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Title: Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA

Abstract

The 2,6-naphthalenedicarboxamide chromophore has been investigated as a fluorescent probe for DNA hairpin and duplex formation and DNA electron transfer. The high fluorescence quantum yield and long singlet lifetime of this chromophore make it an attractive candidate for these studies. The kinetics of intermolecular quenching of a naphthalenedicarboxamide by nucleosides is dependent upon the nucleoside oxidation potential and solvent. Bis(oligonucleotide) conjugates containing naphthalene linkers have been prepared by means of conventional phosphoramidite chemistry. The base-sequence dependence of the naphthalene fluorescence intensity and decay times in both single-strand and hairpin conjugates indicates that singlet naphthalene is quenched by neighboring dA more efficiently than by dT, in accord with an electron-transfer quenching mechanism. These data are analyzed by means of a three-state model which includes a nonemissive dark state. Duplexes formed between complementary naphthalene-linked oligonucleotides display naphthalene excimer emission. The base-sequence dependence of the excimer emission quantum yields indicates that the excimer is not quenched by neighboring dA but that distance-dependent electron-transfer quenching by dG may occur. Quenching serves to protect the naphthalene chromophore from photobleaching in both single strand and duplex structures.

Authors:
; ; ; ;  [1]
  1. Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry
Publication Date:
Sponsoring Org.:
USDOE, Washington, DC (United States)
OSTI Identifier:
345119
DOE Contract Number:  
FG02-96ER14604
Resource Type:
Journal Article
Journal Name:
Journal of Physical Chemistry B: Materials, Surfaces, Interfaces, amp Biophysical
Additional Journal Information:
Journal Volume: 103; Journal Issue: 13; Other Information: PBD: 1 Apr 1999
Country of Publication:
United States
Language:
English
Subject:
55 BIOLOGY AND MEDICINE, BASIC STUDIES; SYNTHESIS; ELECTRON TRANSFER; OLIGONUCLEOTIDES; NAPHTHALENE; DICARBOXYLIC ACIDS; AMIDES; FLUORESCENCE; MATHEMATICAL MODELS; REACTION KINETICS

Citation Formats

Lewis, F D, Zhang, Y, Liu, X, Xu, N, and Letsinger, R L. Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA. United States: N. p., 1999. Web. doi:10.1021/jp9845423.
Lewis, F D, Zhang, Y, Liu, X, Xu, N, & Letsinger, R L. Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA. United States. https://doi.org/10.1021/jp9845423
Lewis, F D, Zhang, Y, Liu, X, Xu, N, and Letsinger, R L. Thu . "Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA". United States. https://doi.org/10.1021/jp9845423.
@article{osti_345119,
title = {Naphthalenedicarboxamides as fluorescent probes of inter- and intramolecular electron transfer in single strand, hairpin, and duplex DNA},
author = {Lewis, F D and Zhang, Y and Liu, X and Xu, N and Letsinger, R L},
abstractNote = {The 2,6-naphthalenedicarboxamide chromophore has been investigated as a fluorescent probe for DNA hairpin and duplex formation and DNA electron transfer. The high fluorescence quantum yield and long singlet lifetime of this chromophore make it an attractive candidate for these studies. The kinetics of intermolecular quenching of a naphthalenedicarboxamide by nucleosides is dependent upon the nucleoside oxidation potential and solvent. Bis(oligonucleotide) conjugates containing naphthalene linkers have been prepared by means of conventional phosphoramidite chemistry. The base-sequence dependence of the naphthalene fluorescence intensity and decay times in both single-strand and hairpin conjugates indicates that singlet naphthalene is quenched by neighboring dA more efficiently than by dT, in accord with an electron-transfer quenching mechanism. These data are analyzed by means of a three-state model which includes a nonemissive dark state. Duplexes formed between complementary naphthalene-linked oligonucleotides display naphthalene excimer emission. The base-sequence dependence of the excimer emission quantum yields indicates that the excimer is not quenched by neighboring dA but that distance-dependent electron-transfer quenching by dG may occur. Quenching serves to protect the naphthalene chromophore from photobleaching in both single strand and duplex structures.},
doi = {10.1021/jp9845423},
url = {https://www.osti.gov/biblio/345119}, journal = {Journal of Physical Chemistry B: Materials, Surfaces, Interfaces, amp Biophysical},
number = 13,
volume = 103,
place = {United States},
year = {1999},
month = {4}
}