Minor RNA Phosphoramidites (TBDMS Protected)

Inosine and 5-Methyl-Uridine are useful for analyzing RNA structure and activity relationships. 5-Bromo-Uridine and 5-Iodo-Uridine have been used for crystallography studies and cross-linking experiments. 6-Thioguanosine (6-thio-G) has applications in ribozyme and siRNA research, as well as in RNA-protein interactions. The removal of the silyl protecting group without interfering with the sulfur is critical. This is removed1 cleanly by triethylamine trihydrofluoride in DMSO but t-butylammonium fluoride (TBAF) leads to degradation of the thio-nucleotide analogue and should not be used. 2-Aminopurine riboside is useful for analyzing RNA structure and activity relationships, for example, in ribozyme studies.

8-Aza-7-deaza-Adenosine is an isomer of Adenosine with virtually identical electron density. The N7 nitrogen is not available for hydrogen bonding.

Ribozyme activity is substantially affected by the substitution of modified pyrimidine bases. Zebularine (pyrimidin-2-one ribonucleoside) may be regarded as a Cytidine derivative lacking the exocyclic amino group. Zebularine and Pyridin-2-one Ribonucleoside, the 3-deaza analogue of Zebularine, are prime candidates for use in evaluating ribozyme activity and function. It should be noted that Zebularine is mildly fluorescent, absorbing at 298nm and emitting at 367nm.

PseudoUridine is one of the most common modified nucleosides found in RNA. The availability of a phosphoramidite will allow detailed research into the effects of this modified base on RNA structure and activity.

rSpacer is used to introduce an abasic site to an RNA sequence.

Methylation of adenosine at position 1 produces a drastic functional change in the nucleobase. 1-Methyladenosine (pKa 8.25) is a much stronger base than adenosine (pKa 3.5). N-1 methylation excludes participation of the adenine base in canonical Watson–Crick base pairing and provides a positive charge to the nucleobase. This modification also alters the hydrophobicity of the base, the stacking properties, the ordering of water molecules and the chelation properties. The base may become involved in non-canonical hydrogen bonding, in electrostatic interactions and, in general, it may contribute to the conformational dynamics of the tRNA.

In the central dogma of molecular biology, genetic information flows from DNA to RNA and then to protein. Reversible epigenetic modifications on genomic DNA and histone have been known to substantially regulate gene expression. On the other hand, there exists more than 100 naturally occurring chemical modifications in RNA; however, the functions of these RNA modifications are largely unknown. Whether some of these modifications in RNA can be reversed and could impact gene expression in the central dogma was unknown until the recent discovery of N6-methyladenosine (N6-Me-A) as the first example of reversible RNA methylation.1 We offer the N6-Me-A RNA monomer with a phenoxyacetyl protecting group to minimize potential branching. We have shown N6-Me-A-CE Phosphoramidite to be completely compatible with all popular RNA synthesis and deprotection methods, from UltraMild to the most popular procedure using AMA for deprotection.

RNA methylation occurs in a large selection of RNA nucleosides and this post transcriptional modification of RNA, carried out by a variety of RNA methyltransferases, appears in a wide variety of RNA species - including tRNA, mRNA, miRNA and RNA viruses. Over 90 methylated nucleosides have been found in tRNA and these play many significant roles in tRNA structure. In addition, methylation appears to mark the tRNA as mature, preventing its degradation as well as directing localization within the cell. mRNA, modified with 1-methylpseudouridine (1-Me-Y) alone or in combination with 5-methylcytidine (5-Me-C), significantly increases protein expression in cells and mouse models. 1-Me-Y is also a modified nucleobase that can greatly enhance the properties of mRNA by reducing immunogenicity and increasing stability.

The bright fluorescent tricyclic cytosine analogues tC and tCO stand out among fluorescent bases due to their virtually unquenched fluorescence inside single- or double-stranded DNA. Until recently, this family of tricyclic cytosines had only been studied and used in DNA contexts and, importantly, introduced as possible donors of the first DNA base analogue FRET-pair with tCnitro. Fluorescent base analogues for RNA are limited in number compared to their DNA counterparts. To facilitate the application of such analogues, characterization of their structural and dynamics behavior in RNA compared to the corresponding natural nucleoside is important. We now introduce the tCO ribonucleoside, which has been incorprated into a range of RNA sequences, where it was shown to be a very potent and useful fluorophore in this context.1 Glen Research offers this useful fluorescent ribonucleoside analogue in cooperation with ModyBase HB.