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| Product Number | Product Name | Molecular Formula | Cas. No. |
5'-Tetrachlorofluorescein CEP |
C46H54Cl4N3O10P |
877049-90-6 |
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Alternate Name(s):TET CEP |
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5-(2-Hydroxyethyl) dU CEP |
C47H65N4O9PSi |
None Assigned |
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DescriptionFor more information on this product and its use, download a Product Information Sheet here.NotesUseful tool for introducing a branch point at defined locations within an oligonucleotide. |
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(5'S)-8,5'-Cyclodeoxyguanosine |
C28H42N7O7P |
None Assigned |
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DescriptionThe 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.NotesThis phosphoramidite is used for standard 3’ to 5’ oligonucleotide synthesis.Alternate Name(s):Cyclo dG CEP |
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5'-Biotin barbell spacer 12 CEP |
C54H74N7O8PS |
None Assigned |
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DescriptionOur 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. |
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BBQ-650®-dT CEP |
C76H89N12O15P |
905554-46-3 |
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DescriptionOur 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) is 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.NotesBBQ-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 |
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5'-BBQ-650®CEP |
C41H55N8O7P |
1027512-25-9 |
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DescriptionOur 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) is 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 1020 here. NotesFor installation of a BlackBerry® quencher at the 5'-terminus of an oligonucleotide.Alternate Name(s):5'-BlackBerry® Quencher 650 CEP |
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BBQ-650®(DMT) CEP |
C59H67N8O10P |
905554-45-2 |
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DescriptionOur 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) is 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. NotesFor 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 |
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3'-BBQ-650® CPG |
N/A |
None Assigned |
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DescriptionOur 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) is 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.NotesBlackBerry® 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 |
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3'-BBQ-650® CPG II |
N/A |
None Assigned |
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DescriptionOur 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) is 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.NotesBlackBerry® 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 |
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3'-BBQ-650® CPG III |
N/A |
None Assigned |
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DescriptionOur 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.NotesBlackBerry® 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 |
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Fmoc-Lysine(BBQ-650®)- |
C53H58N8O10 |
None Assigned |
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BBQ-650®N-hydroxysuccinimide |
C36H39N7O9 |
1027512-30-6 |
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DescriptionOur 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, this BBQ-650®NHS Ester (BL 3010) is 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.NotesDark 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 |
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BBQ-650®TEG azide |
C40H52N10O9 |
1333148-80-3 |
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DescriptionFor 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.NotesA 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 |
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D-(+)Biotin N-Hydroxysuccinimide |
C14H19N3O5S |
35013-72-0 |
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NotesBiotinylation reagent for labeling nucleic acids or proteins. |
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D-(+)Biotin 2-Nitrophenyl Ester |
C16H19N3O5S |
131303-71-4 |
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NotesBiotinylation reagent for labeling nucleic acids or proteins. |
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N-(16-(Dimethoxytrityl)oxy-15- |
C43H59N3O10S |
869354-57-4 |
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N-(15,16-Dihydroxy-4,7,10,13- |
C22H41N3O8S |
869354-59-6 |
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N1-(4-(t-Butyl)benzoyl)-D-(+) |
C27H31N3O6S |
869354-61-0 |
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N1-(Dimethoxytrityl)-D-(+) |
C37H37N3O7S |
869354-63-2 |
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D-Desthiobiotin |
C10H18N2O3 |
533-48-2 |
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DescriptionDesthiobiotin 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. NotesFor affinity capture via the biotin-streotavidin interaction. |
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Desthiobiotin N- |
C14H21N3O5 |
80750-24-9 |
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DescriptionDesthiobiotin 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 desthiobiotin, see BT 1060 .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. NotesFor affinity capture via the biotin-streotavidin interaction. |
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Desthiobiotin-TEG azide |
C18H34N6O5 |
1306615-47-3 |
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DescriptionFor a complete listing of our reagents for click chemistry, please see our Click-matesTM Collection page. 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.NotesA useful tool from our Click-matesTM collection for ligation of desthiobiotin via Saudinger ligation or click chemistry. |
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N1-(D-(+)-Biotinyl)-1,19- |
C24H46N4O7S |
869354-65-4 |
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Alternate Name(s):3-[[N-(D-(+)-Biotinyl)-3-aminopropoxy(ethoxy)ethoxy]-ethoxy-1-aminopropane |
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Biotin-TEG azide |
C18H32N6O5S |
875770-34-6 |
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DescriptionFor a complete listing of our reagents for click chemistry, please see our Click-matesTM Collection page. 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.NotesA useful tool from our Click-matesTM collection for ligation of biotin via Saudinger ligation or click chemistry.Alternate Name(s):N-(11-Azido-3,6,9-trioxa-undecylamine)-D-(+)-biotinamide |
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Thiol cleavable biotin |
C22H42N4O4S3 |
None Assigned |
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Alternate Name(s):Aminooxy-S-S-cleavable biotin |
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6-Chlorosalicylic acid |
C7H5ClO3 |
56961-31-0 |
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DescriptionTheherbicide Dicamba, 3,6-dichloro-2-methoxybenzoic acid, is biodegraded under anaerobic conditions, proceeding by demethylation to 3,6-dichlorosalicylic acid and reductive dechlorination to 6-chlorosalicylic acid. See: Taraban, R. H.; Berry, D. F.; Berry, D. A.; Walker, H. L, Jr. Applied and Environmental Microbiology, 1993, 59, 2332-2334. NotesBiodegredation product of the herbicide Dicamba.Alternate Name(s):2-Chloro-6-hydroxybenzoic acid |
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