Fluorescent pteridine nucleoside analogs: a window on DNA interactions

Cell Biochemistry and Biophysics

Volumn 34, Issue 2, 2001, Pages 257-281

  Hawkins, Mary E ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; DNA; FLUORESCENT DYE; GUANOSINE; OLIGONUCLEOTIDE; PTERIDINE DERIVATIVE;

ANISOTROPY; CHEMICAL MODEL; CHEMISTRY; METABOLISM; METHODOLOGY; REVIEW; SPECTROFLUOROMETRY; TEMPERATURE; TIME;

ADENINE; ANISOTROPY; DNA; FLUORESCENT DYES; GUANOSINE; MODELS, CHEMICAL; OLIGONUCLEOTIDES; PTERIDINES; SPECTROMETRY, FLUORESCENCE; TEMPERATURE; TIME FACTORS;

EID: 0035754097     PISSN: 10859195     EISSN: None     Source Type: Journal    
DOI: 10.1385/CBB:34:2:257     Document Type: Review

References (40)

1. Hawkins, M. E., Pfleiderer, W., Balis, F. M., Porter, D. and Knutson, J. R. (1997) Fluorescence Properties of Pteridine Nucleoside Analogs as Monomers and Incorporated into Oligonucleotides. Analytical Biochemistry 244, 86-95.
2. Hawkins, M. E., Pfleiderer, W., Mazumder, A., Pommier, Y. G., and Balis, F. M. (1995) Incorporation of a Fluorescent Guanosine Analog into Oligonucleotides and Its Application to a Real Time Assay for the HIV-I Integrase 3′-processing Reaction. Nucleic Acids Research 23, 2872-2880.
3. 2a. Wojtuszewski, K., Hawkins, M., Cole, J. L., Mukerji, I. (2001) Hu binding to DNA: evidence for multiple complex formation and DNA bending. Biochemistry. 40, 2588-2598.
4. 6-Alkylguanine-DNA Alkyltransferase. Analytical Biochemistry 281, 216-222.
5. Stryer, L. and Haugland, R. P. (1967) Energy transfer: a spectroscopic ruler. Proc. Natl. Acad. Sci. 58, 719-726.
6. Driscoll, S. L., Hawkins, M. E., Balis, F. M., Pfleiderer, W., and Laws, W. R. (1997) Fluorescence Properties of a New Guanosine Analog Incorporated into Small Oligonucleotides. Biophysical Journal 73, 3277-3286.
7. Garcia de la Torre, J. S., Navarro, M. C., Martinez, L., Diaz, F. G., and Cascales, J. J. L. (1994) HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophysical Journal 14, 81-139.
8. Espositio, D. and Craigie, R. (1999) HIV integrase structure and function. Adv Virus Res 52, 319-333.
9. Asante-Appiah, E. and Skalka, A. (1999) HIV-1 integrase: structural organization, conformational changes, and catalysis. Adv. Virus Res. 52,
10. Fujiwara, T. and Craigie, R. (1989) Integration of Mini-retroviral DNA: A Cell-free Reaction for Biochemical Analysis of Retroviral Integration. Proceedings of the National Academy of Sciences 86, 3065-3069.
11. Brown, P. O., Bowerman, B., Varmus, H. E., and Bishop, J. M. (1987) Correct Integration of Retroviral DNA In Vitro. Cell 49, 347-356.
12. Brown, P. O., Bowerman, B., Varmus, H. E., and Bishop, J. M. (1989) Retroviral Integration: Structure of the Initial Covalent Product and Its Precursor, and a Role for the Viral IN Protein. Proceedings of the National Academy of Sciences 86, 2525-2529.
13. Vink, C., Banks, M., Bethell, R., and Plasterk, R. H. A. (1994) Nucleic Acids Research 22, 2176-2177.
14. 6-alkylguanine-DNA alkyltransferase. Proc. Natl. Acad. Sci. 86, 8620-8624.
15. 6-methylguanine lesions in methylated DNA. Nucleic Acids Research 9, 3089-3103.
16. 6-methylguanine from DNA by human liver fractions. Proc. Natl. Acad. Sci. 79, 5162-5165.
17. 6 -alkylguanine-DNA alkyltransferase based on restriction endonucleoase inhibition and magnetic bead separation of products. Carcinogenesis 15, 2143-2148.
18. Bewley, C. A., Gronenborn, A. M., and Clore, G. M. (1998) Minor Groove-Binding Architectural Proteins: Structure, Function and DNA Recognition. Ann. Rev. Biophys. Biomol. Struct. 27, 105-131.
19. Fried, M. and Crothers, D. M. (1981) Equilibria and Kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucl. Acids Res. 9, 6505-6525.
20. Fried, M. G. and Liu, G. (1994) Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis. Nucl. Acids Res. 22, 5054-5059.
21. Paull, T., Haykinson, M., and Johnson, R. (1993) The nonspecific DNA-binding and bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structure. Genes Dev. 7, 1521-1534.
22. Hodges-Garcia, Y., Hagerman, P. J., and Pettijohn, D. E. (1989) DNA Ring Closure Mediated by Protein HU. J. Biol. Chem. 264, 14621-14623.
23. Crothers, D. M. and Shakked, Z. DNA Bending by adenine-thymine tracts (ed. Neidle, S.) (Oxford university Press, Oxford, 1999).
24. Chan, S. S., Breslauer, K. J., Austin, R. H., and Hogan, M. E. (1993) Thermodynamics and Premelting Conformational Changes of Phased (dA)5 Tracts. Biochemistry 29, 6161-61171.
25. Chan, S. S., Austin, R. H., Mukerji, I., and Spiro, T. G. (1997) Temperature-Dependent Ultraviolet Resonance Raman Spectroscopy of the Premelting State of dA.dT DNA. Biophysical Journal 72, 1512-1520.
26. Park, Y. W. and Breslaueer, K. J. (1991) A Spectroscopic and Calorimetric Study of the Melting Behaviors of a 'bent' and 'normal' DNA Duplex:[d(GA4T4C)]2 versus [d(GT4A4C)]2. Proceedings of the National Academy of Sciences 88, 1551-1555.
27. deHaseth, P. L., Zupancic, M., and Record Jr., M. T. (1998) RNA polymerase-promoter interaction: the cmings and goings of RNA polymerase. J. Bacteriol 180, 3019-3025.
28. Marr, M. T. and Roberts, J. W. (1997) Promoter recognition as measured by binding of RNA polymerase to nontemplate strand oligonucleotides. Science 276, 1258-1260.
29. Savinkova, L. K. et al. (1993) Eschericia coli RNA polymerase interaction with the oligonribonucleotides homologous to "-10" and "-35" regions of bacterial spc promoters. Mol. Biol. 27, 33-37.
30. Sullivan, J. J., Bjornson, K. P., Sowers, L. C., and deHaseth, P. L. (1997) Spectroscopic determination of open complex formation at promoters for Escherichia coli RNA polymerase. Biochemistry 36, 8005-8012.
31. Strainic, J., M. G., Sullivan, J. J., Velevis, A., and deHaseth, P. L. (1998) Promoter recognition by Esherichia coli RNA polymerase: Effects of the UP element on open complex formation and promoter clearance. Biochemistry 37, 18074-18080.
32. Fedoriw, A. M., Liu, H., Anderson, V. E., and deHaseth, P. L. (1998) Equilibrium and kinetic parameters of the sequence-specific interaction of Escherichia coli RNA polymerase with non-template strand oligodeoxyribonucleotides. Biochemistry 37, 11971-11979.
33. McClure, W., Hawley, D., and Malan, T. P. (1984) The Mechanism of RNA Polymerase Activation on the Lambda PRM and lac P+ promoters.,
34. Rao, L. et al. (1994) Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J. Mo.. Biol. 235, 1421-1435.
35. Cossum, P. A. et al. (1993) Disposition of the 14C-labeled phosphorothioate oligonucleotide ISIS 2105 after intravenous administration to rats. J. Pharmacol. Exp. Ther. 267, 1181-1190.
36. Meeker, R., Legrand, G., Ramirez, J., Smith, T., and Shih, Y. H. (1995) Antisense vasopressin oligonucleotides: Uptake, turnover, distribution, toxicity and behavior. Journal of Neuroendocrinology 7, 419-428.
37. Obeibauer, R., Schreiner, G. F., and Meyer, T. W. (1995) Renal uptake of an 18-mer phosphorothioate oligonucleotide. Kidney International 48, 1226-1232.
38. Ogawa, S., Brown, H. E., Okano, H. J., and Pfaff, D. W. (1995) Cellular uptake of intracerebrally administered oligodeoxynucleotides in mouse brain. Regul. Pept. 59, 143-149.
39. Rappaport, J. et al. (1995) Transport of phosphorothioate oligonucleotides in kidney: implications for molecular therapy. Kidney Internat. 47, 1462-1469.
40. Zhao, Q., Waldschmidt, T., Fisher, E., Herrera, C. J., and Krieg, A. M. (1994) Stage-specific oligonucleotide uptake in murine bone marrow B-Cell precursors. Blood 84, 3660-3666.