Emission kinetics of fluorescent nucleoside analogs

Edward L. Rachofsky, Lawrence Sowers, Mary E. Hawkins, Frank M. Balis, William R. Laws, J. B Alexander Ross

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

Fluorescent analogs of nucleic acid bases are useful probes for observation of DNA structure, interactions, and dynamics. 2-aminopurine (2AP) and 3-methylisoxanthopterin (3MI) are analogs of adenine and guanine, respectively, which have single exponential fluorescence intensity decay kinetics when free in buffer at neutral pH but complex multi-exponential decays when incorporated into oligonucleotides. We have investigated the mechanisms underlying the complexity of the emission kinetics of these probes in DNA by observing decays as a function of local nucleic acid sequence and emission wavelength. For both probes, the intensity-averaged lifetime increases smoothly with increasing emission wavelength. Analysis of these data as a time-resolved emission spectrum (TRES) demonstrates that the complex decay law can be described as resulting from dipolar relaxation of the local environment of the probe on the same timescale as emission. While the mean fluorescence lifetime shows no dependence on nucleic acid sequence 5' or 3' of the probe, the mean time constant for dipolar relaxation is correlated with the identity of the neighboring bases. These results suggest that 2AP and 3MI may be sensitive probes of the local dynamics of nucleic acids, bound water, and counterions.

Original languageEnglish (US)
Title of host publicationProceedings of SPIE - The International Society for Optical Engineering
EditorsJ.R. Lakowicz, J.B. Alexander Ross
Pages68-75
Number of pages8
Volume3256
DOIs
StatePublished - 1998
Externally publishedYes
EventAdvances in Optical Biophysics - San Jose, CA, United States
Duration: Jan 25 1998Jan 26 1998

Other

OtherAdvances in Optical Biophysics
CountryUnited States
CitySan Jose, CA
Period1/25/981/26/98

Fingerprint

nucleosides
nucleic acids
analogs
Kinetics
probes
kinetics
Nucleic acid sequences
Nucleic acids
decay
DNA
deoxyribonucleic acid
Fluorescence
life (durability)
Wavelength
fluorescence
oligonucleotides
guanines
Oligonucleotides
adenines
wavelengths

Keywords

  • Dipolar relaxation
  • Fluorescence decay
  • Fluorescent nucleoside analogs
  • Kinetic models

ASJC Scopus subject areas

  • Electrical and Electronic Engineering
  • Condensed Matter Physics

Cite this

Rachofsky, E. L., Sowers, L., Hawkins, M. E., Balis, F. M., Laws, W. R., & Ross, J. B. A. (1998). Emission kinetics of fluorescent nucleoside analogs. In J. R. Lakowicz, & J. B. Alexander Ross (Eds.), Proceedings of SPIE - The International Society for Optical Engineering (Vol. 3256, pp. 68-75) https://doi.org/10.1117/12.307079

Emission kinetics of fluorescent nucleoside analogs. / Rachofsky, Edward L.; Sowers, Lawrence; Hawkins, Mary E.; Balis, Frank M.; Laws, William R.; Ross, J. B Alexander.

Proceedings of SPIE - The International Society for Optical Engineering. ed. / J.R. Lakowicz; J.B. Alexander Ross. Vol. 3256 1998. p. 68-75.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Rachofsky, EL, Sowers, L, Hawkins, ME, Balis, FM, Laws, WR & Ross, JBA 1998, Emission kinetics of fluorescent nucleoside analogs. in JR Lakowicz & JB Alexander Ross (eds), Proceedings of SPIE - The International Society for Optical Engineering. vol. 3256, pp. 68-75, Advances in Optical Biophysics, San Jose, CA, United States, 1/25/98. https://doi.org/10.1117/12.307079
Rachofsky EL, Sowers L, Hawkins ME, Balis FM, Laws WR, Ross JBA. Emission kinetics of fluorescent nucleoside analogs. In Lakowicz JR, Alexander Ross JB, editors, Proceedings of SPIE - The International Society for Optical Engineering. Vol. 3256. 1998. p. 68-75 https://doi.org/10.1117/12.307079
Rachofsky, Edward L. ; Sowers, Lawrence ; Hawkins, Mary E. ; Balis, Frank M. ; Laws, William R. ; Ross, J. B Alexander. / Emission kinetics of fluorescent nucleoside analogs. Proceedings of SPIE - The International Society for Optical Engineering. editor / J.R. Lakowicz ; J.B. Alexander Ross. Vol. 3256 1998. pp. 68-75
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