Amino Acids

, Volume 43, Issue 3, pp 1141–1146 | Cite as

Advances in the study of protein–DNA interaction

Review Article

Abstract

Protein–DNA interaction plays an important role in many biological processes. The classical methods and the novel technologies advanced have been developed for the interaction of protein–DNA. Recent developments of these methods and research achievements have been reviewed in this paper.

Keywords

Protein–DNA interaction Biotechnology EMSA SELEX 

Notes

Conflict of interest

We declare that we have no conflict of interest about this manuscript.

References

  1. Betzig E, Trautman JK, Harris TD, Weiner JS, Kostelak RL (1991) Breaking the diffraction barrier: optical microscopy on a nanometric scale. Science 251(5000):1468–1470. doi: 10.1126/science.251.5000.1468 PubMedCrossRefGoogle Scholar
  2. Binnig G, Rohrer H, Gerber C, Weibel E (1982) Tunneling through a controllable vacuum gap. Appl Phys Lett 40:178–180CrossRefGoogle Scholar
  3. Binnig G, Quate CF, Gerber C (1986) Atomic force microscope. Phys Rev Lett 56(9):930–933PubMedCrossRefGoogle Scholar
  4. Brenowitz M, Senear DF, Shea MA, Ackers GK (1986) Quantitative DNase footprint titration: a method for studying protein–DNA interactions. Meth Enzymol 130:132–181PubMedCrossRefGoogle Scholar
  5. Brenowitz M, Senear DF, Kingston RE (2001) DNase I footprint analysis of protein–DNA binding, Chap. 12, Unit 12–14. In: Ausubel FM et al (eds) Current protocols in molecular biology. doi: 10.1002/0471142727.mb1204s07
  6. Brown D, Brown J, Kang C, Gold L, Allen P (1997) Single-stranded RNA recognition by the bacteriophage T4 translational repressor, regA. J Biol Chem 272(23):14969–14974PubMedCrossRefGoogle Scholar
  7. Buck MJ, Nobel AB, Lieb JD (2005) ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol 6(11):R97. doi: 10.1186/gb-2005-6-11-r97 PubMedCrossRefGoogle Scholar
  8. Carey M, Smale ST (2007) Methylation interference assay. CSH protocols 2007. doi: 10.1101/pdb.prot4812
  9. Connaghan-Jones KD, Moody AD, Bain DL (2008) Quantitative DNase footprint titration: a tool for analyzing the energetics of protein–DNA interactions. Nat Protoc 3(5):900–914. doi: 10.1038/nprot.2008.53 PubMedCrossRefGoogle Scholar
  10. Dahlberg AE, Dingman CW, Peacock AC (1969) Electrophoretic characterization of bacterial polyribosomes in agarose–acrylamide composite gels. J Mol Biol 41(1):139–147PubMedCrossRefGoogle Scholar
  11. Deplancke B, Dupuy D, Vidal M, Walhout AJ (2004) A gateway-compatible yeast one-hybrid system. Genome Res 14(10B):2093–2101. doi: 10.1101/gr.2445504 Google Scholar
  12. Despeyroux D, Walker N, Pearce M, Fisher M, McDonnell M, Bailey SC, Griffiths GD, Watts P (2000) Characterization of ricin heterogeneity by electrospray mass spectrometry, capillary electrophoresis, and resonant mirror. Anal Biochem 279(1):23–36. doi: 10.1006/abio.1999.4423 PubMedCrossRefGoogle Scholar
  13. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346(6287):818–822. doi: 10.1038/346818a0 PubMedCrossRefGoogle Scholar
  14. Feng SY, Ota K, Ito T (2010) A yeast one-hybrid system to screen for methylated DNA-binding proteins. Nucleic Acids Res 38(20):e189. doi: 10.1093/nar/gkq757 PubMedCrossRefGoogle Scholar
  15. Feng H, Beck J, Nassal M, Hu KH (2011) A SELEX-screened aptamer of human hepatitis B virus RNA encapsidation signal suppresses viral replication. PLoS One 6(11):e27862. doi: 10.1371/journal.pone.0027862 PubMedCrossRefGoogle Scholar
  16. Fields S, Song O (1989) A novel genetic system to detect protein–protein interactions. Nature 340(6230):245–246. doi: 10.1038/340245a0 PubMedCrossRefGoogle Scholar
  17. Fullwood MJ, Ruan Y (2009) ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem 107(1):30–39. doi: 10.1002/jcb.22116 PubMedCrossRefGoogle Scholar
  18. Gupta G, Sharma PK, Sikarwar B, Merwyn S, Kaushik S, Boopathi M, Agarwal GS, Singh B (2012) Surface plasmon resonance immunosensor for the detection of Salmonella typhi antibodies in buffer and patient serum. Biosens Bioelectron 36(1):95–102. doi: 10.1016/j.bios.2012.03.046 PubMedCrossRefGoogle Scholar
  19. Hayano T, Yamauchi Y, Asano K, Tsujimura T, Hashimoto S, Isobe T, Takahashi N (2008) Automated SPR-LC-MS/MS system for protein interaction analysis. J Proteome Res 7(9):4183–4190. doi: 10.1021/pr700834n PubMedCrossRefGoogle Scholar
  20. Hellman LM, Fried MG (2007) Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions. Nat Protoc 2(8):1849–1861. doi: 10.1038/nprot.2007.249 PubMedCrossRefGoogle Scholar
  21. Henriksson-Peltola P, Sehlen W, Haggard-Ljungquist E (2007) Determination of the DNA-binding kinetics of three related but heteroimmune bacteriophage repressors using EMSA and SPR analysis. Nucleic Acids Res 35(10):3181–3191. doi: 10.1093/nar/gkm172 PubMedCrossRefGoogle Scholar
  22. Hoa XD, Kirk AG, Tabrizian M (2007) Towards integrated and sensitive surface plasmon resonance biosensors: a review of recent progress. Biosens Bioelectron 23(2):151–160. doi: 10.1016/j.bios.2007.07.001 PubMedCrossRefGoogle Scholar
  23. Horak CE, Snyder M (2002) ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 350:469–483PubMedCrossRefGoogle Scholar
  24. Jahanmir J, Haggar BG, Hayes JB (1992) The scanning probe microscope. Scanning Microsc 6(3):625–660PubMedGoogle Scholar
  25. Khan SH, Farkas K, Kumar R, Ling J (2012) A versatile method to measure the binding to basic proteins by surface plasmon resonance. Anal Biochem 421(2):385–390. doi: 10.1016/j.ab.2011.12.006 PubMedCrossRefGoogle Scholar
  26. Kim SH, Hwang SB, Chung IK, Lee J (2003) Sequence-specific binding to telomeric DNA by CEH-37, a homeodomain protein in the nematode Caenorhabditis elegans. J Biol Chem 278(30):28038–28044. doi: 10.1074/jbc.M302192200 PubMedCrossRefGoogle Scholar
  27. Lane D, Prentki P, Chandler M (1992) Use of gel retardation to analyze protein–nucleic acid interactions. Microbiol Rev 56(4):509–528PubMedGoogle Scholar
  28. Lehming N, Thanos D, Brickman JM, Ma J, Maniatis T, Ptashne M (1994) An HMG-like protein that can switch a transcriptional activator to a repressor. Nature 371(6493):175–179. doi: 10.1038/371175a0 PubMedCrossRefGoogle Scholar
  29. Li JJ, Herskowitz I (1993) Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science 262(5141):1870–1874PubMedCrossRefGoogle Scholar
  30. Ling J, Liao H, Clark R, Wong MS, Lo DD (2008) Structural constraints for the binding of short peptides to claudin-4 revealed by surface plasmon resonance. J Biol Chem 283(45):30585–30595. doi: 10.1074/jbc.M803548200 PubMedCrossRefGoogle Scholar
  31. Liu Y, Dong Y, Jauw J, Linman MJ, Cheng Q (2010) Highly sensitive detection of protein toxins by surface plasmon resonance with biotinylation-based inline atom transfer radical polymerization amplification. Anal Chem 82(9):3679–3685. doi: 10.1021/ac1000114 PubMedCrossRefGoogle Scholar
  32. Matos RG, Barbas A, Arraiano CM (2010) Comparison of EMSA and SPR for the characterization of RNA–RNase II complexes. Protein J 29(6):394–397. doi: 10.1007/s10930-010-9265-1 PubMedCrossRefGoogle Scholar
  33. Mueller PR, Wold B (1989) In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246(4931):780–786PubMedCrossRefGoogle Scholar
  34. Muller J, Isermann B, Ducker C, Salehi M, Meyer M, Friedrich M, Madhusudhan T, Oldenburg J, Mayer G, Potzsch B (2009) An exosite-specific ssDNA aptamer inhibits the anticoagulant functions of activated protein C and enhances inhibition by protein C inhibitor. Chem Biol 16(4):442–451. doi: 10.1016/j.chembiol.2009.03.007 PubMedCrossRefGoogle Scholar
  35. Murphy MB, Fuller ST, Richardson PM, Doyle SA (2003) An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res 31(18):e110PubMedCrossRefGoogle Scholar
  36. Nagaraj VH, O’Flanagan RA, Sengupta AM (2008) Better estimation of protein–DNA interaction parameters improve prediction of functional sites. BMC Biotechnol 8:94. doi: 10.1186/1472-6750-8-94 PubMedCrossRefGoogle Scholar
  37. Okorafor M, Clayton GM (2011) Modeling scanning probe microscope lateral dynamics using the probe-surface interaction signal. Rev Sci Instrum 82(3):033707. doi: 10.1063/1.3548835 PubMedCrossRefGoogle Scholar
  38. Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25(3):99–104PubMedCrossRefGoogle Scholar
  39. Pan Y, Wang L, He X, Tian Y, Liu G, Tan H (2011) SabR enhances nikkomycin production via regulating the transcriptional level of sanG, a pathway-specific regulatory gene in Streptomyces ansochromogenes. BMC Microbiol 11:164. doi: 10.1186/1471-2180-11-164 PubMedCrossRefGoogle Scholar
  40. Pollet J, Delport F, Janssen KP, Jans K, Maes G, Pfeiffer H, Wevers M, Lammertyn J (2009) Fiber optic SPR biosensing of DNA hybridization and DNA–protein interactions. Biosens Bioelectron 25(4):864–869. doi: 10.1016/j.bios.2009.08.045 PubMedCrossRefGoogle Scholar
  41. Reimer JJ, Turck F (2010) Genome-wide mapping of protein–DNA interaction by chromatin immunoprecipitation and DNA microarray hybridization (ChIP-chip). Part A: ChIP-chip molecular methods. Methods Mol Biol (Clifton, NJ) 631:139–160. doi: 10.1007/978-1-60761-646-7_12 Google Scholar
  42. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4(8):651–657. doi: 10.1038/nmeth1068 PubMedCrossRefGoogle Scholar
  43. Schaup HW, Green M, Kurland CG (1970) Molecular interactions of ribosomal components. I. Identification of RNA binding sites for individual 30S ribosomal proteins. Mol Gen Genet MGG 109(3):193–205CrossRefGoogle Scholar
  44. Sengupta AM, Djordjevic M, Shraiman BI (2002) Specificity and robustness in transcription control networks. Proc Natl Acad Sci USA 99(4):2072–2077. doi: 10.1073/pnas.022388499 PubMedCrossRefGoogle Scholar
  45. Smith AJP, Humphries SE (2009) Characterization of DNA-binding proteins using multiplexed competitor EMSA. J Mol Biol 385(3):714–717. doi: 10.1016/j.jmb.2008.11.035 PubMedCrossRefGoogle Scholar
  46. Stenger D, Gruissem W, Baginsky S (2004) Mass spectrometric identification of RNA binding proteins from dried EMSA gels. J Proteome Res 3(3):662–664PubMedCrossRefGoogle Scholar
  47. Stormo GD, Fields DS (1998) Specificity, free energy and information content in protein–DNA interactions. Trends Biochem Sci 23(3):109–113PubMedCrossRefGoogle Scholar
  48. Strong CL, Lanchy JM, Lodmell JS (2011) Viral SELEX reveals individual and cooperative roles of the C-box and G-box in HIV-2 replication. RNA 17(7):1307–1320. doi: 10.1261/rna.2564311 PubMedCrossRefGoogle Scholar
  49. Surina ER, Morozkina EV, Marchenko EV, Ter-Avanesian MD, Benevolenskii SV (2009) Selection of DNA aptamers, specifically interacting with fibrillar form of the yeast Sup35 protein. Mol Biol 43(4):682–688CrossRefGoogle Scholar
  50. Szabo A, Stolz L, Granzow R (1995) Surface plasmon resonance and its use in biomolecular interaction analysis (BIA). Curr Opin Struct Biol 5(5):699–705PubMedCrossRefGoogle Scholar
  51. Tong Y, Falk J (2009) Genome-wide analysis for protein–DNA interaction: ChIP-chip. Methods Mol Biol (Clifton, NJ) 590:235–251. doi: 10.1007/978-1-60327-378-7_15 Google Scholar
  52. Truax AD, Greer SF (2012) ChIP and Re-ChIP assays: investigating interactions between regulatory proteins, histone modifications, and the DNA sequences to which they bind. Methods Mol Biol (Clifton, NJ) 809:175–188. doi: 10.1007/978-1-61779-376-9_12
  53. Wilson S, Howell S (2002) High-throughput screening in the diagnostics industry. Biochem Soc Trans 30(4):794–797. doi: 10.1042/ PubMedCrossRefGoogle Scholar
  54. Won J, Kim TK (2006) Histone modifications and transcription factor binding on chromatin ChIP-PCR assays. Methods Mol Biol (Clifton, NJ) 325:273–283Google Scholar
  55. Wu S, Wang J, Zhao W, Pounds S, Cheng C (2010) ChIP-PaM: an algorithm to identify protein–DNA interaction using ChIP-Seq data. Theor Biol Med Model 7:18. doi: 10.1186/1742-4682-7-18 PubMedCrossRefGoogle Scholar
  56. Xia N, Liu L, Yi X, Wang J (2009) Studies of interaction of tumor suppressor p53 with apo-MT using surface plasmon resonance. Anal Bioanal Chem 395(8):2569–2575. doi: 10.1007/s00216-009-3174-1 PubMedCrossRefGoogle Scholar
  57. Yan J, Burgess SM (2012) Using a yeast inverse one-hybrid system to identify functional binding sites of transcription factors. Methods Mol Biol (Clifton, NJ) 786:275–290. doi: 10.1007/978-1-61779-292-2_17
  58. Zhang Y, Zou Q (2012) High-speed force load in force measurement in liquid using scanning probe microscope. Rev Sci Instrum 83(1):013707. doi: 10.1063/1.3678320 PubMedCrossRefGoogle Scholar
  59. Zhang JF, Ma L, Liu X, Lu YT (2004) Using capillary electrophoresis with laser-induced fluorescence to study the interaction of green fluorescent protein-labeled calmodulin with Ca2+- and calmodulin-binding protein. J Chromatogr B Anal Technol Biomed Life Sci 804(2):413–420. doi: 10.1016/j.jchromb.2004.01.054 CrossRefGoogle Scholar
  60. Zhao Y, Granas D, Stormo GD (2009) Inferring binding energies from selected binding sites. PLoS Comput Biol 5(12):e1000590. doi: 10.1371/journal.pcbi.1000590 PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Department of Biological Engineering and Key Laboratory of Systems Bioengineering of the Ministry of EducationSchool of Chemical Engineering and Technology, Tianjin UniversityTianjinChina

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