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Chemical Synthesis of RNA Molecules. Molecules of ssRNA are produced by automated solid-phase synthesis employing -hydroxyl protecting groups that provide ribonucleoside phosphoramitides (Beaucage, ). Following the synthesis step, cognate ssRNAs are hybridized to form RNA duplexes.

Design, synthesis and evaluation of novel, branched trident small interfering RNA nanostructures for sequence-specific RNAi activity. Akash Chandela a and Yoshihito Ueno * ab a The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan b Course of Applied Life Science, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu , Japan.

//&#;&#;The close proximity of a protected -hydroxyl to the internucleotide phosphate may present problems, both in terms of formation of the internucleotide linkage and in the removal of the -protecting group once the oligoribonucleotide is synthesized. In addition, the internucleotide bond in RNA is less stable than that in DNA.

With the aim of circumventing this, the sterically less hindered and more reactive -(-cyanoethyl- N-ethyl-N-methylamino phosphoramidite), in conjunction with a -O-tBDMS group, has been tried, but without favorable results Therefore, the design of an ideal -OH protecting group for Scheme The -OH protecting groups used in oligo-RNA synthesis. improving RNA synthesis has been a key ...

//&#;&#;The direct functionalization of RNA by selective acylation at the -hydroxyl position is a powerful tool for structural and functional studies. This Review describes the chemical properties and ...

oligonucleotide synthesis is a commonly used approach to generate small and large-scale single strand material and has been established as a robust method for synthesizing oligonucleotide at various scales. In this process, to ensure correct chain growth, acid labile Di-methoxy-trityl (DMT) group is utilized to protect the Hydroxyl (OH) group

Evaluation of '-hydroxyl protection in RNA-synthesis using the H-phosphonate approach.

//&#;&#;That is the reason why all modern methods of RNA synthesis that employ different RNA phosphoramidite monomers have protective groups at the hydroxyl group. This protective group needs to be stable in basic conditions during base deprotection and can be easily removed to completion on the next processing step using different or orthogonal conditions.

T. W. Green, P. G. M. Wuts, Protective Groups in Organic Synthesis, Wiley-Interscience, New York, , , .

the -OH protecting group must be stable to the reagents and conditions used during solid-phase DNA/RNA synthesis in addition to those required for nucleobase and phosphate deprotection. Last, the -OH protecting group must be cleaved under conditions that will not harm the oligoribo-nucleotide. Thus, the search for an ideal -OH protecting

The problem for many years with RNA has been identifying appropriate protection of reactive sites on the nucleosides, especially an orthogonal set that includes protection of the -hydroxyl during synthesis. After various false starts, Steve Scaringe developed the -O-silyl-O-orthoester RNA synthesis chemistry in my laboratory

//&#;&#;In a study of potential prebiotic RNA synthesis, Sutherland and colleagues , showed that the -OH group of RNA can be acetylated under

or no bridge modifications (figure ). H NMR analysis of final compounds confirmed their structure and homogeneity (details on synthesis and purification in electronic supplementary material). Figure . Synthesis of cap analogues and . (i) . POCl ( equiv.), (MeO) PO, C, h; . H O, NaHCO ; (ii) CH I ( equiv.), DMSO, h ...

Figure . A) Depiction of the three modified RNA nucleosides hmC (), fC () and caC () together with the corresponding DNA ones d, d, and d.B) Sequence of an oligonucleotide (ON) containing all three modifications. Due to the sensitivity of RNA compared to DNA, a modified protecting group strategy to the one applied in our analogous DNA PA building

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treated with a solution of ortho-chlorobenzoyl chloride to protect the ' hydroxyl group, followed by succinic anhydride in the presence of -dimethylaminopyridine (DMAP) to form a mixture of protected and ' succinates. All new compounds were analyzed and characterized using NMR techniques. The protected amino uridine succinate was then

H . G O B I N D K H O R A N A Nucleic acid synthesis in the study of the genetic code Nobel Lecture, December , . Introduction Recent progress in the understanding of the genetic code is the result of the efforts of a large number of workers professing a variety of scientific disci-plines.

//&#;&#;Evaluation of '-hydroxyl protection in RNA-synthesis using the H-phosphonate approach. E Rozners Department of Organic Chemistry,

//&#;&#;Synthesis of RNA is less efficient owing to problems caused by the presence of the -hydroxyl group of ribose, which requires selective protection during oligonucleotide assembly. This reduces the coupling efficiency of RNA phosphoramidite monomers due to steric hindrance.

//&#;&#;The -Cyano,-dimethylethanimine- N-oxymethyl Group for the -Hydroxyl Protection of Ribonucleosides in the Solid-Phase Synthesis of RNA Sequences journal, February . Cielak, Jacek; Aus&#;n, Cristina; Grajkowski, Andrzej; Chemistry - A European Journal, Vol. , Issue ; DOI: /chem

Preparation of Solutions (,) Preparation of solutions using the following suggestions can help prevent RNase contamination: As an alternative to the historic use of DEPC, which can inhibit enzymatic reactions if not completely removed, we have found that Milli-Q (Millipore) purified water is sufficiently free of RNases for most RNA work.

RNA can be chemically synthesized by automated DNA / RNA synthesizers, using protected ribonucleosides activated as phosphoramidites. The efficiency of the synthesis depends greatly on the protecting groups used, especially the protecting group on the -hydroxyl functionality. The strategies employed to place the protecting groups on the desired functionality are quite inefficient ...

//&#;&#;In the second part, we describe our research on RNA, including synthetic approaches to stereodefined backbone-modified oligoribonucleotides with chiral linkages, and the development of a method for the synthesis of RNA based on the use of -cyanoethoxymethyl (CEM) as the -hydroxyl protecting group.

//&#;&#;Functional Group Protection. Martin D. Burke at the University of Illinois at Urbana-Champaign reported (Nature Chem. , , .) that the amphotericin B derivative could be site-selectively acylated at the C, C, or C hydroxyls by electronic tuning of the acylating agent (e.g. leading to ).Another impressive example of selective protection was disclosed (Nature Chem. ,

//&#;&#;Further functionalization of for RNA synthesis required selective -O-silylation to deliver derivative with free -OH group, which then can be converted to the phosphoramidite prior to use at the RNA synthesizer. Protocols for selective -O-silylation are available, however, the standard procedure using AgNO

//&#;&#;Evaluation of -hydroxyl protection in RNA-synthesis using the H-phosphonate approach

phosphoramidite synthesis using -t-butyldimethylsilyl (TBS) protected monomers for the RNA tracts. The TBS method of RNA synthesis () was chosen as it is widely used, the requisite reagents are readily available, and it has been shown to be effec-tive in the synthesis of a wide range of chemically modified RNA analogues ().

//&#;&#;Nucleic acid material of adequate quality is crucial for successful high-throughput sequencing (HTS) analysis. DNA and RNA isolated from archival FFPE material are frequently degraded and not readily amplifiable due to chemical damage introduced during fixation. To identify optimal nucleic acid extraction kits, DNA and RNA quantity, quality and performance in HTS applications were evaluated.

Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). E Westman and R Str&#;mberg

//&#;&#;Rozners E, Westman E, Str&#;mberg R. Evaluation of '-hydroxyl protection in RNA-synthesis using the H-phosphonate approach. Nucleic Acids Res. Jan ; ():. [ PMC free article ] [ PubMed ]

//&#;&#;Abstract. Recent studies on the chemical synthesis of RNA and related derivatives are reviewed. In particular, a variety of new -hydroxyl protecting groups that are developed during the past decade are described and compared with the conventional ones

//&#;&#;The RNA microarrays will be synthesized in situ on glass substrates using the recently developed RNA phosphoramidite monomers incorporating acetal levulinyl ester

methylsilyl for '-hydroxyl protection. It is noteworthy that the use of protecting groups common to both ribo- and deoxyribonucleotides renders the two types of structure compatible from the viewpoint of automated synthesis and deprotection. This consideration prompted the synthesis and evaluation

This chapter enables the reader to carry out the solid-phase synthesis of ribonucleic acid (RNA) using -cyanoethyl phosphoramidite chemistry combined with

protected intermediate, Amt(Boc) -Nea,Nea was treated with TFA/TIS/H O :: for h at room temperature and the expected ligand, Amt-Nea,Nea, was isolated by HPLC with an overall % yield. Regarding the synthesis of the compound containing three different RNA-binding