Fluorescent Pteridine Nucleoside Analogs: A Window on DNA Interactions

Hawkins, Mary E.

doi:10.1385/cbb:34:2:257

Cited by 152 publications

(117 citation statements)

References 37 publications

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“…A recently developed group of fluorescent base analogues are the pteridines (for recent review see Hawkins) 20 . Of the available pteridines the two guanine analogs 3-methylisoxanthopterine (3-MI) and 6-methylisoxanthopterine (6-MI) have been synthesized as phosphoramidites and incorporated into DNA oligonucleotides.…”

Section: Introductionmentioning

confidence: 99%

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

et al. 2003

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The neutral, base-pairing form of tC, having a fluorescence quantum yield of 0.2, is found to be the totally predominant species in a wide pH interval, 4-12. We show that the absorption band of tC at lowest energy, centred at 26700 cm -1 and well separated from the nucleobase absorption, is due to a single electronic transition polarized approximately at 35 from the long-axis of the molecule. The 2-deoxyribonucleoside of 1,3-diaza-2-oxophenothiazine, synthesized for further incorporation into DNA was found to display a fluorescence quantum yield nearly the same as in the form of tC that was incorporated into PNA, confirming the notion of the tC nucleoside being a probe with very promising fluorescence properties essentially invariant of environment, also upon incorporation into a DNA strand and upon hybridization.2

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Section: Introductionmentioning

confidence: 99%

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

et al. 2003

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“…Hawkins and co-workers have described substituted pteridines as fluorescent analogues of DNA bases (see ref 8 for review), and they have identified 3-methylisoxanthopterin (3MI) and 6-methylisoxanthopterin (6MI) as two particularly promising guanine analogues. Both analogues have absorbance bands that are at lower energies (red-shifted) than those of the naturally occurring nucleic acids and amino acids, allowing selective excitation of the analogues.…”

Section: Introductionmentioning

confidence: 99%

pH-Dependent Spectroscopy and Electronic Structure of the Guanine Analogue 6,8-Dimethylisoxanthopterin

et al. 2002

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Fluorescent nucleic acid analogues are valuable tools for studying DNA dynamics, protein-DNA interactions and nucleotide-dependent enzyme activities. The recent development of guanine analogues based on the isoxanthopterin structure offers new opportunities to investigate these dynamics, interactions, and activities. Our combined experimental/theoretical investigation of one such analogue, 6,8-dimethylisoxanthopterin (6,8DMI), has shown that absorbance and fluorescence emission spectra of 6,8DMI shift to lower energies as the pH is increased, yielding pK a values of 8.3 and 8.5, respectively. We show that these pH-dependent spectral changes result from protonation/deprotonation of the nitrogen at position 3 of 6,8DMI on the basis of pH-dependent iodide ion quenching of 6,8DMI fluorescence and pH-independent absorption and fluorescence properties of 3,6,8-trimethylisoxanthopterin. Quantum mechanical calculations on the neutral and deprotonated forms of 6,8DMI confirm the observed spectral changes.

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“…We have used the available high resolution structures of UP1 to incorporate the fluorescent guanosine analog 6-methyl-8-(2-deoxy-␤-ribofuranosyl)isoxanthopteridine (6-MI) into the oligonucleotide d(TTAGGG) 2 as a probe for studying UP1 interactions to hTR DNA (33,34). Previous fluorescence studies using either the quenching of intrinsic tryptophan fluorescence or the fluorescent nucleotide riboethanoadenylic acid have shown that UP1 binds promiscuously to single-stranded nucleic acids as part of its in vivo role in RNA processing and transport (22,23,27).…”

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Structure-based Incorporation of 6-Methyl-8-(2-deoxy-β-ribofuranosyl)isoxanthopteridine into the Human Telomeric Repeat DNA as a Probe for UP1 Binding and Destabilization of G-tetrad Structures

Myers

Moore

Shamoo

2003

Journal of Biological Chemistry

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Heterogeneous ribonucleoprotein A1 (hnRNP A1) is an abundant nuclear protein that participates in RNA processing, alternative splicing, and chromosome maintenance. hnRNP A1 can be proteolyzed to unwinding protein (UP1), a 22.1-kDa protein that retains a high affinity for purine-rich single-stranded nucleic acids, including the human telomeric repeat (hTR) d(T-TAGGG) n . Using the structure of UP1 bound to hTR as a guide, we have incorporated the fluorescent guanine analog 6-MI at one of two positions within the DNA to facilitate binding studies. One is where 6-MI remains stacked with an adjacent purine, and another is where it becomes fully unstacked upon UP1 binding. The structures of both modified oligonucleotides complexed to UP1 were determined by x-ray crystallography to validate the efficacy of our design, and 6-MI has proven to be an excellent reporter molecule for single-stranded nucleic acid interactions in positions where there is a change in stacking environment upon complex formation. We have shown that UP1 affinity for d(TTAGGG) 2 is ϳ5 nM at 100 mM NaCl, pH 6.0, and our binding studies with d(TTAGG(6-MI)TTAGGG) show that binding is only modestly sensitive to salt and pH. UP1 also has a potent G-tetrad destabilizing activity that reduces the T m of the hTR sequence d(TAGGGT) 4 from 67.0°C to 36.1°C at physiological conditions (150 mM KCl, pH 7.0). Consistent with the structures determined by x-ray crystallography, UP1 is able to bind the hTR sequence in solution as a dimer and supports a model for hnRNP A1 binding to nucleic acids in arrays that may make a contiguous set of anti-parallel single-stranded nucleic acid binding clefts. These data suggest that seemingly disparate roles for hnRNP A1 in alternative splice site selection, RNA processing, RNA transport, and chromosome maintenance reflect its ability to bind a purine-rich consensus sequence (nYAGGn) and destabilize potentially deleterious G-tetrad structures.

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Fluorescent Pteridine Nucleoside Analogs: A Window on DNA Interactions

Cited by 152 publications

References 37 publications

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

Photophysical Characterization of Fluorescent DNA Base Analogue, tC

pH-Dependent Spectroscopy and Electronic Structure of the Guanine Analogue 6,8-Dimethylisoxanthopterin

Structure-based Incorporation of 6-Methyl-8-(2-deoxy-β-ribofuranosyl)isoxanthopteridine into the Human Telomeric Repeat DNA as a Probe for UP1 Binding and Destabilization of G-tetrad Structures

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