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RNA is susceptible to this base-catalyzed hydrolysis because the ribose sugar in RNA has a hydroxyl group at the 2’ position. [1] This feature makes RNA chemically unstable compared to DNA, which does not have this 2’ -OH group and thus is not susceptible to base-catalyzed hydrolysis. [1] Mechanism of base catalyzed RNA hydrolysis.
This is likely why nature has "chosen" a four base alphabet: fewer than four would not allow the creation of all structures, while more than four bases are not necessary to do so. Since RNA is charged, metal ions such as Mg 2+ are needed to stabilise many secondary and tertiary structures. [17]
This is due to the fact that the coding strand is single-stranded during transcription, which is chemically more unstable than double-stranded DNA. During elongation of transcription, supercoiling can occur behind an elongating RNA polymerase, leading to single-stranded breaks.
RNA is notoriously unstable and vulnerable to ribonucleases, which has thus been an obstacle to the production and analysis of the cellular transcriptome.First referenced by Berger et al., the substance was used to prevent the digestion of RNA during isolation from white blood cells, and was rapidly adopted for such purposes as the acquisition of RNA from green beans.
AREs are one of the most common determinants of RNA stability in mammalian cells. [1] The function of AREs was originally discovered by Shaw and Kamen in 1986. [2] AREs are defined as a region with frequent adenine and uridine bases in a mRNA. They usually target the mRNA for rapid degradation.
The structural hierarchy in RNA is usually described in terms of a stem-loop 2D secondary structure, which further folds to form its 3D tertiary structure, stabilized by what are referred to as long range tertiary contacts. Most often the non-canonical base pairs are involved in those tertiary contacts or extra-stem base pairs.
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Cryptic unstable transcripts (CUTs) are a subset of non-coding RNAs (ncRNAs) that are produced from intergenic and intragenic regions. CUTs were first observed in S. cerevisiae yeast models and are found in most eukaryotes . [ 1 ]