Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis

Analytical Biochemistry

Volumn 439, Issue 2, 2013, Pages 99-101

  He, Gaofei ^a   Vasilieva, Elena ^a   Bashkin, James K ^a   Dupureur, Cynthia M ^a  

^a UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

Capillary electrophoresis; DNA; Footprinting; Ligand DNA interactions; Sequencing

Indexed keywords

CAPILLARY ELECTROPHORESIS; DNA; INDEXING (OF INFORMATION); LIGANDS; MAPPING;

CLEAVAGE PRODUCTS; CLEAVAGE SITES; FOOTPRINTING; HYDROXYL RADICAL FOOTPRINTING; LENGTH DEPENDENCE; LIGAND-DNA INTERACTIONS; SEQUENCING;

GENE ENCODING;

DEOXYRIBONUCLEASE I; HYDROXYL RADICAL; LIGAND;

ARTICLE; BINDING AFFINITY; CAPILLARY ELECTROPHORESIS; CHEMICAL MODIFICATION; DNA BINDING; DNA CLEAVAGE; DNA FOOTPRINTING; DNA SEQUENCE; GENE INTERACTION; GENE MAPPING; GENOME; HUMAN PAPILLOMAVIRUS TYPE 16; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; SANGER DIDEOXY CHAIN TERMINATION;

EID: 84879211294     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2013.04.011     Document Type: Article

References (21)

1. M. Brenowitz, D.F. Senear, M.A. Shea, G.K. Ackers, Quantitative DNase footprint titration: a method for studying protein-DNA interactions, Methods Enzymol. 130 (1986) 132-181.
2. J.W. Trauger, P.B. Dervan, Footprinting methods for analysis of pyrrole-imidazole polyamide/DNA complexes, Methods Enzymol. 340 (2001) 450-466. (Pubitemid 32751714)
3. P. Schultz, J. Taylor, P. Dervan, Design and synthesis of a sequence-specific DNA cleaving molecule, (distamycin-EDTA)iron(II), J. Am. Chem. Soc. 104 (1982) 6861-6863. (Pubitemid 13182925)
4. W.S. Wade, M. Mrksich, P.B. Dervan, Binding affinities of synthetic peptides, pyridine-2-carboxamidonetropsin and 1-methylimidazole-2- carboxamidonetropsin, that form 2:1 complexes in the minor groove of double-helical DNA, Biochemistry 32 (1993) 11385-11389. (Pubitemid 23332050)
5. K.D. Leslie, K.R. Fox, Interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments containing isolated ligand binding sites, Biochemistry 41 (2002) 3484-3497. (Pubitemid 34218138)
6. J.K. Bashkin, K. Aston, J.P. Ramos, K.J. Koeller, R. Nanjunda, G. He, C.M. Dupureur, W.D. Wilson, Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-Alanine, Biochimie 95 (2013) 271-279.
7. Y. Liu, Y. Chai, A. Kumar, R. Tidwell, D. Boykin, W.D. Wilson, Designed compounds for recognition of 10 base pairs of DNA with two AT binding sites, J. Am. Chem. Soc. 134 (2012) 5290-5299.
8. J. Stubbe, J. Kozarich, W. Wu, D. Vanderwall, Bleomycins: a structural model for specificity, binding, and double strand cleavage, Acc. Chem. Res. 29 (1996) 322-330. (Pubitemid 126453207)
9. K. Fox, DNaseI Footprinting, vol. 90, Humana Press, Totowa, NJ, 1997. pp. 1-22.
10. S.C. Parker, L. Hansen, H.O. Abaan, T.D. Tullius, E.H. Margulies, Local DNA topography correlates with functional noncoding regions of the human genome, Science 324 (2009) 389-392.
11. M. Hancock, E.A. Shephard, Detection of regulatory polymorphisms: Highthroughput capillary DNase I footprinting, Methods Mol. Biol. 987 (2013) 269-282.
12. S. Mitra, I.V. Shcherbakova, R.B. Altman, M. Brenowitz, A. Laederach, Highthroughput single-nucleotide structural mapping by capillary automated footprinting analysis, Nucleic Acids Res. 36 (2008) e63.
13. O. Tu, T. Knott, M. Marsh, K. Bechtol, D. Harris, D. Barker, J. Bashkin, The influence of fluorescent dye structure on the electrophoretic mobility of endlabeled DNA, Nucleic Acids Res. 26 (1998) 2797-2802. (Pubitemid 28297398)
14. M. Hahn, J. Wilhelm, A. Pingoud, Influence of fluorophor dye labels on the migration behavior of polymerase chain reaction-Amplified short tandem repeats during denaturing capillary electrophoresis, Electrophoresis 22 (2001) 2691-2700. (Pubitemid 32798933)
15. M. Marsh, O. Tu, V. Dolnik, D. Roach, N. Solomon, K. Bechtol, P. Smietana, L. Wang, X. Li, P. Cartwright, A. Marks, D. Barker, D. Harris, J. Bashkin, Highthroughput DNA sequencing on a capillary array electrophoresis system, J. Capillary Electrophor. 4 (1997) 83-89.
16. F. Sanger, S. Nicklen, A.R. Coulson, DNA sequencing with chain-Terminating inhibitors, Proc. Natl. Acad. Sci. USA 74 (1977) 5463-5467.
17. S. Basak, V. Nagaraja, A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes, Nucleic Acids Res. 29 (2001) e105.
18. R.P. Hertzberg, P.B. Dervan, Cleavage of DNA with methidiumpropyl-EDTA- iron(II): reaction conditions and product analyses, Biochemistry 23 (1984) 3934-3945.
19. B. Balasubramanian, W.K. Pogozelski, T.D. Tullius, DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone, Proc. Natl. Acad. Sci. USA 95 (1998) 9738-9743. (Pubitemid 28415239)
20. S.S. Jain, T.D. Tullius, Footprinting protein-DNA complexes using the hydroxyl radical, Nat. Protoc. 3 (2008) 1092-1100. (Pubitemid 351818696)
21. A.M. Maxam, W. Gilbert, Sequencing end-labeled DNA with base-specific chemical cleavages, Methods Enzymol. 65 (1980) 499-560.