Fluorescence of the Purine and Pyrimidine Bases of the Nucleic Acids in Neutral Aqueous Solution at 300°K

Daniels, Malcolm; Hauswirth, William W.

doi:10.1126/science.171.3972.675

Cited by 262 publications

(220 citation statements)

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“…1 The nucleobases fluoresce extremely weakly and this has led to the conclusion that their excited states must be very short-lived. 2 This is supported by femtosecond transient visible absorption 3 and fluorescence upconversion 4 measurements that reveal that the bases and mononucleotides possess sub-picosecond excited state lifetimes. However, the reasons for the short lifetimes are still a matter of debate, with theoretical studies emphasising the importance of ultrafast non-radiative processes.…”

mentioning

confidence: 88%

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

et al. 2007

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A strong infrared band at 1574 cm 21 is observed following 267 nm excitation of 29-deoxycytidine (t = 37 ¡ 4 ps) or 29-deoxycytidine 59-monophosphate (t = 33 ¡ 4 ps); this band is provisionally attributed to an 1 n N p* state and is absent for cytosine.The nature of the electronic excited states of DNA continues to be a focus of significant interest because of their role in UV-light induced modifications that could potentially be mutagenic. 1 The nucleobases fluoresce extremely weakly and this has led to the conclusion that their excited states must be very short-lived. 2 This is supported by femtosecond transient visible absorption 3 and fluorescence upconversion 4 measurements that reveal that the bases and mononucleotides possess sub-picosecond excited state lifetimes. However, the reasons for the short lifetimes are still a matter of debate, with theoretical studies emphasising the importance of ultrafast non-radiative processes. 5 IR methods, including 2D-IR, are proving an increasingly valuable tool for the study of DNA systems. 6,7 Time-resolved IR (TRIR) absorption spectroscopy 8 can provide structural as well as kinetic information on the ultrafast processes in DNA and our first paper in this area allowed the observation of the vibrationally excited ground states formed from nucleotides excited at 267 nm. 9 Subsequently the method has been used to identify the products of the photoionisation of GMP after excitation at 200 nm 10 and very recently the formation of thymine dimers. 11 In this paper we probe the transient species formed from 29-deoxycytidine 59-monophosphate (dCMP), 29-deoxycytidine (dCyd) and cytosine (Cyt) using vibrational spectroscopy. The presence of a new short-lived species is shown for both dCyd and dCMP but not for the nucleobase Cyt. Fig. 1 shows the transient IR difference spectra recorded between 2 ps and 1000 ps after 267 nm (150 fs) excitation of the mononucleotide dCyd in neutral (buffered pH 6.9) solution. (Identical spectra were also recorded at pH 8.5). The spectrum shows areas corresponding to ground state depletion (bands at 1505, 1524, 1617 and 1652 cm 21 as found in the FTIR) and ones where the transient absorbs more strongly. Similar behaviour is observed for dCMP (see ESI).The transient decay (and the ground state recovery) is essentially complete over the 1000 ps time scale of the experiment. However, in contrast to the results for other nucleotides such as dAMP and dGMP, 9 the kinetics are distinctly biphasic (see Fig. 2). At short times (2-8 ps -shown in red in Fig. 1) the transient absorption bands are observed to shift to higher wavenumber, behaviour which is consistent with relaxation of vibrationally excited ground states, as previously proposed. 9 The time constant for this is determined to be 2.6 ¡ 0.3 ps for dCyd.After this cooling process is complete a strong transient absorption at 1574 cm 21 persists. This band is the only one observable in the IR absorption spectrum in the region 1450-1750 cm 21 (assuming that there is no accidental overlap of other band...

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confidence: 88%

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

et al. 2007

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“…Guanine was directly dissolved in MilliQ water rather than buffer as a means to minimize external variables and to be able to cross compare our values with those reported by Danies and Hauswirth. 47 The fluorescence spectrum of at least three samples was collected at every concentration. All spectra were corrected using the correction file for the instrument, the solvent spectrum was subtracted, and an average of at least three spectra was used to calculate final values.…”

Section: Quantum Yield Measurementsmentioning

confidence: 99%

“…For the quantum yield spectral collection, the following parameters were used: excitation bandwidth 5 nm, emission bandwidth 5 nm (the same bandwidth was used for the absorbance spectra), integration time of 0.1 s. Samples were excited at 275.5 nm to match the conditions in Daniels and Hauswirth. 47 The quantum yield of G9 was measured in 10 mKPi, 50 mM KCl buffer, pH 7.2.…”

Section: Quantum Yield Measurementsmentioning

confidence: 99%

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Méndez

Szalai

2009

Biopolymers

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Fluorescence of unmodified oligonucleotides has not been exploited for guanine‐quadruplex (G‐quadruplex) characterization. We observe that G‐rich sequences fluoresce more strongly than duplex or single‐stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G‐quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5′‐T4GnT4‐3′ (n = 4–10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5′‐GGGT‐3′, which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan‐Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5′‐TGGG‐3′, the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G‐rich sequences can be probed using fluorescence signatures of unmodified oligonucleotides. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 841–850, 2009.This article was originally published online as an accepted preprint. The ”Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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“…Product: white solid (18.6 mg, 0.056 mmol, 9% yield). 1 , 3′-OH, 1H), 5.14-5.08 (m, H-2′, 1H), 4.12-4.17 (m, H-3′, 1H 9. 8-(fur-2-yl)-guanosine (4)-To a suspension of 12 (139 mg, 0.4 mmol) and ammonium sulfate (21 mg) in anhydrous 1,1,1,3,3,3-hexamethyldisilazane (10 ml) was added anhydrous pyridine (1 ml).…”

Section: -(Fur-2-yl)-adenosine (3)mentioning

confidence: 99%

“…The product was purified by flash column chromatography (1/1 ethyl acetate/ hexanes, 1% Et 3 N). Product: light brown foam (50 mg, 0.063 mmol, 65% yield) 1 Iowa) and purified by PAGE as described below. Modified oligonucleotides were synthesized on a 1.0 μmole scale (500 Å CPG column) using a Biosearch Cyclone Plus DNA synthesizer.…”

Section: ′-(2-cyanoethyl)diisopropylphosphoramidite-5′-dimethoxytritmentioning

confidence: 99%

Furan Decorated Nucleoside Analogues as Fluorescent Probes: Synthesis, Photophysical Evaluation, and Site‐Specific Incorporation.

Greco

Tor

2007

ChemInform

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The synthesis and photophysical evaluation of modified nucleoside analogues in which a fivemembered heterocycle (furan, thiophene, oxazole and thiazole) is attached to the 5 position of 2′-deoxyuridine are reported. The furan containing derivative is identified as the most promising responsive nucleoside of this family due to its emission quantum efficiency and degree of sensitivity to its microenvironment. The furan moiety was then attached to the 5 position of 2′-deoxycytidine as well as the 8 position of adenosine and guanosine. Photophysical evaluation of these four furan containing nucleoside analogues reveal distinct differences in the absorption, emission and quantum efficiency depending upon the class of nucleoside (pyrimidine or purine). Comparing the photophysical properties of all furan containing nucleosides, identifies the furan thymidine analogue, 5-(fur-2-yl)-2′-deoxyuridine, as the best candidate for use as a responsive fluorescent probe in nucleic acids. 5-(fur-2-yl)-2′-deoxyuridine was then converted to the corresponding phosphoramidite and site specifically incorporated into DNA oligonucleotides with greater than 88% coupling efficiency. Such furan-modified oligonucleotides form stable duplexes upon hybridization to their complementary DNA strands and display favorable fluorescent features.

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Fluorescence of the Purine and Pyrimidine Bases of the Nucleic Acids in Neutral Aqueous Solution at 300°K

Cited by 262 publications

References 15 publications

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

Fluorescence of unmodified oligonucleotides: A tool to probe G‐quadruplex DNA structure

Furan Decorated Nucleoside Analogues as Fluorescent Probes: Synthesis, Photophysical Evaluation, and Site‐Specific Incorporation.

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