Biophysical characterization of DNA and RNA aptamer interactions with hen egg lysozyme

International Journal of Biological Macromolecules

Volumn 48, Issue 3, 2011, Pages 392-397

  Potty, Ajish S R ^a,d   Kourentzi, Katerina ^a   Fang, Han ^b   Schuck, Peter ^c   Willson, Richard C ^a  

^a UNIVERSITY OF HOUSTON   (United States)

^b University of Houston   (United States)

^c NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING   (United States)

^d MILLIPORE CORPORATION   (United States)

Author keywords

Aptamers; Fluorescence anisotropy; Hen egg white lysozyme; Isothermal titration calorimetry

Indexed keywords

APTAMER; CYTOCHROME C; DNA APTAMER; LYSOZYME; RNA APTAMER; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

ANISOTROPY; ARTICLE; BINDING AFFINITY; BIOPHYSICS; CONTROLLED STUDY; EGG; EMISSION ANISOTROPY; ENTHALPY; ENTROPY; ENZYME SPECIFICITY; IONIC STRENGTH; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; MOLECULAR RECOGNITION; PH; PROTEIN DNA BINDING; PROTEIN RNA BINDING; TEMPERATURE DEPENDENCE; ULTRACENTRIFUGATION;

EID: 79952101633     PISSN: 01418130     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijbiomac.2010.12.007     Document Type: Article

References (40)

1. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
2. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-510.
3. Ellington A.D., Szostak J.W. Selection in vitro of single-stranded DNA molecules that fold into specific ligand-binding structures. Nature 1992, 355:850-852.
4. Davies D.R., Cohen G.H. Interactions of protein antigens with antibodies. Proc. Natl. Acad. Sci. USA 1996, 93:7-12.
5. Wibbenmeyer J.A., Schuck P., Smith-Gill S.J., Willson R.C. Salt links dominate affinity of antibody HyHEL-5 for lysozyme through enthalpic contributions. J. Biol. Chem. 1999, 274:26838-26842.
6. Xavier K.A., Willson R.C. Association and dissociation kinetics of anti-hen egg lysozyme monoclonal antibodies HyHEL-5 and HyHEL-10. Biophys. J. 1998, 74:2036-2045.
7. Shick K.A., Xavier K.A., Rajpal A., Smith-Gill S.J., Willson R.C. Association of the anti-hen egg lysozyme antibody HyHEL-5 with avian species variant and mutant lysozymes. Biochim. Biophys. Acta 1997, 1340:205-214.
8. Hibbits K.A., Gill D.S., Willson R.C. Isothermal titration calorimetric study of the association of hen egg lysozyme and the anti-lysozyme antibody HyHEL-5. Biochemistry 1994, 33:3584-3590.
9. Sinha N., Mohan S., Lipschultz C.A., Smith-Gill S.J. Differences in electrostatic properties at antibody-antigen binding sites: implications for specificity and cross-reactivity. Biophys. J. 2002, 83:2946-2968.
10. Kawde A.-N., Rodriguez M.C., Lee T.M.H., Wang J. Label-free bioelectronic detection of aptamer-protein interactions. Electrochem. Commun. 2005, 7:537-540.
11. Cheng A.K.H., Ge B., Yu H.-Z. Aptamer-based biosensors for label-free voltammetric detection of lysozyme. Anal. Chem. 2007, 79:5158-5164.
12. Potty A.S., Kourentzi K., Fang H., Jackson G.W., Zhang X., Legge G.B., Willson R.C. Biophysical characterization of DNA aptamer interactions with vascular endothelial growth factor. Biopolymers 2009, 91:145-156.
13. Cox J.C., Ellington A.D. Automated selection of anti-Protein aptamers. Bioorg. Med. Chem. 2001, 9:2525-2531.
14. Kirby R., Cho E.J., Gehrke B., Bayer T., Park Y.S., Neikirk D.P., McDevitt J.T., Ellington A.D. Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal. Chem. 2004, 76:4066-4075.
15. Canfield R.E. The amino acid sequence of egg white lysozyme. J. Biol. Chem. 1963, 238:2698-2707.
16. Wetter L.R., Deutsch H.F. Immunological studies on egg white proteins. IV. Immunochemical and physical studies of lysozyme. J. Biol. Chem. 1951, 192:237-242.
17. Titolo S., Welchner E., White P.W., Archambault J. Characterization of the DNA-binding properties of the origin-binding domain of simian virus 40 large T antigen by fluorescence anisotropy. J. Virol. 2003, 77:5512-5518.
18. Balbo A., Minor K.H., Velikovsky C.A., Mariuzza R.A., Peterson C.B., Schuck P. Studying multiprotein complexes by multisignal sedimentation velocity analytical ultracentrifugation. Proc. Natl. Acad. Sci. USA 2005, 102:81-86.
19. Record M.T., Lohman T.M., De Haseth P. Ion effects on ligand-nucleic acid interactions. J. Mol. Biol. 1976, 107:145-158.
20. Steinrauf L.K., Shiuan D., Yang W.J., Chiang M.Y. Lysozyme association with nucleic acids. Biochem. Biophys. Res. Commun. 1999, 266:366-370.
21. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.
22. Law M.J., Linde M.E., Chambers E.J., Oubridge C., Katsamba P.S., Nilsson L., Haworth I.S., Laird-Offringa I.A. The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res. 2006, 34:275-285.
23. Tinoco I., Bustamante C. How RNA Folds. J. Mol. Biol. 1999, 293:271-281.
24. SantaLucia J., Hicks D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 2004, 33:415-440.
25. Tan Z.-J., Chen S.-J. Nucleic acid helix stability: effects of salt concentration, cation valence and size, and chain length. Biophys. J. 2006, 90:1175-1190.
26. Girardot M., Gareil P., Varenne A. Interaction study of a lysozyme-binding aptamer with mono- and divalent cations by ACE. Electrophoresis 2010, 31:546-555.
27. Ahmad R., Arakawa H., Tajmir-Riahi H.A. A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: major and minor grooves bindings. Biophys. J. 2003, 84:2460-2466.
28. Zhai G., Iskandar M., Barilla K., Romaniuk P.J. Characterization of RNA aptamer binding by the Wilms' tumor suppressor protein WT1. Biochemistry 2001, 40:2032-2040.
29. Fried M.G., Stickle D.F. Ion-exchange reactions of proteins during DNA binding. Eur. J. Biochem. 1993, 218:469-475.
30. Taylor N.J., Darugar Q., Kourentzi K., Willson R.C., Landes C.F. Dynamics of an anti-VEGF DNA aptamer: a single-molecule study. Biochem. Biophys. Res. Commun. 2008, 373:213-218.
31. Poland D. Protein-binding polynomials. J. Protein Chem. 2001, 20:91-97.
32. Von Hippel P.H., Berg O.G. Facilitated target location in biological systems. J. Biol. Chem. 1989, 264:675-678.
33. Berk D.A., Yuan F., Leunig M., Jain R.K. Fluorescence photobleaching with spatial Fourier analysis: measurement of diffusion in light-scattering media. Biophys. J. 1993, 65:2428-2436.
34. Tinland B., Pluen A., Sturm J., Weill G. Persistence length of single-stranded DNA. Macromolecules 1997, 30:5763-5765.
35. Gill D.S., Roush D.J., Willson R.C. Presence of a preferred anion-exchange binding site on cytochrome b5: structural and thermodynamic considerations. J. Chromatogr. A 1994, 684:55-63.
36. Jennissen H.P., Heilmeyer L.M.G. General aspects of hydrophobic chromatography. Adsorption and elution characteristics of some skeletal muscle enzymes. Biochemistry 1975, 14:754-760.
37. Fu J.Y., Balan S., Potty A., Nguyen V., Willson R.C. Enhanced protein affinity and selectivity of clustered-charge anion-exchange adsorbents. Anal. Chem. 2007, 79:9060-9065.
38. Connor A.C., McGown L.B. Aptamer stationary phase for protein capture in affinity capillary chromatography. J. Chromatogr. A 2006, 1111:115-119.
39. Murphy M.B., Fuller S.T., Richardson P.M., Doyle S.A. An improved method for the in vitro evolution of aptamers and applications in protein detection and purification. Nucleic Acids Res. 2003, 31:e110.
40. Romig T.S., Bell C., Drolet D.W. Aptamer affinity chromatography: combinatorial chemistry applied to protein purification. J. Chromatogr. B Biomed. Sci. Appl. 1999, 731:275-284.