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| Product Number | Product Name | Molecular Formula | Cas. No. | Description | Notes | Alt. Name | Alt. Name 2 |
| BA 0339 | 8-OxoG clamp CEP | C55H61N6O11P | 1134373-47-9 | The Sasaki labs have identified a variation of Matteucci’s cytosine analog “G-Clamp”1 that is specific for 8-oxoG. This fluorescent phenoxazine analog 8-oxoG Clamp CEP (BA 0339) appears to be highly specific for pairing with 8-oxoG.2 When incorporated into an oligonucleotide, the duplex stabilization was lowered only slightly, and 8-oxoG was selectively detected by fluorescence quenching the 8-oxoG Clamp.3 For more information, download a Product Information Sheet for BA 0339 here.. 1. Lin, K.-Y.; Jones, R.J.; Matteucci, M. J. Am. Chem. Soc., 1995, 117, 3873-3874. 2. Nakagawa, O.; Ono, S.; Li, Z.; Tsujimoto, A.; Sasaki, S. Angew. Chem. Int. Ed., 2007, 46, 4500-4503. 3. Nasr, T.; Li, Z.; Nakagawa, O.; Taniguchi, Y.; Ono, S.; Sasaki, S. Bioorg. & Med. Chem. Lett. 2009, 19, 727-730. |
Fluorescent molecule for the selective recognition of 8-oxoG | 8-Oxo-dG Clamp CEP | |
| BA 0342 | 5-(3-Aminophenyl)-2'-dU CEP | C48H57N6O8P | None assigned | Electrochemical detection is a less expensive alternative to common optical methods in DNA biosensors and chips. Hocek and coworkers1 have shown that when aminophenyl (BA 0342) and nitrophenyl (BA 0355) substituted 2’-deoxyribonucleosides are incorporated into oligonucleotides, they exhibit excellent electrochemical label properties. Both types of markers in the same oligonucleotide can be easily detected and differentiated since the aminophenyl tag is irreversibly oxidized, and the nitophenyl tag is irreversibly reduced. For more information on this product and its use, download a Product Information Sheet here. References 1. Cahova, H.; Havran, L.; Brazdilova, P.; Pivonkova, H.; Pohl, R.; Fojta, M.; Hocek, M. Angew. Chem. Int. Ed. 2008, 47, 2059-2062. | Simple organic 2’-deoxyribonucleoside derivatives for use as electroactive DNA markers. | ||
| BA 0343 | dNaM CEP | C46H53N2O7P | 1117893-10-3 | The dNaM (BA 0343) and d5SICS (BA 0344) matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction.
For more information, download a Product
Information Sheet for BA 0343 here.
1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7. 2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52. 3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400. 4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63. 5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9. 6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82. 7. Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43. |
Half of a novel base pair that achieves pair recognition through hydrophobic interactions. | 3-(3-O-[(Diisopropylamino)(2-cyano-ethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-2-methoxy napthalene | |
| BA 0344 | d5SICS CEP | C45H52N3O6PS | 1010689-04-9 | The dNaM (BA 0343) and d5SICS (BA 0344)matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction.
For more information, download a Product
Information Sheet for BA 0344 here.
1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7. 2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52. 3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400. 4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63. 5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9. 6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82. 7. Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43. |
Half of a novel base pair that achieves pair recognition through hydrophobic interactions. | 3-(3-O-[(Diisopropylamino)(2-cyano-ethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-6-methyl-1(2H)-isoquinolinethione | |
| BA 0345 | Carbazole dT CEP | C62H72N7O10P | None Assigned | Template-directed DNA ligation has multiple potential biotechnological applications.1-4 The research of Fujimoto, Saito and coworkers have illustrated the utility of 5-vinyldeoxyuridine5a and a carbazole-tethered 5-carboxyvinyldeoxyuridine5b for photo induced non-enzymatic chemical DNA ligation. This carbazole-tethered analog (BA 0345) gives a photo ligation system where ligation and splitting (at 366 nm) can be repeated without damage to the normal DNA. Data suggests that the carbazole group intercalates in the duplex formed when photo ligation takes place in the presence of template DNA. This intercalation prevents photo induced splitting when in the duplex form, allowing control of the ligation/splitting based on the presence or absence of the template DNA strand. Our Carbazole dT CEP (BA 0345) provides an efficient way to form carbazole-tethered vinyl dU containing oligonucleotides. For more information, download a Product Information Sheet for BA 0345 here. Note: This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research. References 1. (a) Silverman, A.P.; Kool. E.T. Chem. Rev., 2006, 106, 3775-3789. (b) Gartner, Z.J.; Kanan, M.W.; Liu, D.R. J. Am. Chem. Soc. 2002, 124, 10304-10306. 2. (a) Gothelf, K.V.; Brown, R.S. Chem. Eur. J. 2005, 11, 1062-1069. (b) Shih, W.M.; Quispe, Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. Science 2005, 310, 1661-1665. 3. (a) Su, X.; Smith, L.M. Nucleic Acids Res. 2004, 32, 3115-3123. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647. (b) Weizmann, Y.; Elnathan, R.; Lioubashevski, O.; Willner, I. J. Am. Chem. Soc. 2005, 127, 12666-12672. 4. (a) Shin, J.-S.; Pierce, N.A.; Nano Lett., 2004, 4, 905-909. (b) Le, J.D.; Pinto, Y.; Seeman, N.C.; Musier-Forsyth, K.; Taton, T.A.; Kiehl, R.A Nano Lett., 2004, 4, 2343-2347. 5. (a) Fujimoto, K.; Yoshino, H.; Ami, T. Yoshimura, Y.; Saito, I. Org. Lett., 2008, 10(3), 397-400. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647. |
For use as a light-controlled, reversible DNA photoligation tool. | 5'-O-(4,4'-Dimethoxytrityl)-3'-O-[2-cyanoethoxy-(N,N-diisopropylamino)-phosphino]-5-(,em>E)-(2-(6-(2-carbazol-9-yl-acetylamiono)-hexylamino)-carbonylvinyl)-2'-deoxyuridine | |
| BA 0346 | 5-(2-Furyl)-dU CEP | C43H49N4O9P | 863713-51-3 | BA 0346 is a phosphoramidite of a small, fluorescent nucleoside that is an isosteric mimic of thymidine.1,2 This probe has been shown to pair with adenine to form a stable duplex. DNA probes constructed to contain BA 0346 at a selected sequence position show a significant emission enhancement when hybridization results in an opposing abasic residue as compared to an opposing adenine residue.1 This property makes BA 0346 useful for the preparation of probes that are designed to detect sequence-specific depurination and depyrimidination. For more information, download a Product Information Sheet for BA 0346 here. 1) Greco, N.J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785. 2) Greco, N.J.; Tor, Y. Nature Protocols, 2007, 2, 305-316. |
Small, fluorescent natural base mimic that can signal the presence of abasic sites in hybridized DNA oligonucleotides. | 5-Furan-2-yl dU CEP | |
| BA 0347 | 5-(Furan-2-yl)-dC CEP | C50H54N5O9P | 1119734-65-4 | Tor and co-workers have reported on the preparation and photophysical characteristics of a number of small, fluorescent isosteric nucleosides that are capable of normal Watson-Crick base paring in unaltered duplexes.1-6 These probes are useful tools for studying nucleic acid sequence, structure, dynamics and recognition. BA 0347 is the phosphoramidite of one such nucleoside.1,2 This probe is a minimally disruptive fluorescent dC analog that can be used in vitro for analysis of oxidative damage caused by reactive oxygen species.6 When incorporated into an oligonucleotide and hybridized, BA 0347 can photophysically distinguish between G, 8-oxoG, or T on the complementary strand. When paired with 8-oxoG, which is the major mutagenic product of oxidative damage, significant emission quenching is observed. When paired with T, the transversion mutation resulting from failure to repair the oxidation, enhanced emission is observed from BA 0347. For more information, download a Product Information Sheet for BA 0347 here. 1) Greco, N.J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785. 2) Greco, N.J.; Tor, Y. Nature Protocols, 2007, 2, 305-316. 3) Greco, N.J.; Tor, Y. Tetrahedron, 2007, 63, 3515-3527. 4) Sinkeldam, R.W.; Greco, N.J.; Tor, Y. ChemBioChem. 2008, 9, 706-709. 5) Srivastan, S.G.; Tor, Y. Tetrahedron, 2007, 63, 3601-3607. 6) Greco, N.J.; Sinkeldam, R.W.; Tor, Y. Org. Lett. 2009, 11, 1115-1118. |
Small, fluorescent natural base mimic that can be used as an in vitro signal the presence of G, 8-oxoG, or T on a complementary strand in hybridized DNA oligonucleotides. | N4-Benzoyl-5-(furan-2-yl)-dC CEP | 4-Benzoyl-5-(2-furyl)-dC CEP |
| BA 0348 | 2'-Fluoro-5'-iodo deoxyuridine CEP | C18H27FIN4O5P | None Assigned | This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research. |
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| BA 0350 | 5'-Aminooxy-modifier-11 CEP | C38H54N3O8P | None Found |
The use of oxime formation in ligation reactions of oligonucleotides has been widely established in the literature for over a decade.1 As examples, 5’-aminooxy-modifiers have been used in oxime ligation for peptide-oligonucleotide conjugates,2 attachment of nucleosides to solid supports,3 and head to tail cyclization of oligonucleotides.4
The concurrent use of BA 0350 at the 5’-terminus and an indole aldehyde modification elsewhere in an oligonucleotide should permit on-support head to tail cyclization upon cleavage of the N-DMT protecting group. See Formylindole-dTCEP (BA 0301) for an example of an appropriate indole aldehyde.
For more information, download a Product Information Sheet for BA 0350 here. References 1) For recent reviews see: a) Zatsepin, T.S.; Stetsenko, D.A.; Gait, M.J.; Oretskaya, T.S. Bioconjugate Chem., 2005, 16(3), 471-89. b) Singh, Y.; Edupuganti, O.P.; Villen, M.; Defrancq, E.; Dumy, P. Comptes RendusChim., 2005, 8(5), 789-96. 2) a) Cebon, B.; Lambert, J.N.; Leung, D.; Mackie, K.; McCluskey, K.L.; Nguyen, H.; Tassone, C. Aust J. Chem., 2000, 53, 3333-40. b) Prater, C.E.; Miller, P.S. Bioconjugate Chem., 2003, 14(2), 320-30. c) Prater, C.E.; Miller, P.S. Bioconjugate Chem., 2004, 15(2), 498-507. 3) a) Salo, H.; Virta, P.; Hakala, H.; Prakash, T.P.; Kawasaki, A.M.; Manoharan, M.; Lönnberg, H. Bioconjugate Chem., 1999, 10(5), 815-23. b) Defrancq, E.; Hoang, a.; Vinet, F.; Dumy, P.; Bioorg. Med. Chem. Lett., 2003, 13, 2683-6. c) Bincheva, M.; Scheibler, L.; Lincoln, P.; Vogel, H.; Akerman, B. Langmuir, 1999, 15, 4317-20. 4) Edupuganti, O.P.; Defrancq, E.; Dumy, P. J. Org. Chem, 2003, 68, 8708-10. |
For the synthesis of oligonucleotides bearing a 5’-aminooxy group. | 5'-Aminooxy TEG CEP | |
| BA 0351 | Thiol-modifier-oxa-6-S-S CPG | N/A | None Assigned | For more information, download a Product Information Sheet for BA 0351 here. |
Superior thiol modifier giving higher yeilds and longer oligos. | ||
| BA 0352 | 8-Styryl-dG CEP | C51H59N8O7P | 1101864-12-3 | Ogasawara and co-workers have reported the use of 8-substituted dG derivatives that provide reversible duplex regulation via a light induced trans-cis isomerization.1,2 The trans isomer of 8-styryl-2’-deoxyguanosine (8STG) is one such photochromic nucleoside (PCN). When a 12-bp duplex containing 8STG is irradiated for 5 minutes at 370 nm, the double bond isomerizes to the cis geometry with 86% conversion. Subsequent irradiation for 2 minutes at 254 nm returns the double bond to the trans geometry with 94% conversion. Both trans and cis isomers are thermally stable but readily interconvert at room temperature upon irradiation with light of the appropriate wavelength. The Tm value of the duplex containing a trans -PCN is 7.9oC higher than the Tm value of the same duplex containing a cis-PCN. When three 8STG insertions are inserted into a 20-bp duplex, the trans -PCNs permit duplex formation whereas the cis-PCNs cause denaturation of the duplex. This phenomenon is evidenced by changes in the circular dichroism spectra before and after irradiation of the duplex containing trans -PCNs at 370 nm. Conversely, when the single strands containg cis-PCNs are irradiated at 254 nm hybridization occurs as the trans isomer is formed.
Berry & Associates now offers 8-Styryl-dG CEP (BA 0352) for the in automated synthesis of PCN-containing oligonucleotides. For more information, download a Product Information Sheet for BA 0352 here. Substitution of other aromatic moieties for the phenyl ring provides PCNs that operate at different wavelengths. For example with 8-(2-napthalen-2-yl)vinly-2’-deoxyguanosine (8NVG) the trans to cisconversion occurs with 410 nm irradiation and reverts at 290 nm and with 8-(2-fluoren-2-yl)vinyl-2’-deoxyguanosine (8FVG) ) the trans to cisconversion occurs with 420 nm irradiation and reverts at 310 nm. 8STG, 8NVG, and 8FVG all have the common synthetic precursor 8-vinyl-dG. Thus we now also offer PR 3335. as a versatile synthetic intermediate for the preparation of these and other PCNs.1. Ogasawara, S.; Saito, I.; Maeda, M. Tetr. Lett., 2008, 49, 2479-82. 2. Ogasawara, S.; Maeda, M. Angew. Chem. Int. Ed., 2008, 47, 8839-42. |
Photochromic nucleoside (PCN) that provides reversible duplex regulation via a light induced trans-cis isomerization. | 8-[(1E)-2-Phenylethenyl]-dG CEP | 8STG |
| BA 0353 | 5-Ethynyl uridine CEP | C47H61N4O9PSi | 1193451-06-7 | Oligonucleotides with 5-ethynyl residues may be used in transition metal-catalyzed coupling reactions. Two ethynyl-bearing oligonucleotides can be homo-coupled via a diyne linkage using copper catalysis. Further, the ethynyl groups may be used in copper-catalyzed couplings with arylacetylenes bearing anthraquinone, biotin, or fluorescein appendages.1 Palladium catalyzed cross-coupling of ethynyl-dU-bearing oligonucleotidies with 2-iodoanthraquinone provides anthraquinone-bearing nucleic acids useful in electrochemical applications of DNA.2 For more detail on the use of this product, download a Product Information Sheet here. (1) Minakawa, N.; Ono, Y.; Matsuda, A. J. Am. Chem. Soc. 2003, 125, 11545-11552. (2) Gorodetsky, A. A.; Green, O.; Yavin, E.; Barton, J. K. Bioconjugate Chem. 2007, 18, 1434-1441. | |||
| BA 0354 | Fmoc-5'-amino-modifier-5 CEP | C28H38N3O5P | None Found | The (fluorenylmethyloxy)carbonyl (Fmoc) group has been shown to be useful as an amine protecting group on oligonucleotide amino-modifiers.1 It can be removed by standard cleave-deprotect protocols such as ammonium hydroxide. Alternatively, the Fmoc group can be selectively removed before cleavage of the oligonucleotide from the solid support,2 thereby simplifying labeling of the resulting amino group by acylation. After the acylation is complete and excess reagents are washed away, the labeled oligonucleotide is cleaved from the support and further deprotected with ammonium hydroxide. See the Related Products below for additional product offerings that contain the Fmoc protecting group. For more information on this product and its use, download a Product Information Sheet here. (1) Nelson, P. S.; Kent, M.; Muthini, S. Nucl. Acids Res. 1992, 20, 6253-6259. (2) For example, see: (a) Gartner, Z. J.; Kanan, M. W.; Liu, D. R. J. Am. Chem. Soc. 2002, 124, 10304-10306; see Supporting Information, p. 3. (b) Gartner, Z. J.; Tse, B. N.; Grubina, R.; Doyon, J. B.; Snyder, T. M.; Liu, D. R. Science 2004, 305, 1601-1605; see Supporting Online Material, p. 2. | For 5’- incorporation of an amine that can be deprotected prior to cleaving the oligonucleotide from the solid support. | ||
| BA 0355 | 5-(3-Nitrophenyl)-2'-dA CEP | C50H57N8O8P | None Assigned | Electrochemical detection is a less expensive alternative to common optical methods in DNA biosensors and chips. Hocek and coworkers1 have shown that when aminophenyl (BA 0342) and nitrophenyl (BA 0355) substituted 2’-deoxyribonucleosides are incorporated into oligonucleotides, they exhibit excellent electrochemical label properties. Both types of markers in the same oligonucleotide can be easily detected and differentiated since the aminophenyl tag is irreversibly oxidized, and the nitophenyl tag is irreversibly reduced. For more information on this product and its use, download a Product Information Sheet here. References 1. Cahova, H.; Havran, L.; Brazdilova, P.; Pivonkova, H.; Pohl, R.; Fojta, M.; Hocek, M. Angew. Chem. Int. Ed. 2008, 47, 2059-2062. | Simple organic 2’-deoxyribonucleoside derivatives for use as electroactive DNA markers. | ||
| BA 0356 | 2'-O-Methyl-pyrrolo C CEP | C43H52N5O8P | 644962-95-8 | Pyrrolo-C (PC) is a fluorescent analog of cytidine.1 It is highly fluorescent, the 2'-deoxy version exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. Pyrrolo-C has proven to be useful for monitoring RNA secondary structure formation, where its fluorescence is reversibly quenched upon base-pairing.2 PC has been used to follow the kinetics of formation and dissociation of an RNA/DNA complex and has been used to monitor the thermal denaturation of the central segment of an RNA duplex.2 Most recently, PC has been incorporated into native and minimal hammerhead ribozymes at cleavage site position C17, where it was found to be capable of efficient photocrosslinking to G12, resulting in catalytically active RNA that was useful in structural studies.3 We also offer the 2’-OTBS phosphoramidite of pyrrolo-C (BA 0245) as well as the 2'-deoxyribo version, pyrrolo-dC CEP (BA 0170). These materials are also available from Glen Research (Pyrrolo-C CEP as the 2'-O-TOM version), our development partner for these products. Glen Research also offers the triphosphates of pyrrolo-C and -dC. We offer the two nucleosides (PYA 11090 and PYA 11092) as well as the simple fluorescent pyrrolocytosine heterocycle (i.e., pyrrolo-C aglycone (HC 9060). Thompson and co-workers have studied the photophysical properties of these fluorescent pyrrolopyrimidines.4 2'-O-Me-Pyrrolo-C CEP should behave in oligonucleotide synthesis in a manner similar to the other modified 2'-O-Me nucleoside CEPs, but this has not yet been proven. This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research. For more detail on the use of this product, download a Product Information Sheet here. 1. Berry, D.A.; Jung, K.-Y.; Wise, D.S.; Sercel, A.D.; Pearson, W.H.; Mackie, H.; Randolph, J.B.; Somers, R.J., Tetrahedron Lett. 2004, 45 (11), 2457-2461). 2. Tinsley, R.A.; Walter, N.G., RNA, 2006, 12, 522-529. 3. Lambert, D.; Heckman, J. E.; Burke, J. M., Biochemistry, 2006, 45, 7140-7147. 4. Thompson, K. C.; Miyake, N., J. Phys. Chem. B, 2005, 109, 6012-6019. |
Pyrrolo-C (PC) is a fluorescent analog of cytidine. | ||
| BA 0358 | 2',3'-Di-O-acetyl-U-5'- CEP |
C22H33N4O9P | 208655-84-9 | For more information, download a Product Information Sheet for BA 0358 here. Note: This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research. |
BA 0358 is for oligo synthesis in the reverse direction. | ||
| BL 1010 | BBQ-650-dT CEP | C76H89N12O15P | 905554-46-3 | 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) 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. | 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. | BlackBerry™ Quencher 650-dT CEP | |
| BL 1020 | 5'-BBQ-650 CEP | C41H55N8O7P | 1027512-25-9 | 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) 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. |
For installation of a BlackBerry™ quencher at the 5'-terminus of an oligonucleotide. | 5'-BlackBerry™ Quencher 650 CEP | |
| BL 1030 | BBQ-650(DMT) CEP | C59H67N8O10P | 905554-45-2 | 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) 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. |
For installation of a DMT-bearing BlackBerry® quencher at the 5'-terminus of an oligonucleotide. | 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 Found | 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) 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. | BlackBerry™ Quencher 650 CPG (3'-BBQ-650 CPG) is used to install BBQ-650 at the 3' end of an oligonucleotide. | 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 Found | 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) 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. | 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. | 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 Found | 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-650(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. | 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. | BlackBerry™ Quencher 650 CPG III | |
| BL 3010 | BBQ-650 Nhydroxysuccinimide ester |
C36H39N7O9 | 1027512-30-6 | 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, 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. |
Dark quencher of long-wavelength fluorescence. | 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 |
| BT 1000 | D-(+)Biotin N-Hydroxysuccinimide Ester |
C14H19N3O5S | 35013-72-0 | Biotinylation reagent for labeling nucleic acids or proteins. | |||
| BT 1010 | D-(+)Biotin 2-Nitrophenyl Ester | C16H19N3O5S | 131303-71-4 | Biotinylation reagent for labeling nucleic acids or proteins. | |||
| BT 1020 | N-(16-(Dimethoxytrityl)oxy-15- hydroxy-4,7,10,13- tetraoxahexadecyl)-D-(+)- biotinamidel |
C43H59N3O10S | 869354-57-4 | ||||