Of branched RNAs

The Structure and Folding of Branched RNA Analyzed by Fluorescence Resonance Energy Transfer... 

The hydrolytic stability of branched RNA where the branch-point is a phospho-triester unit revealed that when the triester was embedded within the oligonucleotide it was stable to base-mediated hydrolysis by more than an order of magnitude compared to the simple trinucleotide unit. 5 -Aminoalkyl phosphate nucleotides have been synthesised as analogues of aminoacyl adenylates, and salicyl phospho-diesters of adenylates as potential inhibitors of Mycobacterium tuberculosis. ... 

Damha, M. J, Pon, R. T, and Ogilvie.K. K (1985) Chemical synthesis of branched RNA novel trinucleoside diphosphates containing vicinal 2 -5 and 3 -5 phosphodiester linkages. Tetrahedron Lett 26,4839-4842... 

In the case of hyperphenylalaninaemia, which occurs ia phenylketonuria because of a congenital absence of phenylalanine hydroxylase, the observed phenylalanine inhibition of proteia synthesis may result from competition between T.-phenylalanine and L-methionine for methionyl-/RNA. Patients sufferiag from maple symp urine disease, an inborn lack of branched chain oxo acid decarboxylase, are mentally retarded unless the condition is treated early enough. It is possible that the high level of branched-chain amino acids inhibits uptake of L-tryptophan and L-tyrosiae iato the brain. Brain iajury of mice within ten days after thek bkth was reported as a result of hypodermic kijections of monosodium glutamate (MSG) (0.5—4 g/kg). However, the FDA concluded that MSG is a safe kigredient, because mice are bom with underdeveloped brains regardless of MSG kijections (106). 

The minimal cell, as the simplest system which has all the required properties of life (metabolism, self-reproduction and the ability to evolve), is presently studied as part of a new research discipline synthetic biology. This includes subjects such as synthesis in branches of biological systems, for example, of new RNA species, new peptides and new nucleic acid analogues, as well as the synthesis of peptide nucleic acids. One example is the work of M. R. Ghadiri and G. von Kiedrowski on self-replication of oligonucleotides and oligopeptides (Luisi, 2006b). 

Oskuee RK, Philipp A, Dehshahri A, Wagner E, Ramezani M (2010) The impact of carboxyalkylation of branched polyethylenimine on effectiveness in small interfering RNA delivery. J Gene Med 12 729-738... 

The viral load test quantifies viremia by measuring the amount of viral RNA. There are several methods used for determining the amount of HIV RNA reverse transcriptase-coupled polymerase chain reaction, branched DNA, and nucleic acid sequence-based assay. Each assay has its own lower limit of sensitivity, and results can vary from one assay method to the other therefore, it is recommended that the same assay method be used consistently within patients. 

Of the five snRNAs, U2 and U6 interact with the reaction site (the 5 splice site and the branch point) in the first chemical step. These two snRNAs are known to anneal together to form a stable-based paired structure in the absence of proteins and in the presence of ions as shown in Fig. 13, with U2 acting as an inducer molecule that displaces the U4 (that is an antisense molecule that regulates the catalytic function of U6 RNA) from the initially formed U4-U6 duplex. The secondary (or higher ordered) structure of the U2-U6 complex consists of the active site of the spliceosome. Recent data suggests that these two snRNAs function as the catalytic domain of the spliceosome that catalyzes the first step of the splicing reaction [145]. 

One specific application of branch-forming deoxyribozymes is named DECAL, which stands for deoxyribozyme-catalyzed labeling of RNA (Baum and Silverman, 2007). This section describes the DECAL approach and its implementation. 

The analytical- and preparative-scale DECAL procedures are essentially equivalent to those used for linear RNA ligation by the 9DB1 deoxyribo-zyme (Section 3.3) as well as for branched RNA formation. If degradation of a large target RNA is a concern, then the CHES, pH 9.0, 40 mM Mg2+ conditions may be replaced with HEPES, pH 7.5, 40 mM Mg2-1- a longer incubation time will be required. 

Damha, M. J., Ganeshan, K., Hudson, R. H., and Zabarylo, S. V. (1992). Sobd-phase synthesis of branched oligoribonucleotides related to messenger RNA spbcing intermediates. Nucleic Adds Res. 20, 6565-6573. 

Wang, Y., and Silverman, S. K. (2003). Characterization of deoxyribozymes that synthesize branched RNA. Biochemistry 42, 15252-15263. 

Single-molecule studies have revealed that some branched RNA species exhibit surprisingly heterogeneous dynamics (Lemay et ah, 2006 Tan et ah, 2003 Zhuang et al, 2002), while others (such as a simple 4H RNA junction) do not. Rates of conformational transitions can vary a hundred... 

In a recent development, FRET has been used to study the dynamics of single DNA junctions while under the application of stretching force (Hohng et al, 2007) this experiment should be directly applicable to branched RNA species. 

RNA and DNA, and to study the effects of phosphorylation state and charge on the results. " In the polymer field. Berry et al. used BDE calculations for model alkyl urethanes to identify vulnerable sites to radical attack, and to examine the effect of branching on the photostability of urethane coatings. ... 

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