towards the minor groove. Similar discrimination was observed with the holo-TFIID transcription complex. DNA topology, particularly bending, is determined by many factors including chromatin in cells and may, through changes in the affinity of the TATA factor, be important in the control of transcription.

PubMed Disclaimer

Similar articles

• X-ray crystallographic studies of eukaryotic transcription initiation factors.
  Burley SK. Burley SK. Philos Trans R Soc Lond B Biol Sci. 1996 Apr 29;351(1339):483-9. doi: 10.1098/rstb.1996.0046. Philos Trans R Soc Lond B Biol Sci. 1996. PMID: 8735270 Review.
• Dynamic simulations of 13 TATA variants refine kinetic hypotheses of sequence/activity relationships.
  Qian X, Strahs D, Schlick T. Qian X, et al. J Mol Biol. 2001 May 11;308(4):681-703. doi: 10.1006/jmbi.2001.4617. J Mol Biol. 2001. PMID: 11350169
• Crystal structure of a yeast TBP/TATA-box complex.
  Kim Y, Geiger JH, Hahn S, Sigler PB. Kim Y, et al. Nature. 1993 Oct 7;365(6446):512-20. doi: 10.1038/365512a0. Nature. 1993. PMID: 8413604
• Specific targeting of protein-DNA complexes by DNA-reactive drugs (+)-CC-1065 and pluramycins.
  Henderson D, Hurley LH. Henderson D, et al. J Mol Recognit. 1996 Mar-Apr;9(2):75-87. doi: 10.1002/(sici)1099-1352(199603)9:2<75::aid-jmr247>3.0.co;2-4. J Mol Recognit. 1996. PMID: 8877797 Review.

Cited by

• Cell phenotypes can be predicted from propensities of protein conformations.
  Nussinov R, Liu Y, Zhang W, Jang H. Nussinov R, et al. Curr Opin Struct Biol. 2023 Dec;83:102722. doi: 10.1016/j.sbi.2023.102722. Epub 2023 Oct 21. Curr Opin Struct Biol. 2023. PMID: 37871498 Review.
• RNA conformational propensities determine cellular activity.
  Ken ML, Roy R, Geng A, Ganser LR, Manghrani A, Cullen BR, Schulze-Gahmen U, Herschlag D, Al-Hashimi HM. Ken ML, et al. Nature. 2023 May;617(7962):835-841. doi: 10.1038/s41586-023-06080-x. Epub 2023 May 17. Nature. 2023. PMID: 37198487 Free PMC article.
• Deciphering the mechanical code of the genome and epigenome.
  Basu A, Bobrovnikov DG, Cieza B, Arcon JP, Qureshi Z, Orozco M, Ha T. Basu A, et al. Nat Struct Mol Biol. 2022 Dec;29(12):1178-1187. doi: 10.1038/s41594-022-00877-6. Epub 2022 Dec 5. Nat Struct Mol Biol. 2022. PMID: 36471057 Free PMC article.
• DNAcycP: a deep learning tool for DNA cyclizability prediction.
  Li K, Carroll M, Vafabakhsh R, Wang XA, Wang JP. Li K, et al. Nucleic Acids Res. 2022 Apr 8;50(6):3142-3154. doi: 10.1093/nar/gkac162. Nucleic Acids Res. 2022. PMID: 35288750 Free PMC article.
• DNA mismatches reveal conformational penalties in protein-DNA recognition.
  Afek A, Shi H, Rangadurai A, Sahay H, Senitzki A, Xhani S, Fang M, Salinas R, Mielko Z, Pufall MA, Poon GMK, Haran TE, Schumacher MA, Al-Hashimi HM, Gordân R. Afek A, et al. Nature. 2020 Nov;587(7833):291-296. doi: 10.1038/s41586-020-2843-2. Epub 2020 Oct 21. Nature. 2020. PMID: 33087930 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group
  • Ovid Technologies, Inc.

• Other Literature Sources

  • The Lens - Patent Citations