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Full Catalog (page 9)
Product Number Product Name Molecular Formula Cas. No.

BA 0377

5'-Tetrachlorofluorescein CEP

C46H54Cl4N3O10P 

877049-90-6 

Alternate Name(s):

TET CEP

BA 0378

5-(2-Hydroxyethyl) dU CEP

C47H65N4O9PSi 

None Assigned 

Description

For more information on this product and its use, download a Product Information Sheet here.

Notes

Useful tool for introducing a branch point at defined locations within an oligonucleotide.

BA 0382

(5'S)-8,5'-Cyclodeoxyguanosine
(THP) CEP

C28H42N7O7P 

None Assigned 

Description

The naturally occurring nucleosides, cyclo-dG and cyclo-dA are bridged cyclonucleosides that result from oxidative free radical damage to DNA. This specialized “tandem lesion” encompasses damage to both the sugar and the base moiety of the same purine nucleoside. This oxidative damage plays a significant role in mutagenesis, carcinogenesis and aging.1 Both of the bulky 8,5’-Cyclodeoxyadenosine (cyclo-dA) and the 8,5’-Cyclodeoxyguanosine (cyclo-dG) lesions have been shown to be present in human cells.1,2 Cyclo-dA and Cyclo-dG are both strong blockers of gene expression in CHO and human cells. These lesions can be repaired via nucleoside excision repair mechanisms, but not by base excision repair mechanisms.3 Structural investigations have shown that when incorporated into DNA, cyclo-dG stacks in the DNA duplex, retains Watson-Crick hydrogen bonding with dC, but significantly perturbs the helix structure near the lesion.4

Both cyclo- dA and cyclo-dG are valuable tools for investigations into DNA damage and repair. We offer the traditionally DMT protected cyclo-dA CEP (BA 0329), but the difficulties encountered when developing a practical synthesis for a cyclo-dG phosphoramidite that would be applicable to automated DNA synthesis led us away from the conventional 5’-DMT protection. A better alternative, which dramatically increases the overall yield of the synthesis, is to utilize a 5’-tetrahydropyranyl (THP) protecting group.

For additional information, download a Product Information Sheet.

References

1. a) Jaruga, P.; Dizdaroglu, M. DNA Repair, 2008, 7, 1413-1425. b) Cooke, M. S.; Evans, M. D.; Dizdaroglu, M.; Lunec, J. The FASEB Journal, 2003, 17, 1195-1214.

2. Dizdaroglu, M.; Dirksen, M.L.; Jiang, H.X.; Robbins, J.H. J. Biochem. 1987, 241, 929-932.

3. a) Brooks, P.J.; Wise, D.S.; Berry, D.A.; Kosmoski, J.V.; Smerdon, M.J.; Somers, R.L.; Mackie, H.; Spoonde, A.Y.; Ackerman, E.J.; Coleman, K.; Tarone, R.E.; Robbins, J.H. J. Biol. Chem. 2000, 275 , 22355-22362. b) Swanson, A. L.; Wang, J.; Wang, Y. Chem. Res. Toxicol. 2012, 25, 1682-1691. c) Pande, P.; Das, R.S.; Sheppard, C.; Kow, Y.W.; Basu, A.K. DNA Repair, 2012, 11, 926-931.

4. Huang, H.; Das, R.S.; Basu, A.K.; Stone, M.P. J. Am. Chem. Soc. 2011, 133, 20357-20368.

Notes

This phosphoramidite is used for standard 3’ to 5’ oligonucleotide synthesis.

Alternate Name(s):

Cyclo dG CEP

BA 0383

5'-Biotin barbell spacer 12 CEP

C54H74N7O8PS 

None Assigned 

Description

Our 5’-Biotin barbell spacer 12 CEP is a very stable biotin phosphoramidite for incorporation of a biotin label at the 5’-terminus of an oligonucleotide. The presence of the DMT on the biotin allows for efficient application of RP cartridge or HPLC purification protocols. P>

For additional information, download a Product Information Sheet.

BA 0384

5'-Hydrazide-modifier-6 CEP

C34H45N4O3P 

350716-21-1 

Description

Hydrazides have been useful tools in protein and carbohydrate chemistry, and more recently in oligonucleotide bioconjugation.1 The lack of easily available hydrazide-containing phosphoramidite building blocks has impeded more widespread use of these tools in the post synthetic modification of oligonucleotides. In addition to our amino modifier and aminooxy phosphoramidites (see related products below), we offer 5’-Hydrazide-modifier-6 CEP (BA 0384) for use with post synthetic covalent attachment chemistry.

For additional information, download a Product Information Sheet.

References (1) a) Raddatz, S.; Mueller-Ibeler, J.; Kluge, J.; Wab, L.; Burdinski, G.; Havens, J. R.; Onofrey, T. J.; Wang, D.; Schweitzer, M. Nucleic Acids Research, 2002, 30 (21) 4793-4802. b) Antsypovich, S. I.; Oretskaya, T. S.; von Kiedrowski, G.; Rus. Chem. Bull. Int. Ed. 2005, 54, 2671-2681.

Notes

Our 5’-Hydrazide-modifier-6 CEP allows incorporation of a useful hydrazine moiety for post synthetic modification of oligonucleotides.

BA 0385

5'-Trityl-hydrazide-modifier CEP

C38H50N5O4P 

None Assigned 

Description

Hydrazides have been useful tools in protein and carbohydrate chemistry, and more recently in oligonucleotide bioconjugation.1 The lack of easily available hydrazide-containing phosphoramidite building blocks has impeded more widespread use of these tools in the post synthetic modification of oligonucleotides. In addition to our amino modifier and aminooxy phosphoramidites (see related products below), we now offer 5’-Trityl-hydrazide-modifier CEP (BA 0385) for use with post synthetic covalent attachment chemistry.

For additional information, download a Product Information Sheet.

References (1) a) Raddatz, S.; Mueller-Ibeler, J.; Kluge, J.; Wab, L.; Burdinski, G.; Havens, J. R.; Onofrey, T. J.; Wang, D.; Schweitzer, M. Nucleic Acids Research, 2002, 30 (21) 4793-4802. b) Antsypovich, S. I.; Oretskaya, T. S.; von Kiedrowski, G.; Rus. Chem. Bull. Int. Ed. 2005, 54, 2671-2681.

Notes

Our 5’-Trityl-hydrazide-modifier CEP allows incorporation of a useful hydrazine moiety for post synthetic modification of oligonucleotides.

BA 0387

5'-TAMRA barbell spacer 12 CEP

C48H62N7O8P 

None Assigned 

Description

Phosphoramidite for incorporation of the TAMRA moiety on the 5’ end of an oligonucleotide.

For additional information, download a Product Information Sheet.

BA 0388

5'-TAMRA C4 CEP

C40H50N5O6P 

None Assigned 

Description

Compact phosphoramidite for incorporation of the TAMRA moiety on the 5’ end of an oligonucleotide.

For additional information, download a Product Information Sheet.

BA 0389

8-Bromo-N6-benzoyl-dA
CEP

C47H51BrN7O7P 

None Assigned 

Description

For additional information, download a Product Information Sheet.

Notes

Allows for incorporation of a halogenated nucleoside into oligonucleotides for crystallographic studies and crosslinking studies of protein-DNA and RNA-DNA complexes.

BA 0390

1-Octadecanol CEP

C27H55N2O2P 

207273-84-5 

Description

For additional information, download a Product Information Sheet.

Notes

Allows for efficient incorporation of a lipophilic carrier into oligonucleotides.

Alternate Name(s):

C-18 CEP

Stearyl CEP

BA 0391

3,N4-Etheno-dC
CEP

C41H48N5O7P 

159624-42-7 

Description

3, N4-Etheno-dC CEP (BA 0391), is a fluorescent pyrimidine nucleoside analog that is useful for the investigation of nucleic acid interactions. Due to the similarity in structure between dC and 3, N4-Etheno-dC, the modified nucleoside can be incorporated into DNA with retention of DNA structure and nucleobase recognition.1

For additional information, download a Product Information Sheet.

Reference

1) Ming, X.; Seela, F. Chem. Eur. J. 2012, 18, 9590-9600 and references therein.

Notes

Allows for efficient incorporation of a fluorescent deoxycytidine analog into oligonucleotides.

BA 0393

7-Deaza-7-(2,3-diacetoxypropyl)-dG
CEP

C52H65N6O12P 

1111664-09-5 

Description

DNA interstrand crosslinks (ICLs) prevent DNA strand separation, which in turn inhibits transcription and replication. Many currently used chemotherapeutic agents achieve efficacy via ICL induction, and the study of ICL repair mechanisms and their role in the sensitization of cancer cells and the development of new cancers is an emerging area of research.1 As reported by Angelov and coworkers,2 tools for the preparation of defined ICL adducts are not readily available. 7-Deaza-7-(2,3-diacetoxypropyl)-dG CEP can be used for the site-specific introduction of ICL precursor nucleosides into opposing strands of DNA.

For additional information, download a Product Information Sheet.

Notes

Allows for efficient incorporation of modifiable nucleosides for the formation of interstrand cross links.

BA 0394

5,N4-Etheno-dC
CEP

C41H48N5O7P 

None Assigned 

Description

5, N4-Etheno-dC CEP (BA 0394, also known as Pyrrolo-dC CEP), is a fluorescent pyrimidine nucleoside analog that is useful for the investigation of nucleic acid interactions. Due to the similarity in structure between dC and 5, N4-Etheno-dC, the modified nucleoside can be incorporated into DNA with retention of DNA structure and nucleobase recognition.1

For additional information, download a Product Information Sheet.

Reference

1) Ming, X.; Seela, F. Chem. Eur. J. 2012, 18, 9590-9600 and references therein.

Notes

Allows for efficient incorporation of a fluorescent deoxycytidine analog into oligonucleotides.

BA 0395

2'-TBDMS-U CEP

C45H61N4O9PSi 

118362-03-1 

BA 0396

2'-TBDMS-G CEP

C48H64N7O9PSi 

944138-03-8 

BA 0397

2'-TBDMS-C CEP

C47H64N5O9PSi 

121058-88-6 

BA 0398

2'-TBDMS-A CEP

C53H66N7O8PSi 

104992-55-4 

BA 0399

2'-Fluoro-dU CEP

C39H46FN4O8P 

146954-75-8 

BA 0400

2'-Fluoro-dC CEP

C41H49FN5O8P 

159414-99-0 

BA 0401

2'-Fluoro-dA CEP

C47H51FN7O7P 

136834-22-5 

BA 0402

2'-Fluoro-dG CEP

C43H52FN8O7P 

None Assigned 

BA 0403

1,N2-Etheno-dG
CEP

C63H66N7O9P 

None Assigned 

Description

The etheno bridged ring system results from the reaction of vinyl halide and other vinyl monomer electrophiles with dG, dC or dA nucleotides in DNA.1 Research has shown that the 1,N2etheno dG is mutagenic in both E. coli and mammalian cells. 2 The structure of duplex DNA containing 1,N2etheno dG has been studied and shown to hinder canonical Watson-Crick H-bonding.2-4.

For more information, download a Product Information Sheet for BA 0403 here.

References

1. Barbin, A. Mutat. Res. 2008, 462, 55-69.

2. Shanmugam, G.; Kozekov, I. D.; Guengerich, F. P.; Rizzo, C. J.; Stone, M. P. Chem. Res. Toxicol. 2008, 21, 1795-1805.

3. Shanmugam, G.; Goodeneough, A.K.; Kozekov, I. D.; Guengerich, F. P.; Rizzo, C. J.; Stone, M. P. Chem. Res. Toxicol., 2007, 20(11), 1601-1611.

4. Stone, M. P.; Huang, H.; Brown, K. L.; Shanmigam, G. Chemistry & Biodiversity, 2011, 8, 1571-1615.

Notes

Allows incorporation of an etheno bridged dG moiety internally or at the 5’ end of an oligonucleotide.

BA 0404

X,5'-Cyanine 5 CEP

C66H83N5O7P1B1F4 

None Assigned 

Description

We offer our more versatile Cyanine 5 and Cyanine 3 fluorophores in phosphoramidite (BA 0404 and BA 0407) and CPG (BA 0406 and BA 0408) forms for use in oligonucleotide synthesis. These products feature the traditional aminopropylglycerol linker construct that has been used successfully with other oligo tags such as fluorescein BA 0253 and BA 0147, dabsyl BA 0149, dabcyl BA 0081 and TAMRA BA 0130.

For more information, download a Product Information Sheet for BA 0404 here.

182873-76-3

718594-66-2

351186-76-0

Notes

BA 0404 can be used to incorporate the cyanine 5 fluorophore internally or at the 5’ end of the oligo sequence.

Alternate Name(s):

Cyanine 5 CEP

5'-Cyanine 5 CEP

BA 0405

5'-Deoxythymidine CEP

C19H31N4O5P 

None Assigned 

Description

For more information, download a Product Information Sheet for BA 0405 here.

BA 0406

3'-Cyanine 5 CPG

N/A 

None Assigned 

Description

We offer our more versatile Cyanine 5 and Cyanine 3 fluorophores in phosphoramidite (BA 0404 and BA 0407) and CPG (BA 0406 and BA 0408) forms for use in oligonucleotide synthesis. These products feature the traditional aminopropylglycerol linker construct that has been used successfully with other oligo tags such as fluorescein BA 0253 and BA 0147, dabsyl BA 0149, dabcyl BA 0081 and TAMRA BA 0130.

For more information, download a Product Information Sheet for BA 0406 here.

Notes

BA 0406 can be used to incorporate the cyanine 5 fluorophore at the 3’ end of the oligo sequence.

BA 0407

X,5'-Cyanine 3 CEP

C64H81BF4N5O7P 

None Assigned 

Description

We offer our more versatile Cyanine 5 and Cyanine 3 fluorophores in phosphoramidite (BA 0404 and BA 0407) and CPG (BA 0406 and BA 0408) forms for use in oligonucleotide synthesis. These products feature the traditional aminopropylglycerol linker construct that has been used successfully with other oligo tags such as fluorescein BA 0253 and BA 0147, dabsyl BA 0149, dabcyl BA 0081 and TAMRA BA 0130.

For more information, download a Product Information Sheet for BA 0407 here.

182873-76-3

718594-66-2

351186-76-0

Notes

BA 0407 can be used to incorporate the cyanine 3 fluorophore internally or at the 5’ end of the oligo sequence.

Alternate Name(s):

Cyanine 3 CEP

5'-Cyanine 3 CEP



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