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Full Catalog (page 29)
Product Number Product Name Molecular Formula Cas. No.

PYA 11001

Formycin A

C10H15N5O5 

6742-12-7 

Notes

Sold as the monohydrate.

Alternate Name(s):

D-Ribitol

8-Aza-9-deazaadenosine, or 7-Amino-3-β-D-ribofuranosyl-1H-pyrazolo[4,3-d]pyrimidine

PYA 11002

Formycin B

C10H12N4O5 

13877-76-4 

Notes

Substantial discounts available on multi-gram orders.

Alternate Name(s):

Laurusin, Ohyamycin

1,4-Dihydro-3-β-D-ribofuranosyl-7H-pyrazolo[4,3-d]pyrimidin-1-one

PYA 11004

Pyrazofurin

C9H13N3O6 

30868-30-5 

Notes

Substantial discounts available on multi-gram orders.

Sold as the monohydrate, C9H15N3O7, MW = 278.09.

Alternate Name(s):

4-Hydroxy-3-β-D-ribofuranosyl-1H-pyrazole-5-carboxamide

PYA 11005

2'-Deoxypseudoisocytidine

C9H13N3O4 

65358-18-1 

Description

An isostere of 2'-deoxycytidine that offers an additional hydrogen-bond donor at N3. Download a brief overview here. For the phosphoramidite of 2'-deoxypseudoisocytidine, see BA 0236. For the nucleoside pseudoisocytidine, see PYA 11060.

Notes

An isostere of 2'-deoxycytidine.

Alternate Name(s):

Ψ-iso-dC, pidC

PYA 11010

2'-Deoxypseudouridine

C9H12N2O5 

39967-60-7 

PYA 11020

1-(β-D-2-Deoxyribofuranosyl)-3-
nitropyrrole

C9H12N2O5 

157066-48-3 

PYA 11030

1-(5-O-(Dimethoxytrityl)-β-D-2-
deoxyribofuranosyl)-3-nitropyrrole

C30H30N2O7 

166984-63-0 

PYA 11035

5'-O-(Dimethoxytrityl)-N-
(dimethylamino)methylidene-2'-
deoxypseudoisocytidine

C33H36N4O6 

307314-30-3 

Notes

For the phosphoramidite of 2'-deoxypseudoisocytidine, see BA 0236.

PYA 11040

1,3-Dimethyl-2'-deoxypseudouridine

C11H16N2O5 

65358-16-9 

PYA 11050

1,3-Dimethylpseudouridine

C11H16N2O6 

64272-68-0 

PYA 11052

N1-
Methylpseudouridine

C10H14N2O6 

13860-38-3 

Notes

Gram quantities available. Please inquire.

PYA 11055

6-Methyl-3-(β-D-2-
deoxyribofuranosyl)furano-[2,3-d]
pyrimidin-2-one

C12H14N2O5 

383897-60-7 

Description

6-Methyl-3-(β-D-2-deoxyribofuranosyl)furano[2,3-d]pyrimidin-2-one is a fluorescent nucleoside similar to ethenoadenosine. Upon treatment with ammonia, the furano ring is converted to a pyrrolo ring. See PYA 11090 for the pyrrolo version.

PYA 11056

Showdomycin

C9H11NO6 

16755-07-0 

Alternate Name(s):

3-β-D-Ribofuranosylpyrrole-2,5-dione

PYA 11057

6-Aza-2'-deoxyuridine

C8H11N3O5 

20500-29-2 

Description

The nitrogen atom in place of the methine group at position 6 of the uracil ring in 6-Aza-2'-deoxyuridine (6-aza-dU)1 results in a significant lowering of the pKa of the N3 hydrogen (6.8) vs. that of 2'-deoxyuridine (9.3).2 Unlike dU, 6-aza-dU is deprotonated at neutral pH, thus bestowing the uracil base with a negative charge. Further, there are significant conformational changes imparted by the presence of the 6-aza substitution: 6-Aza-dU has a high-anti conformation and is present in solution with N-type sugar pucker.2

See also 6-Aza-dU CEP, the phosphoramidite version for incorporation of 6-aza-dU residues into oligonucleotides, the nucleoside 6-Azathymidine, and its phosphoramidite 6-Azathymidine CEP.

(1) (a) Kara, J.; Sorm, F. Coll. Czech. Chem. Commun. 1963, 28, 1441-1448. (b) Holy, A.; Cech, D. Coll. Czech. Chem. Commun. 1974, 39, 3157-3167. © Drasar, P.; Hein, L.; Beranek, J. Coll. Czech. Chem. Commun. 1976, 41, 2110-2123. (d) Freskos, J. N. Nucleosides Nucleotides 1989, 8, 549-555.

(2) Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.

Notes

6-Aza-2'-deoxyuridine (6-aza-dU) has a nitrogen atom in place of the methine group at position 6 of the uracil ring.

PYA 11058

6-Azathymidine

C9H13N3O5 

13410-30-5 

Description

The nitrogen atom in place of the methine group at position 6 of the thymine ring in 6-Azathymidine1 results in a significant lowering of the pKa of the N3 hydrogen (7.0)2 vs. that of thymidine (10.0). Hence, 6-azathymidine will be significantly deprotonated at neutral pH.

The phosphoramidite of this nucleoside has been incorporated into oligonucleotides,1 where it imparts nuclease resistance when installed at the 5'-position. Duplexes with DNA or RNA are only slightly destabilized, and heteroduplexes with RNA support RNase-H cleavage.

See also the nucleoside 6-Aza-2'-deoxyuridine and the phosphoramidites 6-Aza-dU CEP and 6-Azathymidine CEP.

(1) Sanghvi, Y.; Hoke, G. D.; Freier, S. M.; Zounes, M. C.; Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P. D. Nucleic Acids Res. 1993, 21, 3197-3203.

(2) Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.

Notes

6-Azathymidine has a nitrogen atom in place of the methine group at position 6 of the thymine ring.

PYA 11060

Pseudoisocytidine hydrochloride

C9H13N3O5·HCl 

57100-18-2 (free base) 57100-20-6 (HCl salt) 

Description

This isostere of cytidine offers an additional hydrogen-bond donor at N3. Download a brief overview here. For the phosphoramidite of 2'-deoxypseudoisocytidine, see BA 0236. For the nucleoside 2'-deoxypseudoisocytidine, see PYA 11005.

Notes

An isostere of cytidine.

Alternate Name(s):

Ψ-iso-C, piC

PYA 11070

Pseudothymidine

C10H14N2O5 

65358-15-8 

PYA 11080

Pseudouridine

C9H12N2O6 

1445-07-4 

Notes

NOTE: This is the beta isomer, and pricing shown is for pseudouridine obtained by fermentation. We also offer synthetic pseudouridine for $1,550.00/g.

PYA 11090

Pyrrolo-dC

C12H15N3O4 

382137-74-8 

Description

Pyrrolo-dC is a fluorescent analog of 2'-deoxycytidine (Berry, et. Al, Tetrahedron Lett. 2004, 45 (11), 2457-2461). It is highly fluorescent, exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. We also offer pyrrolo-C, a fluorescent analog of cytidine.

The phosphoramidites of pyrrolo-C and pyrrolo-dC suitable for oligonucleotide synthesis are available from Berry & Associates (Products BA 0170 and BA 0245) or from Glen Research, our development partner for these products. Glen Research also offers the triphosphates of pyrrolo-C and -dC. We also offer the simple fluorescent pyrrolocytosine heterocycle (i.e., pyrrolo-C aglycone (HC 9060). For photophysical studies on these fluorescent pyrrolopyrimidines, see: Thompson, K. C.; Miyake, N., J. Phys. Chem. B, 2005, 109, 6012-6019.

Notes

Fluorescent analog of 2’-deoxycytidine.

Alternate Name(s):

6-Methyl-3-(β-D-2-deoxyribofuranosyl)pyrrolo[2,3-d]pyrimidin-2-one

PYA 11092

6-Methyl-3-(β-D-2-ribofuranosyl)
pyrrolo[2,3-d]pyrimidin-2-
one

C12H15N3O5 

644962-84-5 

Description

Pyrrolo-C is a fluorescent analog of cytidine (Berry, et. Al, Tetrahedron Lett. 2004, 45 (11), 2457-2461). It is highly fluorescent, exhibiting an emission maximum at approximately 473 nm. We also offer pyrrolo-dC, a fluorescent analog of cytidine. The phosphoramidites of pyrrolo-C and pyrrolo-dC suitable for oligonucleotide synthesis are available from Berry & Associates (Products BA 0170 and BA 0245) or from Glen Research, our development partner for these products. Glen Research also offers the triphosphates of pyrrolo-C and -dC. We also offer the simple fluorescent pyrrolocytosine heterocycle (i.e., pyrrolo-C aglycone (HC 9060). For photophysical studies on these fluorescent pyrrolopyrimidines, see: Thompson, K. C.; Miyake, N., J. Phys. Chem. B, 2005, 109, 6012-6019.

Notes

A fluorescent analog of cytidine.

Alternate Name(s):

Pyrrolo-C

PYA 11095

3-(5'-O-Dimethoxytrityl)-β-D-2-
deoxyribofuranosyl)-6-
methylpyrrolo[2,3-d]pyrimidin-2-
one

C33H33N3O6 

644962-87-8 

PYA 11100

3-(2'-Deoxy-β-D-2-ribofuranosyl)
pyrido[2,3-d]pyrimidine-2,7(8H)
-dione

C12H13N3O5 

99517-98-3 

Description

Download a brief overview here. Known as "dF" or "P". Ribo version fluoresces at 385 nm (Bergstrom, D. E.; Inoue, H.; Reddy, P. A., J. Org. Chem., 1982, 47, 2174-2178; Bergstrom, D., et. Al, Synlett, 1992, 179-188). Has been incorporated into oligonucleotides, where dF pairs with dG, resulting in a higher melting temperature (Inoue, H.; Imura, A.; Ohtsuka, E., Nucleic Acids Res., 1985, 13, 7119-7128). In triple helices, dF pairs well with dA (Staubli, A. B.; Dervan, P. B., Nucleic Acids Res. 1994, 22, 2637-2642). We also offer the phosphoramidite version (Product # BA 0238, CAS Reg. No. 162585-09-3), which has been used for oligonucleotide synthesis (Durland, R. H.; Rao, T. S.; Jayaraman, K.; Revankar, G. R., Bioconjugate Chem., 1995, 6, 278-282), where it is known as "P", and serves as a fluorescent replacement of T in targeting AT base pairs during triplex formation.

Notes

Fluorescent deoxycytidine analog.

Alternate Name(s):

"dF" or "P"

PYA 11115

tCnitro Nucleoside

C15H14N4O6S 

1139889-25-0 

Alternate Name(s):

7-Nitro-3-(2'-deoxyribofuranosyl)-1,3-diazaphenothiazin-2-one

10H-7-Nitro-3-(2'-deoxyribofuranosyl)-pyrimido[5,4-b][1,4]benzothiazin-(2,3H)-one

PYA 11130

3,N4-Etheno-2'-
deoxycytidine

C11H13N3O4 

68498-26-0 



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