Binding properties of peptidic affinity ligands for plasmid DNA capture and detection

AIChE Journal

Volumn 55, Issue 2, 2009, Pages 505-515

  Han, Ying ^a   Gras, Sally ^b   Forde, Gareth M ^a  

^a MONASH UNIVERSITY   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Binding kinetics; Peptide ligand design; Protein nucleic acid interactions; Surface plasmon resonance; Synthetic peptide

Indexed keywords

AFFINITY LIGANDS; AFFINITY PEPTIDES; BINDING CHARACTERISTICS; BINDING KINETICS; BINDING PROPERTIES; DISSOCIATION CONSTANTS; DISSOCIATION RATES; DNA BINDING DOMAINS; EQUILIBRIUM DISSOCIATION CONSTANTS; LAC OPERONS; LAC REPRESSORS; PEPTIDE LIGAND DESIGN; PEPTIDE SEQUENCES; PLASMID DNAS; PROTEIN-NUCLEIC ACID INTERACTIONS; SYNTHETIC PEPTIDE;

AFFINITY CHROMATOGRAPHY; BINDING ENERGY; BIOSENSORS; CHROMATOGRAPHIC ANALYSIS; DISSOCIATION; DNA; EQUILIBRIUM CONSTANTS; ESCHERICHIA COLI; GENES; LIGANDS; NUCLEIC ACIDS; PEPTIDES; PLASMONS; SURFACE PLASMON RESONANCE;

AMINES;

ESCHERICHIA COLI;

EID: 63449083999     PISSN: 00011541     EISSN: 15475905     Source Type: Journal    
DOI: 10.1002/aic.11690     Document Type: Article

References (61)

1. Boniface JJ, Davis MM. The kinetics of binding of peptide/MHC complexes to T-cell receptors: application of surface plasmon resonance to a low -affinity measurement. Methods: A Companion to Methods in Enzymology. 1994;6:168-176.
2. Bouchie A. Box 1 FDA, NCI collaborate to identify biomarkers for cancer trials. Nat Biotechnol. 2003;21:718.
3. Danquah MK, Forde GM. Rapid therapeutic plasmid DNA isolation: addressing the looming vaccine crisis. BIOFORUM EUROPE, ISSN 1611-597X,10:24-27,2006.
4. Diogo MM, Ribeiro SC, Queiroz JA, Monteiro GA, Tordo N, Perrin P, Prazeres DM. Production, purification and analysis of an experimental DNA vaccine against rabies. J Gene Med. 2001;3:577-584.
5. Forde GM. Rapid-response vaccines-does DNA offer a solution? Nat Biotechnol. 2005;23:1059-1062.
6. Fukumoto S, Tamaki Y, Okamura M, Bannai H, Yokoyama N, Suzuki T, Igarashi I, Suzuki H, Xuan X. Prime-boost immunization with DNA followed by a recombinant vaccinia virus expressing P50 induced protective immunity against Babesia gibsoni infection in dogs. Vaccine. 2007;25:1334-1341.
7. Johansen P, Raynaud C, Yang M. Anti-mycobacterial immunity induced by a single injection of M-leprae Hsp65-encoding plasmid DNA in biodegradable microparticles. Immunol Lett. 2003;90:81-85.
8. Michel ML, Davis HL, Schleef M. DNA-mediated immunization to the hepatitis-B surface-antigen in mice-aspects of the humoral response mimic hepatitis-B viral infection in humans. Proc Natl Acad Sci USA. 1995;92:5307-5311.
9. Wolff JA, Malone RW, Williams P, Chong W, Acsadi G, Jani A, Felgner PL. Direct gene transfer into mouse muscle in vivo. Science. 1990;247:1465-1468.
10. Rogers KR. Recent advances in biosensor techniques for environmental monitoring. Anal Chim Acta. 2006;568:222-231.
11. Gilbert W, Müller HB. The lac operator is DNA. Proc Natl Acad Sci USA. 1967;58:2415-2421.
12. Sadler JR, Sasmor H, Betz JL. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc Natl Acad Sci USA. 1983;80:6785-6789.
13. Oehler S, Eismann ER, Krämer H, Müller-Hill B. The three operators of the lac operon cooperate in repression. EMBO J. 1990;9:973-979.
14. Barker A, Fickert R. Operator search by mutant Lac repressors. J Mol Biol. 1998;278:549-558.
15. Barkley MD, Bourgeois S. Repressor Recognition of Operator and Effectors. NY: Cold spring Harbor Laboratory Press, 1980.
16. Bell CE, Lewis M. The Lac repressor: a second generation of structural and functional studies. Curr Opin Struct Biol. 2001;11:19-25.
17. Chakerian AE, Matthew KS. Effect of lac repressor oligomerization on regulatory outcome. Mol Microbiol. 1992;6:963-968.
18. Kisters-Woike B, Lehming N. A model of the lac repressor-operator complex based on physical and genetic data. Eur J Biochem. 1991;198:411-419.
19. Markiewicz P, Kleina LG. Genetic studies of the lac repressor XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence. J Mol Biol. 1994;240:421-433.
20. Steitz TA. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys. 1990;23:205-280.
21. Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brennan RG, Ponzy L. Crystal structure of the lactose operon repressor and its complex with DNA and inducer. Science. 1996; 271:1247-1254.
22. Kleina LG, Miller JH. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J Mol Biol. 1990;212:295-318.
23. David LN, Michael MC. Principles of Biochemistry. New York: W. H. Freeman and Company, 2005.
24. Fried MG, Stickle DF, Smirnakis KV, Adams C, MacDonald D, Lu P. Role of hydration in the binding of lac repressor to DNA. J Biol Chem. 2002;277:50676-50682.
25. Forde GM, Ghose S, Slater NKH, Hine AV, Darby AJ, Hitchcock AG. LacO-LacI interaction in affinity adsorption of plasmid DNA. Biotechnol Bioeng. 2006;95:67-75.
26. Ghose S, Forde GM, Slater NKH. Affinity adsorption of plasmid DNA. Biotechnol Prog. 2004;20:841-850.
27. Clonis YD. Affinity chromatography matures as bioinformatics and combinatorial tools develop. J Chromatogr A. 2006;1101:1-24.
28. Kumar A, Galaev IY, Mattiasson B. Purification of Lac repressor protein using polymer displacement and immobilization of the protein. Bioseparation. 1999;8:307-316.
29. Hasche A, Voβ C. Immobilisation of a repressor protein for binding of plasmid DNA. J Chromatogr A. 2005;1080:76-82.
30. Lundeberg J, Wahlberg J, Uhlen M. Affinity purification of specific DNA fragments using a lac repressor fusion protein. Genet Anal Tech Appl. 1990;7:47-52.
31. Schluep T, Cooney CL. Purification of plasmid DNA by triplex affinity interactions. Nucl Acids Res. 1998;26:4524-4528.
32. Darby RAJ, Hine AV. LacI-mediated sequence-specific affinity purification of plasmid DNA for therapeutic applications. The FASEB J. 2005;19:801-803.
33. Hu MC, Davidson N. Targeting the Escherichia coli lac repressor to the mammalian cell nucleus. Gene. 1991;99:141-150.
34. Ferreira GNM, Monteiro GA, Prazeres DMF, Cabral JMS. Down-stream processing of plasmid DNA for gene therapy and DNA vaccine applications. Trends Biotechnol. 2000;18:380-388.
35. Stadler J, Lemmens R, Nyhammar T. Plasmid DNA purification. J Gene Med. 2004;6:54-66.
36. Lowe CR, Lowe AR, Gupta G. New developments in affinity chromatography with potential application in the production of biopharmaceuticals. J Biochem Biophys Methods. 2001;49:561-574.
37. Majka J, Speck C. Analysis of protein-DNA interactions using sur-face plasmon resonance. Adv Biochem Eng Biotechnol. 2007;104: 13-36.
38. Pattnaik P. Surface plasmon resonance - applications in understanding receptor-ligand interaction Appl Biochem Biotechnol. 2005;126: 79-92.
39. Schubert F, Zettl H, Hafner W. Comparative thermodynamic analysis of DNA-protein interactions using surface plasmon resonance and fluorescence correlation spectroscopy. Biochemistry. 2003;42: 10288-10294.
40. Tweedie JW, Stowell KM. Quantification of DNA by agarose gel electrophoresis and analysis of the topoisomers of plasmid and M13 DNA following treatment with a restriction endonuclease or DNA topoisomerase I. Biochem Mol Biol Educ. 2005;33:28-33.
41. Ciolkowski ML, Fang MM, Lund ME. A surface plasmon resonance method for detecting multiple modes of DNA-ligand interactions. J Pharm Biomed Anal. 2000;22:1037-1045.
42. Rich RL, Myska DG. Advances in surface plasmon resonance biosensor analysis. Curr Opin Biotechnol. 2000;11:54-61.
43. Adamczyk M, Moore JA, Yu Z. Application of surface plasmon resonance toward studies of low molecular weight antigen-antibody binding interactions. Methods. 2000;20:319-328.
44. Karlsson R, Falt A. Experimental design for kinetic analysis of protein-protein interaction with surface plasmid resonance biosensors. J Immunol Methods. 1997;200:121-133.
45. Katsamba PS, Park S, Laird-Offringa IA. Kinetics studies of RNA- protein interactions using surface plasmon resonance. Methods. 2002;26:95-104.
46. Pabbisetty KB, Yue X. Kinetic analysis of the binding of monomeric and dimeric ephrins to Eph receptors: Correlation to function in a growth cone collapse assay. Protein Sci. 2007;16:355-361.
47. Wilkinson CRM, Seeger M, Hartmann-Petersen R, Stone M, Wallace M, Semple C, Gordon C. Proteins containing the UBA domain are able to bind to multi-ubiquitin chains. Nat Cell Biol. 2001;3: 939-943.
48. Winter RB, von Hippel PH. Diffusion-driven mechanism of protein translocation on nucleic acids. II. The E. coil repressor-operator interaction: equilibrium measurements. Biochemistry. 1981;20: 6948-6960.
49. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Structure and flexibility adaptation in nonspecific and specific protein-DNA complexs. Science. 2004;305:386-389.
50. Lauria A, Montalbano A, Barraja P, Dattolo G, Almerico AM. DNA minor groove binders: an overview on molecular modeling and QSAR approaches Curr Med Chem. 2007;14:2136-2160.
51. Normanno D, Vanzi F, Pavone FS. Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping. Nucl Acids Res. 2008;36:2505-2513.
52. Arrondo JLR, Muga A, Castresana J, Goni FM. Quantitative studies of the structure of proteins in solution by Fourier-transform infrared spectroscopy. Prog Biophys Mol Biol. 1993;59:23-56.
53. Haris PI, Chapman D. Does Fourier-transform infrared spectroscopy provide useful information on protein structures? Trends Biochem Sci. 1992;17:328-333.
54. Goormaghtigh R, Caulaux V, Ruysschart JM. Determination of soluble and membrane protein structure by Fourier transform infrared spectroscopy, III. Secondary structures. Subcell Biochem. 1994;23:329-362.
55. Han Y, Forde GM. Single step purification of plasmid DNA using peptide ligand affinity chromatography. J Chromatogr B. (available online doi:10.1016/jchromb.2008.08.025).
56. Branovic K, Forcic D, Ivancic J, Strancar A, Barut M, Kosutic Gulija T, Zgorelec R, Mazuran R. Application of short monolithic columns for fast purification of plasmid DNA. J Chromatogr B. 2004;801:331-337.
57. Danquah MK, Forde GM. The suitability of DEAE-Cl active groups on customized poly(GMA-co-EDMA) continous stationary phase for fast enzyme-free isolation of plasmid DNA. J Chromatogr B. 2007;853:38-46.
58. Danquah MK, Ho J, Forde GM. Performance of R-N(R')-)-R" functionalised poly(glycidyl methacrylate-co-ethylene glycol dimethacry-late) monolithic sorbent for plasmid DNA adsorption. J Separation Sci. 2007;30:2841-2850.
59. Urthaler J, Schlegl R, Podgornik A, Strancar A, Jungbauer A, Necina R. Application of monoliths for plasmid DNA purification: development and transfer to production. J Chromatogr A. 2005; 1065:93-106.
60. Ranbaxy. Jupiter Bioscience Enter into Marketing Tie-Up. New Delhi, India: The Economic Times.
61. Morreale G, Lee EG, Jones DB, Middelberg APJ. Bioprocess-centered molecular design (BMD) for the efficient production of an interfacially active peptide. Biotechnol Bioeng. 2004;87:912-923.