Minor RNA Bases

Minor RNA Phosphoramidites (TOM Protected)

Glen Research offers minor RNA phosphoramidites with either TOM or TBDMS protecting groups. 4-Thio-U, 5-Methyl-Cytidine, and 2-Amino-Adenosine are useful for analyzing RNA structure and activity relationships, for example, in ribozyme studies.

Pyrrolo-C is a fluorescent nucleoside whose fluorescence is sensitive to its environment and is ideal for probing RNA structure. It base-pairs as a normal C nucleotide. It is highly fluorescent and its excitation and emission are well to the red of most fluorescent nucleotide analogs, which eliminates or reduces background fluorescence from proteins. Pyrrolo-CTP has potential uses in biological assay development.

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

The protecting scheme for 2,6-Diaminopurine has been changed and the original product (10-3084) has been replaced with the optimized product (10-3085) below.

Item Catalog No. Pack Price ($)
10-3052-95 50µm 212.50
10-3052-90 100µm 425.00
10-3052-02 0.25g 975.00
10-3064-95 50µm 95.00
10-3064-90 100µm 190.00
10-3064-02 0.25g 475.00
10-3085-95 50µm 212.50
  (2-amino-A) 10-3085-90 100µm 425.00
10-3085-02 0.25g 975.00
10-3017-95 50µm 212.50
10-3017-90 100µm 425.00
10-3017-02 0.25g 975.00
10-3914-95 50µm 90.00
10-3914-90 100µm 180.00
10-3914-02 0.25g 495.00





rSpacer CE

See Also

RNA Sequence Modifier (TOM Protected)

Amino-Modifier C6-U has been added to the growing family of sequence modifiers and we envisage applications in RNA structural studies as well as for labelling siRNA to probe uptake and cellular distribution.

Item Catalog No. Pack Price ($)
10-3039-95 50µm 360.00
10-3039-90 100µm 720.00
10-3039-02 0.25g 1475.00

Amino-Modifier C6-U

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.

Item Catalog No. Pack Price ($)
10-3040-95 50µm 95.00
10-3040-90 100µm 190.00
10-3040-02 0.25g 475.00
10-3050-95 50µm 95.00
  (T) 10-3050-90 100µm 190.00
10-3050-02 0.25g 475.00
10-3090-95 50µm 98.00
10-3090-90 100µm 195.00
10-3090-02 0.25g 475.00
10-3091-95 50µm 98.00
10-3091-90 100µm 195.00
10-3091-02 0.25g 475.00
10-3072-95 50µm 250.00
10-3072-90 100µm 500.00
10-3072-02 0.25g 1200.00
10-3070-95 50µm 212.50
10-3070-90 100µm 425.00
10-3070-02 0.25g 975.00







See Also


  1. C.J. Adams, J.B. Murray, M.A. Farrow, J.R.P. Arnold, and P.G. Stockley, Tetrahedron Lett., 1995, 36, 5421-5424.
  2. D.A. Berry, et al., Tetrahedron Lett, 2004, 45, 2457-2461.

Minor RNA (TBDMS Protected) (Part 2)

7-Deaza-Adenosine is lacking nitrogen at the 7-position, which is replaced by carbon. The N7 position in adenosine takes part in non-Watson and Crick hydrogen bonding, which may be relevant to RNA folding and subsequent activity. This Adenosine analogue is also known as Tubercidin. 8-Aza-7-deaza-Adenosine is an isomer of Adenosine with virtually identical electron density. Again, the N7 nitrogen is not available for hydrogen bonding. Nebularine or Purine Nucleoside can be viewed as an Adenosine derivative that is lacking the exocyclic amino group. This molecule allows researchers to determine the relevance of the exocyclic amine of Adenosine to RNA structure and function.

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.

Item Catalog No. Pack Price ($)
10-3011-95 50µm 125.00
10-3011-90 100µm 250.00
10-3011-02 0.25g 650.00
10-3012-95 50µm 210.00
10-3012-90 100µm 420.00
10-3012-02 0.25g 1200.00
10-3055-95 50µm 175.00
10-3055-90 100µm 350.00
10-3055-02 0.25g 995.00
10-3083-95 50µm 300.00
10-3083-90 100µm 600.00
10-3083-02 0.25g 1500.00





Minor RNA (TBDMS Protected) (Part 3)

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.

Item Catalog No. Pack Price ($)
10-3501-95 50µm 190.00
10-3501-90 100µm 380.00
10-3501-02 0.25g 975.00
10-3005-95 50µm 285.00
10-3005-90 100µm 550.00
10-3005-02 0.25g 1295.00



See Also

Minor RNA (TBDMS Protected) (Part 4)

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-Ψ ) alone or in combination with 5-methylcytidine (5-Me-C), significantly increases protein expression in cells and mouse models. 1-Me-Ψ is also a modified nucleobase that can greatly enhance the properties of mRNA by reducing immunogenicity and increasing stability.

Item Catalog No. Pack Price ($)
10-3056-95 50µm 420.00
10-3056-90 100µm 820.00
10-3056-02 0.25g 2300.00



  1. (1) Y. Fu, D. Dominissini, G. Rechavi, and C. He,
    Nat Rev Genet, 2014, 15, 293-306.

Minor RNA Triphosphates

Pyrrolo-dC is a fluorescent nucleoside that codes as dC and base pairs efficiently with dG. Preliminary evidence indicates that pyrrolo-dC triphosphate is an excellent substrate for Taq, Pfu and Vent polymerases and is incorporated specifically opposite dG. Pyrrolo-dCTP has been available for some time and is in use in biological assays. Pyrrolo-CTP is a fluorescent ribonucleotide with fluorescence exquisitely sensitive to its environment and is of great interest for RNA structural research. The pyrrolo-C project is a joint development by Berry and Associates, Inc. and Glen Research Corporation.

Item Catalog No. Pack Price ($)
81-3017-01 0.1mL 270.00

Pyrrolo-CTP (10mM)

See Also



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