The Nonenzymic Hydrolysis of Nucleoside 2',3'-Phosphates<sup>*</sup>

Abrash, Henry I.; Cheung, Chun-Chung S.; Davis, Jesse C.

doi:10.1021/bi00857a011

Cited by 30 publications

(29 citation statements)

References 9 publications

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“…Recently, the extinction coefficients at 260 nm for the nucleoside 5 ′ monophosphates at pH 7 were redetermined using NMR spectroscopy to accurately measure sample concentrations (Cavaluzzi and Borer 2004). While RNA hydrolysis results in an interconverting mixture of nucleoside 3 ′ monophosphates and 2 ′ monophosphates, the extinction coefficients for these species are closely approximated by the values for the 5 ′ monophosphates (Supplemental Table S1), as the location of the phosphate group has little effect (Katz and Comb 1963;Abrash et al 1967;Puglisi and Tinoco 1989;Cavaluzzi and Borer 2004).…”

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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“…1) (Eigner et al, 1961;Abrash et al, 1968). To evaluate the influence of TCAA, the rate constants for both the disappearance of the ribose phosphodiester bond within 5 0 -dCrCdGdG and the disappearance of the deoxyribose phosphodiester bond within dCrC>p and dGdG were calculated by fitting the reaction curves ( Table 2).…”

Section: Reaction Rates Of Oligonucleotides In the Presence Of Tcaamentioning

confidence: 99%

Chemical evolution of RNA under hydrothermal conditions and the role of thermal copolymers of amino acids for the prebiotic degradation and formation of RNA

Kawamura

Nagahama

Kuranoue

2005

Advances in Space Research

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“…2Ј,3Ј-cUMP is highly resistant to hydrolysis. The second order rate constant [30] for the hydroxide-catalysed hydrolysis at 37°C is ca. 6.5⋅10 Ϫ3  Ϫ1 s Ϫ1 .…”

Section: Hydrolysis Of 2ј3ј-cumpmentioning

confidence: 99%