Small stable RNA

Table 35-1. Some of the species of small stable RNAs found in mammalian cells.

A large number of discrete, highly conserved, and small stable RNA species are found in eukaryotic cells. The majority of these molecules are complexed with proteins to form ribonucleoproteins and are distributed in the nucleus, in the cytoplasm, or in both. They range in... 

Eukaryotic transcription uses three distinct RNA polymerases, which are specialized for different RNAs. RNA polymerase I makes Ribosomal RNAs, RNA polymerase II makes messenger RNAs, and RNA polymerase III makes small, stable RNAs such as transfer RNAs and 5S ribosomal RNA. Eukaryotic RNA polymerases are... 

Alluvia S, Weinstein-Eischer D, Zhang A, Postow L, Storz G. A small, stable RNA induced by oxidative stress Role as a pleiotropic regulator and antimutator. Cell 1997 90(1) 43—53. 

Zieve, G. W., 1981, Two groups of small stable RNAs, Cell 25 296. 

There are three major classes of RNA in cells messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). Of these, the latter two are termed stable RNAs, as they have a longer half-life than that of mRNA [1], Ribosomal RNA is the most abundant class of RNA in a cell. In a typical eukaryotic cell (yeast, plant, and animal), there are other RNAs, such as organelle RNA and small RNAs in nuclei (snRNAs) or in the cytoplasm (7S RNA). In eukaryotic cells, most RNAs are synthesized as larger precursor molecules and are then processed into smaller mature RNAs. Total RNA in a human cell may range from 10 to 30 pg, with most of it in the cytoplasm (about 85%), while the rest is in the nucleus. 

RNA polymerase I synthesizes only pre-rRNA. RNA polymerase II synthesizes mRNAs and some of the small nuclear RNAs that participate in mRNA splicing. RNA polymerase III synthesizes tRNAs, 5S rRNA, and several other relatively short, stable RNAs. 

Segments of double helix that are shorter than tetranucleotides (having fewer than about 4 base pairs) are unstable at physiological temperatures due to their small extent of base stacking and small number of interstrand hydrogen bonds. Until the critical length of RNA is synthesized for a stable RNA/DNA double helix, the short initial di- and trinucleotides are susceptible to release. 

RNase A is a single-domain protein, a pancreatic enzyme which catalyses the cleavage of single-stranded RNA. This protein consists of 124 amino acid residues with a molecular mass of 13.7 kDa. It has traditionally served as a model for protein folding because it is small, stable and has a well-known native structure. The el protons of the four RNase A histidine residues are well-resolved from other protons in the H NMR spectrum of the native protein in D2O they have been used in this work to monitor the structural changes of four distinct segments in the molecule during cold, heat and pressure denaturation processes. His-12 and His-119 are part of the catalytic... 

Variously astatinated nucleic acids, At-DNA and At-RNA, have been obtained via their chloromercuri derivatives with radiochemical yields of >90%. These compounds have been isolated and proved stable to purification by gel filtration. There was no evidence of any deastatination at pH 2-11 on incubation for 20 hours, nor at neutral pH in the presence of small amounts of reductants or oxidants at room temperature. However, heating to 50° C caused slow deastatination with 15-20% astatine loss in 20 hours. On heating of the At-nucleic acids there was some degree of degradation hut this did not appear to involve breakage of the C—At bond (i 70). 

Figure 10.22 Vesicle size selection by RNA added to a mixture of small ( 80 nm diameter) and large vesicles ( 160 nm) from 0.5 mM POPC-3.5% CTAB in 20 mM sodium phosphate buffer (pH 7.0). (a) The initial size distribution of the 1 1 mixture (b) the size distribution 4 min after RNA addition, during the selection process (c) the stable final size distribution after 15 min, with one peak for small diameters ( 90 nm) and a second peak indicating aggregates of large vesicles (> 1000 nm). As mentioned in the text, this process is reversible upon addition of RNAase (Thomas and Luisi, 2004.)...

UG pairs provide a very small amount of stabilization to an RNA double helix, while the presence of unpaired bases has a destabilizing effect. The most stable hairpin loops contain four or five bases. Depending upon whether the loop is "closed" by CG or AU, the helix is destabilized by 20-30 kj/mol. "Bulge loops," which protrude from one side of a helix, have a smaller destabilizing effect. An example of the way in which Table 5-2 can be used to estimate the energies of formation of a loop in a straight-chain RNA is illustrated in Fig. 5-9. Similar analysis of base pairing in DNA can also be done.53 55... 

The genetic instructions contained in DNA are transcribed into RNA when a small portion of the DNA double helix unwinds and one of the two DNA strands acts as a template for complementary ribonucleotides to line up, a process similar to that of DNA replication (Figure 24.20). The only difference is that uracil (U) rather than thymine lines up opposite adenine. Once completed, the RNA molecule separates from the DNA template, and the DNA rewinds to its stable doublehelix conformation. 

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