A force-based, parallel assay for the quantification of protein-DNA interactions

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Limmer, Katja ^a,b   Pippig, Diana A ^a   Aschenbrenner, Daniela ^a   Gaub, Hermann E ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b Munich Center for Integrated Protein Science   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ZINC FINGER PROTEIN;

ARTICLE; ASSAY; BASE PAIRING; BINDING AFFINITY; CONTROLLED STUDY; DNA SEQUENCE; DOUBLE STRANDED DNA BREAK; FORCE BASED ASSAY; MOLECULAR FORCE ASSAY; MOLECULAR INTERACTION; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS; SPECTROSCOPY;

BINDING SITES; DNA; DNA-BINDING PROTEINS; HIGH-THROUGHPUT SCREENING ASSAYS; PROTEIN BINDING; TRANSCRIPTION FACTORS; ZINC FINGERS;

EID: 84897893577     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0089626     Document Type: Article

References (35)

1. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science 324: 1720-1723.
2. Tanay A (2006) Extensive low-affinity transcriptional interactions in the yeast genome. Genome Res 16: 962-972.
3. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535-540. (Pubitemid 351186263)
4. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309. (Pubitemid 32041573)
5. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538. (Pubitemid 32144361)
6. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
7. Bulyk ML, Huang X, Choo Y, Church GM (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sci U S A 98: 7158-7163. (Pubitemid 32567919)
8. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat Genet 36: 1331-1339. (Pubitemid 39577944)
9. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat Biotechnol 24: 1429-1435. (Pubitemid 44722107)
10. Berger MF, Bulyk ML (2009) Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc 4: 393-411.
11. Fordyce PM, Gerber D, Tran D, Zheng J, Li H, et al. (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28: 970-975.
12. Nutiu R, Friedman RC, Luo S, Khrebtukova I, Silva D, et al. (2011) Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol 29: 659-664.
13. Stormo GD, Zhao Y (2010) Determining the specificity of protein-DNA interactions. Nat Rev Genet 11: 751-760.
14. Koch SJ, Shundrovsky A, Jantzen BC, Wang MD (2002) Probing protein-DNA Interactions by Unzipping a Single DNA Double Helix. Biophysical Journal 83: 1098-1105. (Pubitemid 34803640)
15. Bartels FW, Baumgarth B, Anselmetti D, Ros R, Becker A (2003) Specific binding of the regulatory protein ExpG to promoter regions of the galactoglucan biosynthesis gene cluster of Sinorhizobium meliloti - a combined molecular biology and force spectroscopy investigation. Journal of Structural Biology 143: 145-152. (Pubitemid 37102962)
16. Kuhner F, Costa LT, Bisch PM, Thalhammer S, Heckl WM, et al. (2004) LexA-DNA bond strength by single molecule force spectroscopy. Biophys J 87: 2683-2690.
17. Bizzarri AR, Cannistraro S (2010) The application of atomic force spectroscopy to the study of biological complexes undergoing a biorecognition process. Chem Soc Rev 39: 734-749.
18. Moy VT, Florin EL, Gaub HE (1994) Intermolecular forces and energies between ligands and receptors. Science 266: 257-259. (Pubitemid 24343509)
19. Albrecht C, Blank K, Lalic-Multhaler M, Hirler S, Mai T, et al. (2003) DNA: a programmable force sensor. Science 301: 367-370. (Pubitemid 36877071)
20. Blank K, Mai T, Gilbert I, Schiffmann S, Rankl J, et al. (2003) A force-based protein biochip. Proc Natl Acad Sci U S A 100: 11356-11360. (Pubitemid 37205939)
21. Pavletich NP, Pabo CO (1991) Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 A. Science 252: 809-817. (Pubitemid 121000517)
22. Kim J-S, Pabo CO (1998) Getting a handhold on DNA: Design of poly-zinc finger proteins with femtomolar dissociation constant. Proc Natl Acad Sci U S A 95: 2812-2817. (Pubitemid 28135811)
23. Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO (1996) Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions. Structure 4: 1171-1180. (Pubitemid 27005385)
24. Greisman HA, Pabo CO (1997) A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science 275: 657-661. (Pubitemid 27061331)
25. Carrion-Vazquez M, Oberhauser AF, Fowler SB, Marszalek PE, Broedel SE, et al. (1999) Mechanical and chemical unfolding of a single protein: a comparison. Proc Natl Acad Sci U S A 96: 3694-3699. (Pubitemid 29168972)
26. Ho D, Dose C, Albrecht CH, Severin P, Falter K, et al. (2009) Quantitative detection of small molecule/DNA complexes employing a force-based and label-free DNA-microarray. Biophys J 96: 4661-4671.
27. Severin PM, Ho D, Gaub HE (2011) A high throughput molecular force assay for protein-DNA interactions. Lab Chip 11: 856-862.
28. Ho D, Falter K, Severin P, Gaub HE (2009) DNA as a force sensor in an aptamer-based biochip for adenosine. Anal Chem 81: 3159-3164.
29. Limmer K, Aschenbrenner D, Gaub HE (2013) Sequence-specific inhibition of Dicer measured with a force-based microarray for RNA ligands. Nucleic Acids Res 41: e69.
30. Severin PM, Gaub HE (2012) DNA-Protein Binding Force Chip. Small.
31. Otten M, Wolf P, Gaub HE (2013) Protein-DNA force assay in a microfluidic format. Lab Chip 13: 4198-4204.
32. Yin J, Lin AJ, Golan DE, Walsh CT (2006) Site-specific protein labeling by Sfp phosphopantetheinyl transferase. Nat Protoc 1: 280-285.
33. Pedelacq JD, Cabantous S, Tran T, Terwilliger TC, Waldo GS (2006) Engineering and characterization of a superfolder green fluorescent protein. Nat Biotechnol 24: 79-88. (Pubitemid 43083170)
34. Wong LS, Thirlway J, Micklefield J (2008) Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase. J Am Chem Soc 130: 12456-12464.
35. Wiegand G, Neumaier KR, Sackmann E (1998) Microinterferometry: three-dimensional reconstruction of surface microtopography for thin-film and wetting studies by interference contrast microscopy (RICM). Appl Opt 37: 6892-6905. (Pubitemid 128658856)