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MINOR RNA BASES

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MINOR RNA PHOSPHORAMIDITES (TOM PROTECTED)

Glen Research offers minor RNA phosphoramidites with either TOM or TBDMS protecting groups. 4-Thio-U, 5-Methyl-Cytidine, 2-Aminopurine riboside 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 ($)
4-Thio-U-TOM-CE Phosphoramidite	10-3052-95	50 �mole	212.50
	10-3052-90	100 �mole	425.00
	10-3052-02	0.25g	975.00
5-Me-C-TOM-CE Phosphoramidite	10-3064-95	50�mole	95.00
	10-3064-90	100�mole	190.00
	10-3064-02	0.25g	475.00
2-Aminopurine-TOM-CE Phosphoramidite	10-3074
(Product has been changed to TBDMS protection, 10-3070.)
2,6-Diaminopurine-TOM-CE Phosphoramidite (Discontinued - Use 10-3085)	10-3084		DISCONTINUED
2,6-Diaminopurine-TOM-CE Phosphoramidite	10-3085-95	50�mole	212.50
(2-Amino-A)	10-3085-90	100�mole	425.00
	10-3085-02	0.25g	975.00
Pyrrolo-C-TOM-CE Phosphoramidite	10-3017-95	50�mole	212.50
	10-3017-90	100�mole	425.00
	10-3017-02	0.25g	975.00
rSpacer CE Phosphoramidite	10-3914-95	50 µmole	90.00
	10-3914-90	100 µmole	180.00
	10-3914-02	0.25g	495.00

Also See

Minor TBDMS Monomers p100

2-Aminopurine TBDMS p100

Pyrrolo-CTP p102

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septum-capped 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
Beckman Oligo 1000	B
Pharmacia Gene Assembler	P
Mermade	M
	Columns
For Instrument type	Add
Applied Biosystems 3900	A
Expedite	E
Mermade	M
Please inquire for availability of columns for other instrument types.

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 ($)
Amino-Modifier C6-U Phosphoramidite	10-3039-95	50�mole	360.00
	10-3039-90	100�mole	720.00
	10-3039-02	0.25g	1475.00

Also See

Pyrrolo-dC p60

OTHER INSTRUMENT TYPES

	Monomers
For Instrument type	Add
Expedite	E
Beckman Oligo 1000	B
Pharmacia Gene Assembler	P
Mermade	M
	Columns
For Instrument type	Add
Applied Biosystems 3900	A
Expedite	E
Mermade	M
Please inquire for availability of columns for other instrument types.

Also See

Minor TOM Monomers p96

References

(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.

Also See

Pyrrolo-dC p 60

Pyrrolo-C p99

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 ($)
I-CE Phosphoramidite	10-3040-95	50 �mole	95.00
	10-3040-90	100 �mole	190.00
	10-3040-02	0.25g	475.00
5-Me-U-CE Phosphoramidite	10-3050-95	50 �mole	95.00
(T)	10-3050-90	100 �mole	190.00
	10-3050-02	0.25g	475.00
Br-U-CE Phosphoramidite	10-3090-95	50 �mole	98.00
	10-3090-90	100 �mole	195.00
	10-3090-02	0.25g	475.00
I-U-CE Phosphoramidite	10-3091-95	50 �mole	98.00
	10-3091-90	100 �mole	195.00
	10-3091-02	0.25g	475.00
6-Thio-G-CE Phosphoramidite	10-3072-95	50 �mole	250.00
	10-3072-90	100 �mole	500.00
	10-3072-02	0.25g	1200.00
2-Aminopurine-TBDMS-CE Phosphoramidite	10-3070-95	50 �mole	212.50
	10-3070-90	100 �mole	425.00
	10-3070-02	0.25g	975.00

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 ($)
7-Deaza-A-CE Phosphoramidite	10-3001-95	50 �mole	225.00
	10-3001-90	100 �mole	450.00
	10-3001-02	0.25g	1100.00
Zebularine-CE Phosphoramidite	10-3011-95	50 �mole	125.00
	10-3011-90	100 �mole	250.00
	10-3011-02	0.25g	650.00
Pyridin-2-one-CE Phosphoramidite	10-3012-95	50 �mole	210.00
	10-3012-90	100 �mole	420.00
	10-3012-02	0.25g	1200.00
Nebularine-CE Phosphoramidite	10-3041-95	50 �mole	225.00
(Purine Ribonucleoside)	10-3041-90	100 �mole	450.00
	10-3041-02	0.25g	1250.00
PseudoUridine-CE Phosphoramidite	10-3055-95	50 �mole	175.00
	10-3055-90	100 �mole	350.00
	10-3055-02	0.25g	995.00
8-Aza-7-deaza-A-CE Phosphoramidite	10-3083-95	50 �mole	300.00
	10-3083-90	100 �mole	600.00
	10-3083-02	0.25g	1500.00

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.

Item	Catalog No.	Pack	Price ($)
1-Me-A-CE Phosphoramidite<	10-3501-95	50 �mole	190.00
	10-3501-90	100 �mole	380.00
	10-3501-02	0.25g	975.00

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.