Literature DB >> 19997887

In vitro footprinting of promoter regions within supercoiled plasmid DNA.

Daekyu Sun1.   

Abstract

Polypurine/polypyrimidine (pPu/pPy) tracts, which exist in the promoter regions of many growth-related genes, have been proposed to be very dynamic in their conformation. In this chapter, we describe a detailed protocol for DNase I and S1 nuclease footprinting experiments with supercoiled plasmid DNA containing the promoter regions to probe whether there are conformational transitions to B-type DNA, melted DNA, and G-quadruplex structures within this tract. This is demonstrated with the proximal promoter region of the human vascular endothelial growth factor (VEGF) gene, which also contains multiple binding sites for Sp1 and Egr-1 transcription factors.

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Year:  2010        PMID： 19997887      PMCID： PMC2807360          DOI： 10.1007/978-1-60327-418-0_14

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  33 in total

1.  Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo.

Authors:  G A Michelotti; E F Michelotti; A Pullner; R C Duncan; D Eick; D Levens
Journal:  Mol Cell Biol       Date:  1996-06       Impact factor: 4.272

2.  Supercoiling of the DNA template during transcription.

Authors:  L F Liu; J C Wang
Journal:  Proc Natl Acad Sci U S A       Date:  1987-10       Impact factor: 11.205

3.  Vascular endothelial growth factor-B and vascular endothelial growth factor-C expression in renal cell carcinomas: regulation by the von Hippel-Lindau gene and hypoxia.

Authors:  S P Gunningham; M J Currie; C Han; K Turner; P A Scott; B A Robinson; A L Harris; S B Fox
Journal:  Cancer Res       Date:  2001-04-01       Impact factor: 12.701

4.  Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex.

Authors:  T Evans; A Efstratiadis
Journal:  J Biol Chem       Date:  1986-11-05       Impact factor: 5.157

5.  Chromatin structure and protein binding in the putative regulatory region of the c-myc gene in Burkitt lymphoma.

Authors:  U Siebenlist; L Hennighausen; J Battey; P Leder
Journal:  Cell       Date:  1984-06       Impact factor: 41.582

6.  A long polypyrimidine/polypurine tract induces an altered DNA conformation on the 3' coding region of the adjacent myosin heavy chain gene.

Authors:  J G McCarthy; S M Heywood
Journal:  Nucleic Acids Res       Date:  1987-10-12       Impact factor: 16.971

Review 7.  VEGF-mediated tumour angiogenesis: a new target for cancer therapy.

Authors:  G Martiny-Baron; D Marmé
Journal:  Curr Opin Biotechnol       Date:  1995-12       Impact factor: 9.740

Review 8.  Approaches to characterize protein-DNA interactions in vivo.

Authors:  H P Saluz; J P Jost
Journal:  Crit Rev Eukaryot Gene Expr       Date:  1993       Impact factor: 1.807

9.  Easily unwound DNA sequences and hairpin structures in the Epstein-Barr virus origin of plasmid replication.

Authors:  D L Williams; D Kowalski
Journal:  J Virol       Date:  1993-05       Impact factor: 5.103

10.  Modulation of transcription of the platelet-derived growth factor A-chain gene by a promoter region sensitive to S1 nuclease.

Authors:  Z Wang; X H Lin; Q Q Qiu; T F Deuel
Journal:  J Biol Chem       Date:  1992-08-25       Impact factor: 5.157
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  6 in total

1.  G-quadruplex deconvolution with physiological mimicry enhances primary screening: Optimizing the FRET Melt2 assay.

Authors:  Rhianna K Morgan; Alexandra Maria Psaras; Quinea Lassiter; Kelsey Raymer; Tracy A Brooks
Journal:  Biochim Biophys Acta Gene Regul Mech       Date:  2019-12-28       Impact factor: 4.490

2.  Yin Yang 1 contains G-quadruplex structures in its promoter and 5'-UTR and its expression is modulated by G4 resolvase 1.

Authors:  Weiwei Huang; Philip J Smaldino; Qiang Zhang; Lance D Miller; Paul Cao; Kristin Stadelman; Meimei Wan; Banabihari Giri; Ming Lei; Yoshikuni Nagamine; James P Vaughn; Steven A Akman; Guangchao Sui
Journal:  Nucleic Acids Res       Date:  2011-10-12       Impact factor: 16.971

3.  The effects of DNA supercoiling on G-quadruplex formation.

Authors:  Doreen A T Sekibo; Keith R Fox
Journal:  Nucleic Acids Res       Date:  2017-12-01       Impact factor: 16.971

4.  Possible regulatory roles of promoter g-quadruplexes in cardiac function-related genes - human TnIc as a model.

Authors:  Wenhua Zhou; Kogularamanan Suntharalingam; Nigel J Brand; Paul J R Barton; Ramon Vilar; Liming Ying
Journal:  PLoS One       Date:  2013-01-09       Impact factor: 3.240

5.  Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures.

Authors:  Rhianna K Morgan; Michael M Molnar; Harshul Batra; Bethany Summerford; Randy M Wadkins; Tracy A Brooks
Journal:  J Nucleic Acids       Date:  2018-05-16

Review 6.  Impact of G-Quadruplexes on the Regulation of Genome Integrity, DNA Damage and Repair.

Authors:  Anzhela V Pavlova; Elena A Kubareva; Mayya V Monakhova; Maria I Zvereva; Nina G Dolinnaya
Journal:  Biomolecules       Date:  2021-08-27
  6 in total

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