Depyrimidination of synthetic poly(uridylic acid) analogue

Han, Man Jung; Cho, Tae Joon; Kim, Ki Ho; Yoo, Kyung Soo; Park, Young Dong; Chang, Ji Young

doi:10.1002/(sici)1099-0518(20000201)38:3<423::aid-pola5>3.0.co;2-r

Cited by 3 publications

(4 citation statements)

References 20 publications

(18 reference statements)

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“…For example, dephosphorylation half-lives for 2 ′ or 3 ′ UMP and 2 ′ or 3 ′ AMP are between 20 and 200 h at pH 7 and 90°C Lonnberg 1989, 1990). Both depurination and depyrimidination of DNA have been found to occur on a timescale on the order of years (t 1/2 ∼ 5-20 yr) at physiological pH and 70°C and 80°C, respectively (Lindahl and Nyberg 1972;Han et al 2000). By comparison, our work indicates that RNA hydrolysis to mononucleotides occurs with a half-life of ∼40 min at pH 7 and 95°C.…”

Section: Resultsmentioning

confidence: 99%

A neutral pH thermal hydrolysis method for quantification of structured RNAs

Wilson

Cohen

Wang

et al. 2014

RNA

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Riboswitch aptamers adopt diverse and complex tertiary structural folds that contain both single-stranded and double-stranded regions. We observe that this high degree of secondary structure leads to an appreciable hypochromicity that is not accounted for in the standard method to calculate extinction coefficients using nearest-neighbor effects, which results in a systematic underestimation of RNA concentrations. Here we present a practical method for quantifying riboswitch RNAs using thermal hydrolysis to generate the corresponding pool of mononucleotides, for which precise extinction coefficients have been measured. Thermal hydrolysis can be performed at neutral pH without reaction quenching, avoids the use of nucleases or expensive fluorescent dyes, and does not require generation of calibration curves. The accuracy of this method for determining RNA concentrations has been validated using quantitative 31 P-NMR calibrated to an external standard. We expect that this simple procedure will be generally useful for the accurate quantification of any sequence-defined RNA sample, which is often a critical parameter for in vitro binding and kinetic assays.

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Section: Resultsmentioning

confidence: 99%

A neutral pH thermal hydrolysis method for quantification of structured RNAs

Wilson

Cohen

Wang

et al. 2014

RNA

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“…The 1 H-and the 13 C-NMR spectra for AQMDA were completely interpreted in our earlier publication. 16 The interpretation of the spectra for AQODA is in Table II. The 1 H resonances were assigned with the aid of NOE experiments.…”

Section: Resultsmentioning

confidence: 99%

“…14,15 Recently we prepared an amine-quinone dianiline monomer (AQMDA) and used this monomer to prepare an amine-quinone polyimide (AQPI-2) by a two-stage condensation with 3,3Ј,4,4Ј-benzophenonetetracarboxylic dianhydride. 16 Our objective was to demonstrate whether we could combine the hightemperature properties inherent with polyimides with the corrosion protection of metal afforded by the amine-quinone functional group. Indeed, the AQPI-2 protected iron against corrosion by sodium chloride electrolyte.…”

Section: Introductionmentioning

confidence: 99%

Amine–quinone polyimides

Han

Nikles

2001

J. Polym. Sci. A Polym. Chem.

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Two dianiline monomers were prepared by the reaction of either 4,4Јmethylenedianiline or 4,4Ј-oxydianiline with 1,4-benzoquinone. These monomers were used to synthesize a series of amine-quinone polyimides by condensation with either 3,3Ј,4,4Ј-benzophenonetetracarboxylic dianhydride or 4,4Ј-(hexafluoroisopropylidene) diphthalic anhydride to make the corresponding polyamic acid. The polyamic acids were converted to the polyimides by thermal imidization at 290°C. The amine-quinone polyimides gave freestanding films with tensile strengths in the range of 90 to 150 MPa and Young's moduli of 0.9 to 1.5 GPa. The thermal decomposition temperature under nitrogen was 440 to 480°C and the glass-transition temperature was in the range of 280 to 310°C. The amine-quinone polyimides had the excellent thermal and mechanical properties that one expects for polyimides.

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“…The environmental fluctuations and reactive alterations experienced by nucleic acids (Fig. 1) are both wide ranging and complex including, but not limited to: base flipping [1], methylation [2][3][4][5][6], depurination [7,8] and depyrimidination [9], and ligand binding [10]. These changes to the local environment occur both in concert with, and independent of, the expected changes experienced throughout the normal function of nucleic acids; namely, the -stacking interactions observed upon accumulation into a strand of DNA [11][12][13][14][15][16], and the hydrogen bonding necessary for combining two strands into the double helix [17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective

Malcomson

2022

Photochem Photobiol Sci

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With the prevalence of fluorescence spectroscopy in biological systems, and the benefits of two-photon absorption techniques, presented here is an assessment of the two-photon accessibility of modern fluorescent nucleobase analogues utilising quadratic response DFT. Due to the complex environment experienced by these nucleobases, the two-photon spectra of each analogue has been assessed in the presence of both $$\pi $$ π -stacked and hydrogen-bonding interactions involving the canonical nucleobases. Findings suggest that the $$\pi $$ π -stacking environment provides a more significant effect on the spectra of the analogues studies than a hydrogen-bonding environment; analogue structures presenting high two-photon cross-section values for one or more states coincide with polycyclic extensions to preserved canonical base structure, as observed in the qA family of analogues, while analogue structures more closely resembling the structure of the base in question present a much more muted spectra in comparison. Results from this investigation have also allowed for the derivation of a number of design rules for the development of potential, two-photon specific, analogues for future use in both imaging and potential photochemical activation. Graphical abstract

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Depyrimidination of synthetic poly(uridylic acid) analogue

Cited by 3 publications

References 20 publications

A neutral pH thermal hydrolysis method for quantification of structured RNAs

A neutral pH thermal hydrolysis method for quantification of structured RNAs

Amine–quinone polyimides

Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective

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