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Full Catalog (page 30)
Product Number Product Name Molecular Formula Cas. No.

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 11110

tC Nucleoside

C15H15N3O4S 

162902-04-7 

Alternate Name(s):

3-(2'-Deoxy-β-D-ribofuranosyl)-1,3-diaza-2-oxophenothiazine

PYA 11112

8-OxoG Clamp

C25H26N4O8 

None Assigned 

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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