A novel fluorescent guanine derivative distinguishable of three structures, single strand, duplex, and quadruplex

Okamoto, Akimitsu; Kanatani, Keiichiro; Ochi, Yuji; Saitō, Yoshio; Saito, Isao

doi:10.1016/j.tetlet.2004.05.136

Cited by 17 publications

(7 citation statements)

References 24 publications

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“…The melting temperature ( T m ) of 3 / 3 ‘ suggests that the fluorophore is bound to the minor groove. The duplex showed a surprisingly low T m (41 °C), which was much lower than that of a nonmodified T/A duplex (60 °C) and close to those observed for mismatched duplexes containing 2 /N base pairs (N = G, C, or T) (43−48 °C). , It has been reported that the duplex containing a pyrene-tethered nucleotide, Py U, forms a structure in which the glycosyl bond of Py U is rotated to the syn conformation when Py U forms an unstable base pair . The pyrene fluorophore of Py U is located in the minor groove.…”

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confidence: 57%

Monitoring DNA Structures by Dual Fluorescence of Pyrene Derivatives

et al. 2005

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We have developed a nucleotide modified by a pyrene derivative with dual fluorescence. The dual fluorescence of the fluorophore, which was incorporated into DNA, was effectively controlled at ambient temperature according to DNA structural status. Our nucleoside with dual fluorescence is effective as a conceptually new probe for monitoring DNA hybridization by the color change without multilabeling with fluorescent dyes.

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confidence: 57%

Monitoring DNA Structures by Dual Fluorescence of Pyrene Derivatives

et al. 2005

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“…8P G (Figure A) adopts a syn conformation and upon incorporation into an antiparallel G-quadruplex, dT 3 G 2 T 3 8P GGT 3 8P GGT 3 G 2 , results in an increased thermal stability from 40 to 47 °C . In the folded form, maximum fluorescence intensity was observed at 458 nm (Φ F = 0.116), which was shifted to 505 nm in single-stranded DNA, which corresponds to pyrene excimer fluorescence.…”

Section: Nucleobase Modificationsmentioning

confidence: 99%

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

2013

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“…Under these conditions, a strong excitonic interaction of pyrene with nucleobases induced both bathochromicity and hypochromicity compared with isolated pyrene absorption. 45,46 However, in the cases of H2AP/H2B and H6AP/H6B, isopropylcyclohexane moieties inserted between the pyrene and nucleobases efficiently isolated pyrene and blocked their excitonic interaction. Accordingly, the insertion of the H-H pair induced hypochromicity and hyperchromicity.…”

Section: Insulating Ability Of Cyclohexyl Base Pairsmentioning

confidence: 99%

Cyclohexyl “base pairs” stabilize duplexes and intensify pyrene fluorescence by shielding it from natural base pairs

et al. 2011

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In this study, we investigated the stability and structure of artificial base pairs that contain cyclohexyl rings. The introduction of a single pair of isopropylcyclohexanes into the middle of DNA slightly destabilized the duplex. Interestingly, as the number of the "base pairs" increased, the duplex was remarkably stabilized. A duplex with six base pairs was even more stable than one containing six A-T pairs. Thermodynamic analysis revealed that changes in entropy and not enthalpy contributed to duplex stability, demonstrating that hydrophobic interactions between isopropyl groups facilitated the base pairing, and thus stabilized the duplex. NOESY of a duplex containing an isopropylcyclohexane-methylcyclohexane pair unambiguously demonstrated its "pairing" in the duplex because distinct NOEs between the protons of cyclohexyl moieties and imino protons of both of the neighboring natural base pairs were observed. CD spectra of duplexes tethering cyclohexyl moieties also showed a positive-negative couplet that is characteristic of the B-form DNA duplex. Taken together, these results showed that cyclohexyl moieties formed base pairs in the DNA duplex without severely disturbing the helical structure of natural DNA. Next, we introduced cyclohexyl base pairs between pyrene and nucleobases as an "insulator" that suppresses electron transfer between them. We found a massive increase in the quantum yield of pyrene due to the efficient shielding of pyrene from nucleobases. The cyclohexyl base pairs reported here have the potential to prepare highly fluorescent labeling agents by multiplying fluorophores and insulators alternately into DNA duplexes.

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A novel fluorescent guanine derivative distinguishable of three structures, single strand, duplex, and quadruplex

Cited by 17 publications

References 24 publications

Monitoring DNA Structures by Dual Fluorescence of Pyrene Derivatives

Monitoring DNA Structures by Dual Fluorescence of Pyrene Derivatives

Molecular Engineering of Guanine-Rich Sequences: Z-DNA, DNA Triplexes, and G-Quadruplexes

Cyclohexyl “base pairs” stabilize duplexes and intensify pyrene fluorescence by shielding it from natural base pairs

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