Molecular beacons for detecting DNA binding proteins: Mechanism of action

Analytical Biochemistry

Volumn 316, Issue 1, 2003, Pages 1-10

  Heyduk, Ewa ^a   Knoll, Eric ^a   Heyduk, Tomasz ^a  

^a SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Detection; DNA binding proteins; Fluorescence

Indexed keywords

BIOCHEMISTRY; DNA; ERROR DETECTION; FLUORESCENCE;

DNA-BINDING PROTEIN; KINETIC EXPERIMENT; MECHANISM OF ACTION; MOLECULAR BEACON; PROTEIN-BINDING SITES; RATE-LIMITING STEPS; RATIONAL DESIGN; THEORETICAL SIMULATION;

PROTEINS;

DNA BINDING PROTEIN; DNA FRAGMENT;

ARTICLE; BIOASSAY; CHEMICAL PARAMETERS; DATA ANALYSIS; EXPERIMENTAL TEST; KINETICS; MOLECULAR DYNAMICS; PHYSICAL MODEL; PRIORITY JOURNAL; PROTEIN TARGETING; SPECTROFLUOROMETRY; THEORY;

EID: 0037402264     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0003-2697(03)00004-6     Document Type: Article

References (15)

1. Heyduk T., Heyduk E. Molecular beacons for detecting DNA binding proteins. Nat. Biotechnol. 20:2002;171-176.
2. Lewin B. Genes VII. 2000;Oxford University Press, New York.
3. Brivanlou A.H., Darnell J.E. Jr. Signal transduction and the control of gene expression. Science. 295:2002;813-818.
4. Lakowicz J.R. Principles of Fluorescence Spectroscopy. 1999;Kluwer Academic/Plenum Press, New York.
5. Stryer L. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47:1978;819-846.
6. Heyduk E., Heyduk T. Thiol reactive luminescence europium chelates. Luminescence probes for resonance energy transfer distance measurements in biomolecules. Anal. Biochem. 248:1997;216-227.
7. Heyduk T., Lee J.C. E. coli cAMP receptor protein: evidence for three conformational states with different promoter binding affinities. Biochemistry. 28:1989;6914-6924.
8. Busby S., Ebright R.H. Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293:1999;199-213.
9. Fried M.G., Crothers D.M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 9:1981;6505-6525.
10. N. Peyret, J. SantaLucia Jr., HYTHER, version 1.0. Wayne State University.
11. SantaLucia J. Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1998;1460-1465.
12. Peyret N., Seneviratne P.A., Allawi H.T., SantaLucia J. Jr. Nearest-neighbor thermodynamics and NMR of DNA sequences with internal. A·A, C·C, G·G, and T·T mismatches Biochemistry. 38:1999;3468-3477.
13. Ebright R.H., Ebright Y.W., Gunasakera A. Consensus DNA site for the Escherichia coli catabolite activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. Nucleic Acids Res. 17:1989;10295-10305.
14. Record M.T. Jr., Anderson C.F., Lohman T.M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 2:1978;103-178.
15. Heyduk T., Lee J.C. Application of fluorescence energy transfer and polarization to monitor E. coli cAMP receptor protein and lac promoter interaction. Proc. Natl. Acad. Sci. USA. 87:1990;1744-1748.