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Product Number Product Name Molecular Formula Cas. No.

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

BA 0408

3'-Cyanine 3 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 0408 here.

Notes

BA 0408 can be used to incorporate the cyanine 3 fluorophore at the 3’ end of the oligo sequence.

BA 0409

5'-Methyl dT CEP

C41H51N4O8P 

167080-32-2 

Description

For more information, download a Product Information Sheet for BA 0409 here.

BA 0410

Clickable dSpacer

C37H45N2O6P 

1173797-55-1 

Description

For more information, download a Product Information Sheet for BA 0410 here.

Notes

BA 0410 is for the incorporation of a clickable abasic nucleoside into oligonucleotides.

BA 0413

Nap-dU CEP

C51H56N5O9P 

None Assigned 

Description

Substitution at the 5-position of pyrimidines provides a tool for aptamer applications whose substitution variation does not interfere with base paring. Nap-dU CEP (BA 0413) has been shown to contain a modified sidechain that imparts exceptional thermodynamic and kinetic stability which results in tight binding and slow dissociations rates.1 Nap-dU CEP can be efficiently incorporated into oligonucleotides using standard protocols.

For more information, download a Product Information Sheet for BA 0413 here.

References 1. Gelinas, A.D.; Davies, D.R.; Edwards, T.E.; Rohloff, J.C.; Carter, J.D.; Zhang, C.; Gupta, S.; Ishikawa, Y.; Hiroto, M.; Nakaishi, Y.; Jarvis, T.C.; Janjic, N. J. Biol. Chem. 2014, 289(12/), 8720-8734.

Notes

BA 0413 is for the incorporation of functional diversity into oligonucleotides for aptamer research.

BL 1010

BBQ-650®-dT CEP

C76H89N12O15P 

905554-46-3 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. We offer versions for incorporation into oligonucleotides at the 3'-terminus (3'-BBQ-650®; CPG, BL 2010), internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

For the use of this product, please consult the Product Information Sheet for BL 1010.

Download a brief overview of BlackBerry® Quenchers here.

Notes

BBQ-650®-dT CEP is a dark quencher of long-wavelength fluorescence and may be used to install a BlackBerry® Quencher internally or at the 5'-terminus of an oligonucleotide.

Alternate Name(s):

BlackBerry® Quencher 650-dT CEP

BL 1020

5'-BBQ-650®CEP

C41H55N8O7P 

1027512-25-9 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. We offer versions for incorporation into oligonucleotides at the 3'-terminus (3'-BBQ-650® CPG, BL 2010), internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

Download a brief overview of these dark quenchers of long-wavelength fluorescence here.

Download a Product Information sheet for BL 1022 here.


Notes

For installation of a BlackBerry® quencher at the 5'-terminus of an oligonucleotide.

Alternate Name(s):

5'-BlackBerry® Quencher 650 CEP

BL 1022

5'-BBQ-650®CEP II

C46H62N9O8P 

None Assigned 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. We offer versions for incorporation into oligonucleotides at the 3'-terminus (3'-BBQ-650® CPG, BL 2010), internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

Download a brief overview of these dark quenchers of long-wavelength fluorescence here.

Download a Product Information sheet for BL 1022 here.


Notes

For installation of a BlackBerry® quencher at the 5'-terminus of an oligonucleotide.

Alternate Name(s):

5'-BlackBerry® Quencher 650 CEP II

BL 1030

BBQ-650®(DMT) CEP

C59H67N8O10P 

905554-45-2 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. We offer versions for incorporation into oligonucleotides at the 3'-terminus (3'-BBQ-650® CPG, BL 2010), internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

For more information, download a Product Information sheet for BL 1030.

Download an overview of the BlackBerry® Quencher 650 here.

Notes

For installation of a DMT-bearing BlackBerry® quencher at the 5'-terminus of an oligonucleotide.

Alternate Name(s):

BlackBerry®Quencher 650(DMT) CEP

9-[[2,5-Dimethoxy-4-[(4-nitrophenyl)azo]phenyl]azo]phenyl-8-[3-(4,4'-dimethoxytrityloxy)-2-[diisopropyl(amino)(2-cyanoethoxy)phosphino]-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizine

BL 2010

3'-BBQ-650® CPG

N/A 

None Assigned 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. Due to the lipophilicity of the quencher, cleavage from the support may be slow. Our 3'-BBQ-650® CPG II, BL 2020 contains a diglycolate linker to facilitate cleavage. We also offer versions for incorporation into oligonucleotides internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

Download a product information sheet for BL 2010 here. Download a brief overview of BlackBerry® Quenchers here.

Notes

BlackBerry® Quencher 650 CPG (3'-BBQ-650®CPG) is used to install BBQ-650®at the 3' end of an oligonucleotide.

Alternate Name(s):

BlackBerry® Quencher 650 CPG

9-[[2,5-Dimethoxy-4-[(4-nitrophenyl)azo]phenyl]azo]phenyl-8-[3-(4,4'-dimethoxytrityloxy)-2-[4-(lcaa-CPG)-4-oxobutanoyloxy]propyl]oxy-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizine

BL 2020

3'-BBQ-650® CPG II

N/A 

None Assigned 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. Our 3'-BBQ-650® CPG , BL 2010 containing a succinate linker also allows for incorporation at the 3'-terminus. We also offer versions for incorporation into oligonucleotides internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

Download a product information sheet for BL 2020 here. Download a brief overview of BlackBerry® Quenchers here.

Notes

BlackBerry® Quencher 650 CPG II (3'-BBQ-650® CPG II) is used to install BBQ-650® at the 3' end of an oligonucleotide, and is more rapidly cleaved from the solid support than its predecessor BL 2010.

Alternate Name(s):

BlackBerry®Quencher 650 CPG II

9-[[2,5-Dimethoxy-4-[(4-nitrophenyl)azo]phenyl]azo]phenyl-8-[3-(4,4'-dimethoxytrityloxy)-2-[4-(lcaa-CPG)-5-oxo-3-oxapentanoyl]oxy-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizine

BL 2030

3'-BBQ-650® CPG III

N/A 

None Assigned 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. 3’-BBQ-650® CPG III (BL 2030) utilizes a 1,3,5-triol framework, which is two methylene units longer than the 1,2,3-triol framework that is employed with 3’-BBQ-650® CPG (BL 2010) and 3’-BBQ-650®CPG II (BL 2020). The one-carbon extension between each of the oxygen atoms provides an architecture that allows a one step cleavage with AMA while also minimizing the occurrence of impurities that lack the quencher tag. The oligo purity observed with BL 2030 after cleavage and deprotection rivals that seen with BL 2020 after the two step protocol. Like BL 2020, BL 2030 also has a fast cleaving linker, but AMA appears to provide markedly superior oligo yield as compared to NH4OH. Our 3'-BBQ-650® CPG , BL 2010 containing a succinate linker also allows for incorporation at the 3'-terminus. In addition, we offer versions for incorporation into oligonucleotides internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-®(DMT) CEP, BL 1030). BBQ-650®NHS Ester (BL 3010) is also available for postsynthetic labeling of amine-modified oligonucleotides.

Download a product information sheet for BL 2030 here. Download a brief overview of BlackBerry® Quenchers here.

Notes

BlackBerry® Quencher 650 CPG III (3'-BBQ-650® CPG III) is used to install BBQ-650® at the 3' end of an oligonucleotide, and is more efficiently cleaved from the solid support than its predecessor BL 2020.

Alternate Name(s):

BlackBerry® Quencher 650 CPG III

BL 2040

Fmoc-Lysine(BBQ-650®)-
OH

C53H58N8O10 

None Assigned 

BL 3010

BBQ-650®N-hydroxysuccinimide
ester

C36H39N7O9 

1027512-30-6 

Description

Our BlackBerry® quenchers are excellent quenchers of long-wavelength fluorophores in both FRET and contact modes. They exhibit an absorption maximum at ca. 650 nm and have useful absorbance between 550 and 750 nm. The tricyclic 8-alkoxyjulolidine moiety is a powerful pi-donor that affords a surprising bathochromic shift when compared to related compounds. A key advantage of the BBQ-650® is its stability to ammonia and oxidation conditions. We offer versions for incorporation into oligonucleotides at the 3'-terminus (3'-BBQ-650® CPG, BL 2010), internally (BBQ-650®-dT CEP, BL 1010), or at the 5'-terminus (5'-BBQ-650® CEP, BL 1020 and 5'-BBQ-650®(DMT) CEP, BL 1030). In addition, BBQ-650® NHS Ester (BL 3010) and BBQ-650® TEG azide (BL 3030) are available for postsynthetic labeling of amine-modified oligonucleotides.

Download a product information sheet for BL 3010 here.

Download a brief overview of BlackBerry® Quenchers here.

1.Valanne, A.; Malmi, P.; Appelblom, H.; Niemelä, P.; Soukka, T. Anal. Biochem. 2008, 375, 71-81.

Notes

Dark quencher of long-wavelength fluorescence.

Alternate Name(s):

BlackBerry® Quencher 650 NHS Ester

6-[9-[4-(4-Nitrophenylazo)-2,5-dimethoxyphenylazo]-2,3,6,7-tetrahydro-1H,5H-benzo[ij]quinolizin-8-yloxy]hexanoic acid N-hydroxysuccimidyl ester

BL 3030

BBQ-650®TEG azide

C40H52N10O9 

1333148-80-3 

Description

For a complete listing of our reagents for click chemistry, please see our Click-matesTM Collection page.

Download a brief overview of BlackBerry® Quenchers here.

The purchase of these products for use in applications relating to copper catalyzed azide-alkyne cycloaddition chemistry (“Click Chemistry”) includes a limited, nontransferable license to intellectual property owned by TSRI to use this product solely for internal non-commercial research activities and specifically excludes clinical, therapeutic, or diagnostic use in humans or animals. Information regarding a license for commercial use in Click Chemistry may be obtained directly from The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, or by contacting 858-784-8140 or click@scripps.edu.

Notes

A useful tool from our Click-matesTM collection for adding our long wavelength quencher, BBQ-650®, to a variety of substrates.

Alternate Name(s):

BlackBerry® Quencher 650TEG azide

BLU 00652

Blueberry-C6-ester-652

C20H20N4O10 

None Assigned 

Notes

Blueberry-C6-ester-652 is a pH sensitive quencher dye for use in potassium sensor optode applications.

BLU 00655

Blueberry-cyano-C6-ester

C21H20N4O8 

None Assigned 

Notes

Bluberry-cyano-C6-ester is a pH sensitive quencher dye.

BLU 00675

Blueberry pyridyl-C6-ester

C19H19N5O10 

None Assigned 

Notes

Bluberry-pyridyl-C6-ester is a pH sensitive quencher dye.

BT 1000

D-(+)Biotin N-Hydroxysuccinimide
Ester

C14H19N3O5S 

35013-72-0 

Notes

Biotinylation reagent for labeling nucleic acids or proteins.

BT 1010

D-(+)Biotin 2-Nitrophenyl Ester

C16H19N3O5S 

131303-71-4 

Notes

Biotinylation reagent for labeling nucleic acids or proteins.

BT 1015

D-(+)-Biotin-tyramine amide

C18H25N3O3S 

41994-02-9 

Alternate Name(s):

Biotin phenol

BT 1020

N-(16-(Dimethoxytrityl)oxy-15-
hydroxy-4,7,10,13-
tetraoxahexadecyl)-D-(+)-
biotinamide

C43H59N3O10S 

869354-57-4 

BT 1030

N-(15,16-Dihydroxy-4,7,10,13-
tetraoxahexadecyl-D-(+)-
biotinamide

C22H41N3O8S 

869354-59-6 

BT 1040

N1-(4-(t-Butyl)benzoyl)-D-(+)
biotin 2-Nitrophenyl Ester

C27H31N3O6S 

869354-61-0 

BT 1050

N1-(Dimethoxytrityl)-D-(+)
biotin 2-Nitrophenyl Ester

C37H37N3O7S 

869354-63-2 

BT 1060

D-Desthiobiotin

C10H18N2O3 

533-48-2 

Description

Desthiobiotin allows capture by streptavidin and can be displaced simply by adding biotin.1-3 For phosphoramidite and CPG versions, see BA 0210 and BA 0211. For the NHS ester of desthiobiotin, see BT 1070 .

1. General: Hirsch, J.D.; Eslamizar, L.; Filanoski, B.J.; Malekzadeh, N.; Haughland, R.P.; Beechem, J. M.; Haughland, R.P. Anal. Biochem. 2002, 308, 343-357.

2. Key references on Desthiobiotin NHS Ester: (a) Hofmann, K.; Titus, G.; Montibeller, J.A.; Finn, F.M. Biochemistry, 1982, 21, 978-984. (b) Romovacek, H.; Finn, F.M.; Hofmann, K. Biochemistry, 1983, 22, 904-909. (c) Finn, F.M.; Titua, G.; Hofmann, K. Biochemistry, 1984, 23, 2554-2558.

3. Regarding association constants and kinetics: (a) Busse, S.; Scheumann, V.; Menges, B.; Mittler, S. Biosensors and Bioelectronics, 2002, 17, 704-710. (b) Yoon, H.C.; Hong, M.-Y.; Kim, H.-S. Langmuir, 2001, 17, 1234-1239.

Notes

For affinity capture via the biotin-streotavidin interaction.


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