Minor RNA Bases (Catalog as PDF)

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 TOM protected version has been discontinued and is replaced with the TBDMS version.

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 Discontinued
10-3914-90 100µm Discontinued
10-3914-02 0.25g Discontinued
  rSpacer CE Phosphoramidite has been discontinued. The substitute is : rSpacer TBDMS CE Phosphoramidite
4-Thio-U-TOM
4-Thio-U-TOM
5-Me-C-TOM
5-Me-C-TOM
2,6-Diaminopurine-TOM
2,6-Diaminopurine-TOM
Pyrrolo-C-TOM
Pyrrolo-C-TOM

Intellectual Property

Pyrrolo-dC is a joint development project of Berry & Associates, Inc. and Glen Research Corporation.

Pyrrolo-C-TOM is covered by US Patent No.: 7,144,995. Patented under European patent number 1483280.

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septumcapped vials suitable for ABI and other instruments. If you would like another type of vial/column add the following to the end of the catalog number.

Monomers  

For Instrument type
Add
Expedite
E
Mermade
M

Columns  

For Instrument type
Add
Expedite
E
Applied Biosystems 3900
A
Mermade
M

Please inquire for availability of columns for other instrument types.

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
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
I
I
5-Me-U
5-Me-U
Br-U
Br-U
5-I-U
5-I-U
6-Thio-G
6-Thio-G
2-Aminopurine-TBDMS
2-Aminopurine-TBDMS

Reference(s)

  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.

See Also

Minor RNA (TBDMS Protected) (Part 2)

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.
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
10-3915-95 50µm 80.00
10-3915-90 100µm 135.00
10-3915-02 0.25g 395.00
Zebularine
Zebularine
Pyridin-2-one
Pyridin-2-one
PseudoUridine
PseudoUridine
8-Aza-7-deaza-A
8-Aza-7-deaza-A
rSpacer TBDMS CE
rSpacer TBDMS CE

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septumcapped vials suitable for ABI and other instruments. If you would like another type of vial/column add the following to the end of the catalog number.

Monomers  

For Instrument type
Add
Expedite
E
Mermade
M

Columns  

For Instrument type
Add
Expedite
E
Applied Biosystems 3900
A
Mermade
M

Please inquire for availability of columns for other instrument types.

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
1-Me-A
1-Me-A
N6-Methyl-A
N6-Methyl-A

Reference(s)

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

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-Methyl-PseudoUridine
1-Methyl-PseudoUridine

minor rna (TBDMS PROTECTED) (Part 5)

The bright fluorescent tricyclic cytosine analogues tC and tC° 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.
Item Catalog No. Pack Price ($)
10-3517-95 50µm 245.00
10-3517-90 100µm 470.00
10-3517-02 0.25g 1195.00
Ribo-tC°
Ribo-tC°

See Also

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)
Pyrrolo-CTP (10mM)

See Also


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