Direct Observation of Photoinduced Electron Transfer in Pyrene-Labeled dU Nucleosides and Evidence for Protonated 2'-Deoxyuridine Anion, dU(H).cntdot., as a Primary Electron Transfer Product

Netzel, Thomas L.; Nafisi, Kambiz; Headrick, Jeb; Eaton, Bruce E.

doi:10.1021/j100051a020

Cited by 48 publications

(76 citation statements)

References 9 publications

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“…In the case of alkylated pyrene derivatives, the fluorescence emission of pyrene was previously reported to be quenched by a PET mechanism between the pyrene and the nucleobases, such as guanine, cytosine, and thymine. 14 The fluorescence behaviors of the silylated pyrene derivatives in this study could be explained by the same mechanism. In the absence of the complementary strand, the fluorescence emission was strongly quenched by the interaction of the silylated pyrene moiety with the neighboring thymine base.…”

supporting

confidence: 58%

Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

et al. 2014

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Previously, we reported a novel fluorescence dye, a silylated pyrene derivative, as a DNA labeling agent. In this study, new silylated pyrene derivatives with different linker lengths and different substituents on the silicon atom have been prepared and introduced into oligonucleotides. In particular, when the diphenylsilylpyrene derivative was introduced as a fluorescence dye, the fluorescence intensity of the duplex was enhanced about 20 times compared to the signal in the absence of the target DNA.Fluorescently labeled oligonucleotides have been widely used in the analysis of genetic information.1 Such oligonucleotide probes should exhibit fluorescence emission only in the presence of the fully matched complementary strand, whereas an obvious fluorescent signal will be observed in the presence of the fully matched complementary strand. Various probe DNA and detection systems satisfying this requirement have been developed.2,3 The fluorescence dyes commonly used for fluorescent DNA probes show strong fluorescence intensity and high quantum yield in highly sensitive detection systems that are required for single molecule measurement 4 and in vivo imaging. 5It was reported that the introduction of silyl groups to polyaromatic compounds, such as anthracene and pyrene, induced red shift of the absorption and emission wavelengths, and increased the fluorescence quantum yield. 68 Recently, we reported novel fluorescently labeled oligonucleotides bearing a silylated pyrene derivative at the 5¤-terminus. 9 The silylated pyrene derivative was functionalized by the introduction of a hydroxy group, and the hydroxy group was phosphitylated to give the standard phosphoramidite derivative. The oligonucleotides containing the silylated pyrene derivative showed characteristic spectroscopic properties. While the modified oligonucleotides showed weak emission on the single strand, the presence of the complementary strand induced enhancement of the fluorescent emission. However, the reason for the distinctive spectroscopic behavior is unclear. In this study, in order to elucidate the effect on the fluorescent behavior of the structure, we prepared novel silylated pyrene derivatives, which have different linker lengths to the oligonucleotides and different substituents on the silicon atom instead of the methyl group.First, for elucidation of the relationship between the fluorescent behavior and linker length, we designed various silylated pyrene derivatives having different alkyl linker lengths and different substituents on the silicon atom. Preparation of the silylated pyrene derivatives having different alkyl linker lengths was carried out by the following steps (Scheme 1). The vinyl silane derivative 2a was synthesized from the reaction of 1-bromopyrene with chlorodimethylvinylsilane using the procedure reported previously. 9 The allylsilane derivative 2b was also prepared by the same procedure. The alcohol derivatives 3a and 3b were successfully prepared by using 9-BBN for hydroboration.10

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supporting

confidence: 58%

Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

et al. 2014

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“…The presence of a dual emission from an LE and a CT state with exciplex character is indicated. [26] In basic solution, there is no exciplex emission visible and the spectrum has a pronounced LEtype character.…”

Section: Resultsmentioning

confidence: 99%

Ultrafast Proton‐Coupled Electron‐Transfer Dynamics in Pyrene‐Modified Pyrimidine Nucleosides: Model Studies towards an Understanding of Reductive Electron Transport in DNA

et al. 2004

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5-(Pyren-1-yl)-2'-deoxyuridine (PydU) and 5-(Pyren-1-yl)-2'-deoxycytidine (PydC) were used as model nucleosides for DNA-mediated reductive electron transport (ET) in steady-state fluorescence and femtosecond time-resolved transient absorption spectroscopy studies. Excitation of the pyrene moiety in PydU and PydC leads to an intramolecular electron transfer that yields the pyrenyl radical cation and the corresponding pyrimidine radical anion (dU.- and dC.-. By comparing the excited state dynamics of PydC and PydU, we derived information about the energy difference between the two pyrimidine radical anion states. To determine the influence of protonation on the rates of photoinduced intramolecular ET, the spectroscopic investigations were performed in acetonitrile, MeCN, and in water at different pH values. The results show a significant difference in the basicity of the generated pyrimidine radical anions and imply an involvement of proton transfer during electron hopping in DNA. Our studies revealed that the radical anion dC.- is being protonated even in basic aqueous solution on a picosecond time scale (or faster). These results suggest that protonation of dC.- may also occur in DNA. In contrast, efficient ET in PydU could only be observed at low pH values (< 5). In conclusion, we propose--based on the free energy differences and the different basicities--that only dT.- but not dC.- can participate as an intermediate charge carrier for excess electron migration in DNA.

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“…The fluorescence quantum yield F F of pyrenebutanoic acid (PBA) in MeOH in this experimental setting was measured to be 0.069 relative to 9,10-diphenylanthracene in cyclohexene (F F = 0.95), [17] which is in excellent agreement with the reported value of 0.065. [18] Emission quantum yields F F (ON) of single-stranded ON9-ON12 and the corresponding duplexes with DNA/RNA targets were determined according to Equation (1), 3288), respectively. The reported quantum yields are an average of at least two measurements within (AE 10) %, although low quantum yields (F F < 10 %) may be associated with considerably larger error.…”

Section: Methodsmentioning

confidence: 99%

“…Deoxygenation was deliberately not applied to the samples since the scope of the work was to determine fluorescence enhancement under aerated conditions prevailing in bioassays. In addition, cross-calibrated fluorescence emission quantum yields (F F ) were determined relative to pyrenebutanoic acid in methanol (F F = 0.065) [17] and 9,10-diphenylanthracene in cyclohexane (F F = 0.95) [18] following established protocols (see the Supporting Information). [17] Hybridization of ON5-ON16 to complementary DNA is accompanied by a) hypsochromic shifts in absorption and excitation maxima of the pyrene moiety of 3-7 nm from ap- Table S3 and S4 in the Supporting Information), b) increases in extinction coefficients (hyperchromic shifts) that appear to be most pronounced for a-l-LNA monomer Z and least pronounced for DNA monomer X (Table 2), and c) formation of duplexes that exhibit broad fluorescence emission maxima at approximately 402 nm with a shoulder at approximately 387 nm (Figure 3 as well as Figures S6-S8 and Table S5 in the Supporting Information).…”

Section: Optical Spectroscopy Studiesmentioning

confidence: 99%

C5‐Functionalized DNA, LNA, and α‐L‐LNA: Positional Control of Polarity‐Sensitive Fluorophores Leads to Improved SNP‐Typing

Østergaard

Kumar

Baral

et al. 2011

Chemistry A European J

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Single nucleotide polymorphisms (SNPs) are important markers in disease genetics and pharmacogenomic studies. Oligodeoxyribonucleotides (ONs) modified with 5-[3-(1-pyrenecarboxamido)propynyl]-2'-deoxyuridine monomer X enable detection of SNPs at non-stringent conditions due to differential fluorescence emission of matched versus mismatched nucleic acid duplexes. Herein, the thermal denaturation and optical spectroscopic characteristics of monomer X are compared to the corresponding locked nucleic acid (LNA) and α-L-LNA monomers Y and Z. ONs modified with monomers Y or Z result in a) larger increases in fluorescence intensity upon hybridization to complementary DNA, b) formation of more brightly fluorescent duplexes due to markedly larger fluorescence emission quantum yields (Φ(F)=0.44-0.80) and pyrene extinction coefficients, and c) improved optical discrimination of SNPs in DNA targets. Optical spectroscopy studies suggest that the nucleobase moieties of monomers X-Z adopt anti and syn conformations upon hybridization with matched and mismatched targets, respectively. The polarity-sensitive 1-pyrenecarboxamido fluorophore is, thereby, either positioned in the polar major groove or in the hydrophobic duplex core close to quenching nucleobases. Calculations suggest that the bicyclic skeletons of LNA and α-L-LNA monomers Y and Z influence the glycosidic torsional angle profile leading to altered positional control and photophysical properties of the C5-fluorophore.

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Direct Observation of Photoinduced Electron Transfer in Pyrene-Labeled dU Nucleosides and Evidence for Protonated 2'-Deoxyuridine Anion, dU(H).cntdot., as a Primary Electron Transfer Product

Cited by 48 publications

References 9 publications

Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

Ultrafast Proton‐Coupled Electron‐Transfer Dynamics in Pyrene‐Modified Pyrimidine Nucleosides: Model Studies towards an Understanding of Reductive Electron Transport in DNA

C5‐Functionalized DNA, LNA, and α‐L‐LNA: Positional Control of Polarity‐Sensitive Fluorophores Leads to Improved SNP‐Typing

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