The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence

Kaukinen, Ulla; Lyytikäinen, Sari; Mikkola, Satu; Lönnberg, Harri

doi:10.1093/nar/30.2.468

Cited by 62 publications

(89 citation statements)

References 45 publications

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“…29 This is important as it is known that RNA degradation rates are very heterogeneous in solution, mainly because of the variety of local RNA conformation. 15 The coherence between the rates of degradation of eight different mRNA and rRNA species suggests that, in the minicapsules, RNA may degrade independently of its sequence.…”

Section: Discussionmentioning

confidence: 99%

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An efficient method for long-term room temperature storage of RNA

Fabre

Colotte²,

Luis³

et al. 2013

Eur J Hum Genet

114

110

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RNA is a tool used in many fields, from molecular and cellular biology to medicine and nanotechnology. For most of these uses, the integrity of RNA is required and must be maintained during storage. Even though freezing is currently the storage method of choice, the increasing number of samples to be stored and the costly use of a cold chain have highlighted the need for room temperature preservation methods. Here, we report a new room temperature technology that consists in drying RNA samples in the presence of a stabilizer in stainless steel minicapsules. These air-and water-tight capsules isolate RNA from the atmosphere and maintain an anhydrous and anoxic environment. Through the evaluation of RNA integrity over time at room temperature or 90 1C, we identified atmospheric humidity as a major deleterious factor. The degradation rate dependence in temperature fitted an Arrhenius model, with an activation energy of 28.5 kcal/mol and an extrapolated room temperature degradation rate of 3.2 10 À13 /nt/s (95% confidence interval: 2.3-4.2/nt/s). In these conditions, it is expected that an RNA molecule will be subjected to 0.7-1.3 cut every 1000 nucleotides per century. In addition, we showed that stored RNA is compatible for further analyses, such as reverse transcription-quantitative PCR. No significant change in the C q values was observed over a simulated period of several decades. At last, our data are consistent with a sequence-independent degradation rate of RNA in the solid state.

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Section: Discussionmentioning

confidence: 99%

“…This structural requirement leads up to 10 000-fold rate variations depending on the local secondary and tertiary structures of the molecule. 14,15 In order to prevent degradation, RNA samples are generally stored frozen at À20 1C or À80 1C or under liquid nitrogen. However, even at a low temperature, RNA retains some reactivity.…”

Section: Introductionmentioning

confidence: 99%

An efficient method for long-term room temperature storage of RNA

Fabre

Colotte²,

Luis³

et al. 2013

Eur J Hum Genet

114

110

View full text Add to dashboard Cite

show abstract

“…After about 10 hours in water, faster degradation of the RNA started. The relatively high stability of the PolyA sequence in aqueous solution is well established [18][19][20]. The stability of RNA phosphodiester bonds has repeatedly been associated with the stacking interactions between adjacent bases [21][22][23].…”

Section: Rna Stability In Boron Mineralsmentioning

confidence: 99%

Borate Minerals and RNA Stability

et al. 2010

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Abstract:The abiotic origin of genetic polymers faces two major problems: a prebiotically plausible polymerization mechanism and the maintenance of their polymerized state outside a cellular environment. The stabilizing action of borate on ribose having been reported, we have explored the possibility that borate minerals stabilize RNA. We observe that borate itself does not stabilize RNA. The analysis of a large panel of minerals tested in various physical-chemical conditions shows that in general no protection on RNA backbone is exerted, with the interesting exception of ludwigite (Mg 2 Fe 3 +BO 5 ). Stability is a fundamental property of nucleic polymers and borate is an abundant component of the planet, hence the prebiotic interest of this analysis.

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“…Previous studies of the stability of the backbone of unstructured RNA reported that the sequences 5 0 -UpA-3 0 and 5 0 -CpA-3 0 are >100-and up to 35-fold, respectively, less chemically stable than any other dinucleotide steps. 33,34 The joiner J4/2 sequences of the G76A, G76C, and G76U mutant ribozymes all contain such dinucleotide steps. The 5 0 -C75pA76-3 0 dinucleotide step in the G76A mutant, for example, may therefore be expected to lead to a more intensive peak 3 0 of C75 than the wt sequence, yet the scission pattern of the G76A mutant is similar to that of the wt ribozyme ( Figure 6).…”

Section: Inmentioning

confidence: 99%

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

et al. 2007

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The self-cleaving hepatitis delta virus (HDV) ribozyme is essential for the replication of HDV, a liver disease causing pathogen in humans. The catalytically critical nucleotide C75 of the ribozyme is buttressed by a trefoil turn pivoting around an extruded G76. In all available crystal structures, the conformation of G76 is restricted by stacking with G76 of a neighboring molecule. To test whether this crystal contact introduces a structural perturbation into the catalytic core, we have analyzed approximately 200 ns of molecular dynamics (MD) simulations. In the absence of crystal packing, the simulated G76 fluctuates between several conformations, including one wherein G76 establishes a perpendicular base quadruplet in the major groove of the adjacent P1 stem. Second-site mutagenesis experiments suggest that the identity of the nucleotide in position 76 (N76) indeed contributes to the catalytic activity of a trans-acting HDV ribozyme through its capacity for hydrogen bonding with P1. By contrast, in the cis-cleaving genomic ribozyme the functional relevance of N76 is less pronounced and not correlated with the P1 sequence. Terbium(III) footprinting and additional MD show that the activity differences between N76 mutants of this ribozyme are related instead to changes in average conformation and modified cross-correlations in the trefoil turn.

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The reactivity of phosphodiester bonds within linear single-stranded oligoribonucleotides is strongly dependent on the base sequence

Cited by 62 publications

References 45 publications

An efficient method for long-term room temperature storage of RNA

An efficient method for long-term room temperature storage of RNA

Borate Minerals and RNA Stability

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme

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