Berry & Associates, Inc.

Berry & Associates - Specialty Chemicals to Advance the Life Sciences

Products:

BerrySelect^® Reagents for DNA and RNA Synthesis - Phosphoramidites and derivatized solid supports

BlackBerry^® Quenchers - Stable dark quenchers of long-wavelength fluorophores

Fluorous Affinity Purification of Oligonucleotides - Convenient affinity-based method for the purification of oligonucleotides

Nucleosides and Nucleotides - An extensive collection of natural and modified nucleosides and their derivatives

Other Specialty Chemicals - Biotins, carbohydrates, fluorophores, psoralens, heterocycles, linkers

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Latest Developments :

Our latest newsletter, "Chemistry from Berry & Associates", (Dec. 2007) is now available, featuring anthraquinone phosphoramidites, amine modifiers, 6-azapyrimidine phosphoramidites, alkyne modifiers for click conjugation, fluorous affinity/immobilization products, Pseudo-dG phosphoramidite, and more. Details

Collaboration with Luminos, LLC announced (Jan. 8, 2008) in order to develop luminescent assay kits. Press release

A collection of rare nucleosides has recently become available, e.g., showdomycin, formycin A, formycin B, pseudouridine, pyrazofurin, toyocamycin, tubercidin, allopurinol riboside, 5-iodotubercidin, TCN, TCN-P, and TOG. Gram quantities are available but supplies are limited.

Previous developments

dF CEP >> Fluorescent cytidine analog. Download a brief overview here. 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 offer the phosphoramidite version, 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. We also offer the nucleoside.				5'-Fluorescein II CEP >> For the installation of fluorescein at the 5'-terminus of an oligonucleotide, the phosphoramidite "6-FAM" (5'-Fluorescein CEP, BA 0054), which does not bear a DMT group, is a popular choice. However, the lack of a trityl group precludes multiple additions or assaying the coupling step. We therefore offer 5'-Fluorescein II CEP ("6-FAM II", BA 0253), which features the same tether length as 6-FAM, but includes a DMT group.¹ Use normally, but with a 15 minute coupling. For the highest yields, prepare the oligo DMT-on and remove the trityl group after cleavage and deprotection. The DMT may also be used to facilitate cartridge purification with on-column detritylation, e.g. with Fluoro-Pak columns. Download Product Information here. 1. 5'-Fluorescein II CEP incorporates 6-carboxyfluorescein. The 5-carboxyfluorescein isomer of this product (CA Reg. No. 144676-14-2) is also known. See: Theisen, P.; McCollum, C.; Upadhya, K.; Jacobson, K.; Vu, H.; Andrus, A. Tetrahedron Lett. 1992, 33, 5033-5036.
Zebularine CEP >> Deletion of the C⁴ amino group of cytidine allows dissection of the roles of various hydrogen bonds. Zebularine is also fluorescent. Download Product Information Sheet. For a related 2'-deoxy version, see 5-Methyl-2'-deoxyzebularine CEP.				O⁴-Chlorophenyl-U CEP >> The convertible nucleoside O⁴-Chlorophenyl-U CEP allows the formation of N⁴-alkyl-C residues in RNA for structural studies. After incorporation of this unit into an oligoribonucleotide by standard phosphoramidite chemistry, treatment with ammonia, methylamine, or higher alkylamines, including those bearing tethered functional groups, leads to displacement of 4-chlorophenol with resultant installation of a 4-amino group, i.e., producing the desired N⁴-alkyl-C residues. Download Product Information. Allerson, C. R.; Chen, S. L.; Verdine, G. L. J. Am. Chem. Soc. 1997, 119, 7423-7433.
Pyridin-2-one Riboside CEP >> Beigelman and co-workers have carried out structure-activity studies on hammerhead ribozymes by substituting modified pyrimidines at various positions, where profound effects on ribozyme catalytic activity have been observed.¹ Pyridin-2-one Riboside CEP² was found to be useful in these studies, providing alterations in syn/anti nucleobase orientation, ribose puckering, and stacking ability due to dipole changes.^1-4 Download Product Information. (1) Beigelman, L.; Matulic-Adamic, J.; Karpeisky, A.; Haeberli, P.; Sweedler, D. Methods in Enzymology2000, 317, 39-65. (2) Matulic-Adamic, J.; Gonzalez, C.; Usman, N.; Beigelman, L. Bioorg. Med. Chem. Lett.1996, 6, 373-378. (3) Baidya, N.; Ammons, G. E.; Matulic-Adamic, J.; Karpeisky, A. M.; Beigelman, L.; Uhlenbeck, O. C. RNA1997, 3, 1135-1142. (4) Burgin, A. B., Jr.; Gonzalez, C.; Matulic-Adamic, J.; Karpeisky, A. M.; Usman, N.; McSwiggen, J. A.; Beigelman, L. Biochemistry1996, 35, 14090-14097.				Nebularine CEP >> Nebularine (purine riboside) lacks exocyclic functional groups and offers an altered hydrogen bonding scheme while retaining base stacking ability.^1-4 It can be viewed as an adenosine analog with the hydrogen bond donor deleted. Sequential replacement of conserved adenosine residues in hammerhead ribozymes by nebularine residues^2b,3 suggested the presence of interstrand non-Watson-Crick hydrogen bonding.^2b Depending on the position of the nebularine residue, cleavage rates were either unchanged or diminished.^2b,3 Incorporation of nebularine into a GNRA tetraloop has also been useful for studying this type of RNA structural feature.⁴ Nebularine has been installed into RNA using two different phosphoramidites, one with 2'-O-THP protection¹ and one with 2'-O-TBDMS protection.^2-4 We offer the latter, Nebularine CEP (BA 0265; download Product Information) as well as the 2-deoxy version, 2'-Deoxynebularine CEP (BA 0016). (1) SantaLucia, J., Jr.; Kierzek, R.; Turner, D. H. J. Am. Chem. Soc. 1991, 113, 4313-4322. (2) (a) Slim, G.; Pritchard, C.; Biala, E.; Asseline, U.; Gait, M. J. Nucleic Acids Symp. Ser. 1991, 24, 55-58. (b) Slim, G.; Gait, M. J. Biochem. Biophys. Res. Commun.1991, 183, 605-609. (3) Fu, D.-J.; Rajur, S.; McLaughlin, L. W. Biochemistry1993, 32, 10629-10673. (4) Wörner, K.; Strube, T.; Engels, J. W. Helv. Chim. Acta1999, 82, 2094-2104.
2-Aminopurine Riboside CEP >> Deletion of the O6 carbonyl group of guanosine results in 2-aminopurine riboside (2-AP). The hydrogen bonding pattern of the 2-aminopurine nucleobase (N1 acceptor, H-N2 donor) is isomeric with that of adenosine (N1 acceptor, H-N6 donor). This nucleoside allows the study of the role of exocyclic functional groups, base stacking, and hydrogen bonding patterns in purine-containing nucleic acids. For example, replacement of guanosine residues with 2-AP in the core region of hammerhead ribozymes was useful in determining their role in stabilizing the transition state of ribozyme cleavage.¹ The nature of hydrogen-bonding between G-A mismatches in RNA internal loops was studied with 2-AP.² The role of hydrogen-bonding and stacking interactions in the stability of GNRA loops was probed using 2-AP substitutions.³ The thermodynamic parameters for RNA loops of the type (A)_n were determined using time-resolved spectrofluorimetry on RNAs bearing 2-AP residues in place of A residues, since 2-AP is blue fluorescent and was found to have properties in the (A)_n region that were otherwise very similar to adenosine.⁴ In this sense, 2-AP can be used as a non-invasive conformational probe in RNA studies. Of the different phosphoramidites that have been used for 2-aminopurine riboside incorporation into RNA oligonucleotides,^1-5 we have chosen to offer 2-Aminopurine Riboside CEP in the particular form shown,^1,4 which appears to offer the best results in RNA synthesis yield and purity. Download Product Information. (1) Tuschl, T.; Ng, M. M. P.; Pieken, W.; Benseler, F.; Eckstein, F. Biochemistry1993, 32, 11658-11668. (2) SantaLucia, J., Jr.; Kierzek, R.; Turner, D. H. J. Am. Chem. Soc. 1991, 113, 4313-4322. (3) Wörner, K.; Strube, T.; Engels, J. W. Helv. Chim. Acta1999, 82, 2094-2104. (4) Zagorowska, I.; Adamiak, R. W. Biochemie1996, 78, 123-130. (5) Doudna, J. A.; Szostak, J. W.; Rich, A.; Usman, N. J. Org. Chem. 1990, 55, 5547-5549.				8-Aza-7-deaza-A CEP >> The 2'-deoxyribonucleoside phosphoramidite 8-Aza-7-deaza-dA CEP, also known as PPA CEP, features a nucleobase that is isosteric with adenine but offers a different pi-electron distribution and thus an altered dipole moment, resulting in stronger stacking interactions in oligonucleotides.¹ We now offer the ribonucleoside version, 8-Aza-7-deaza-A CEP (PPA Riboside CEP, BA 0267), a new compound, for use in the synthesis of altered RNA oligonucleotides. Please note: This product is from our Experimental Grab Bag. The compounds in this unique collection have not been validated for any particular purpose, though we have found this particular product to be successfully incorporated into oligonucleotides. We hope that you may find it of interest, but please be aware that its purchase and use is at your own risk. Use: 12 min coupling time, standard dilution, standard cleavage/deprotection. Download Product Information. (1) Seela, F.; Kaiser, K.Helv. Chim. Acta 1988, 71, 1813-1823. Seela describes the N⁶-benzoyl version of the phosphoramidite of 2'-deoxy-8-aza-7-deaza-A. The N-(dimethylamino)methylidene version of the 2'-deoxy version is available from Berry & Associates (BA 0239) or from Glen Research (#1083).
7-Deaza-A CEP >> The N7 imidazole nitrogen of purine nucleosides is known to take part in non-Watson-Crick hydrogen bonding and in metal chelation. "Deleting" the N7 nitrogen by replacing it with a CH group is a useful modification that has been accomplished in DNA and RNA oligonucleotides using the phosphoramidites of 7-deaza-dA (2'-deoxytubercidin) and 7-deaza-A (tubercidin), respectively. Early work by Seela¹ involved 7-Deaza-dA CEP (our product BA 0001), which was useful in showing that N7 of dA is an important hydrogen bond acceptor site for the endodeoxyribonuclease EcoRI. For RNA work, we offer 7-Deaza-A CEP, also known as Tubercidin CEP or C7A CEP (our product BA 0268). This phosphoramidite has been used for studies of the role of the N7 adenosine nitrogen in the structure and function of tRNA and ribozymes.^2,3 Download Product Information. (1) (a) Seela, F.; Kehne, A. Biochemistry1987, 26, 2232-2238. (b) Seela, F.; Berg, H.; Rosemeyer, H. Biochemistry1989, 28, 6193-6198. (2) Fu, D.-J.; McLaughlin, L. W. Biochemistry1992, 31, 10941-10949. (3) Grasby, J. A.; Mersmann, K.; Singh, M.; Gait, M. J. Biochemistry1995, 34, 4068-4076. This work involves a related phosphoramidite using 2'-O-triisopropylsilyl and N⁶-(dimethylamino)methylidene protecting groups.				O⁶-Chlorophenyl-I CEP >> The convertible nucleoside O⁶-Chlorophenyl-I CEP allows the formation of N⁶-alkyl-A residues in RNA. After incorporation of this unit into an oligoribonucleotide by standard phosphoramidite chemistry, treatment with ammonia, methylamine, or higher alkylamines, including those bearing tethered functional groups, leads to displacement of 4-chlorophenol with resultant installation of a 6-amino group, i.e., producing the desired N⁶-alkyl-A residues. Download Product Information. Allerson, C. R.; Chen, S. L.; Verdine, G. L. J. Am. Chem. Soc. 1997, 119, 7423-7433.
8-Vinyl-dA CEP >> This phosphoramidite has been used to incorporate fluorescent 8-vinyl-deoxyadenosine (8vdA) residues into oligonucleotides and has been proposed as an alternative to 2'-deoxyribofuranosyl-2-aminopurine (2AP).¹ The 8vdA-labeled oligonucleotides form more stable duplexes than 2AP-labeled versions when flanked by dA or T residues. The fluorescence quantum yield of 8vdA-labeled oligonucleotides is significantly higher than the 2AP versions. Oligonucleotide synthesis using this phosphoramidite requires UltraMILD phosphoramidites and alternate deblock, Cap A, and Ox as well as a 4 h deprotection with ammonium hydroxide at rt. See Product Information for more information. 1. Ben Gaied, N.; Glasser, N.; Ramalanjaona, N.; Beltz, H.; Wolff, P.; Marquet, R.; Burger, A.; Mely, Y. 8-Vinyl-deoxyadenosine, an alternative fluorescent nucleoside analog to 2'-deoxyribosyl-2-aminopurine with improved properties. Nucl. Acids Res. 2005, 33, 1031-1039.				2-Fluoro-I CEP >> The convertible nucleoside 2-Fluoro-I CEP allows the formation of N²-alkyl-G residues in RNA for structural studies. After incorporation of this unit into an oligoribonucleotide by standard phosphoramidite chemistry, treatment with ammonia, methylamine, or a higher alkylamine, including one bearing a tethered functional group, leads to displacement of fluoride ion with resultant installation of a 2-amino group, i.e., producing a guanosine or an N²-alkyl-G residue. Download Product Information. Allerson, C. R.; Chen, S. L.; Verdine, G. L. J. Am. Chem. Soc. 1997, 119, 7423-7433.
Pseudouridine CEP >> Pseudouridine (ψ) is one of the most common modified nucleosides found in RNA.¹ The uracil nucleobase is identical to that found in uridine except that it is attached to the ribose ring via C5 rather than N1, i.e., it is a C-nucleoside. Thus, in addition to the ability to form Watson-Crick base pairs with adenosine in the normal manner, ψ has an additional hydrogen bond donor at N1. This difference can strongly influence the overall structure of an RNA oligonucleotide. The ability to install a ψ residue site-specifically allows the systematic study of its effect on the structure, function and stability of RNA. Several strategies have been reported for the incorporation of ψ during the chemical synthesis of RNA oligonucleotides.^2-6 We now offer Pseudouridine CEP (ψ CEP, BA 0280) for this purpose. This particular version^2,5 of pseudouridine phosphoramidite relies on standard cyanoethyl phosphoramidite coupling chemistry, 2'-O-TBDMS protection, and no nucleobase protecting groups.⁴ Download Product Information. (1) Charette, M.; Gray, M. W. IUBMB Life 2000, 49, 341-351. (2) Hall, K. B.; McLaughlin, L. W. Nucleic Acids Res. 1992, 20, 1883-1889. See also reference 3 for a closely related phosphoramidite (NEtMe rather than N(i-Pr)2). (3) Gasparutto, D.; Livache, T.; Bazin, H.; Duplaa, A.-M.; Guy, A.; Khorlin, A.; Molko, D.; Roget, A.; Teoule, R. Nucleic Acids Res. 1992, 20, 5159-5166. This work describes a phosphoramidite similar to Pseudouridine CEP, but with an N-ethyl-N-methyl phosphoramidite. (4) Pieles, U.; Beijer, B.; Bohmann, K.; Weston, S.; O'Loughlin, S.; Adam, V.; Sproat, B. S. J. Chem. Soc., Perkin Trans. 1 1994, 3423-3429. This report describes a pseudouridine phosphoramidite bearing pivaloyloxymethyl protecting groups at N1 and N3 and an Fpmp group at the 2'-oxygen. See also the references provided therein for early non-phosphoramidite routes to pseudouridine incorporation. (5) Agris, P. F.; Malkiewicz, A.; Kraszewski, A.; Everett, K.; Nawrot, B.; Sochacka, E.; Jankowska, J.; Guenther, R. Biochemie 1995, 77, 125-134. (6) (a) Meroueh, M.; Grohar, P. J.; Qiu, J.; SantaLucia, J., Jr.; Scaringe, S. A.; Chow, C. S. Nucleic Acids Res. 2000, 28, 2075-2083. This paper describes pseudouridine incorporation using the Scaringe/Dharmacon 2'-O-ACE method for RNA synthesis. See also: (b) Chui, H. M.-P.; Meroueh, M.; Scaringe, S. A.; Chow, C. S. Bioorg. Med. Chem. 2002, 10, 325-332 and (c) Chui, H. M.-P.; Desaulniers, J.-P.; Scaringe, S. A.; Chow, C. S. J. Org. Chem. 2002, 67, 8847-8854.				2'-O-Aminolinker-U CEP >> We offer three uridine-based amino-modifiers for the synthesis of amine-modified RNA, Amino-modifier-C6-U CEP (BA 0247), 5-Aminoallyl-U CEP (BA 0269), and 2'-O-Aminolinker-U CEP (BA 0281). If tethering a reporter group to the 2' oxygen of uridine via an amine is preferred, 2'-O-Aminolinker-U CEP offers an alternative to 2'-aminouridine and 2'-O-(2-aminoethoxy)uridine. Placing the amino group farther from the sugar ring may be advantageous in post-synthetic acylation reactions. Couple using normal dilution and protocols for RNA, i.e., 12 minute coupling time. Please note: This product is from our Experimental Grab Bag. The compounds in this unique collection have not been validated for any particular purpose and have not been proven in oligonucleotide synthesis. We hope that you may find them of interest, but please be aware that their purchase and use is at your own risk. Download Product Information.
3-Methyl-dC CEP >> The formation and repair of alkylated DNA continues to be an important area of research. It has been shown that 3-methyl-2'-deoxycytidine (m3C) residues may be introduced site-specifically into DNA using the phosphoramidite 3-Methyl-dC CEP (BA 0282).¹ Download Product Information. (1) See for example "Mutagenesis, genotoxicity, and repair of 1-methyladenine, 3-alkylcytosines, 1-methylguanine, and 3-methylthymine in alkB Escherichia coli," Delaney, J.; Essigmann, J. M., PNAS, 2004, 101s, 14051-14056. The supporting information of this paper includes the experimental details for the incorporation of m3C into oligonucleotides.				5'-O-Dabsyl-T CEP >> Improved methods for the detection of nucleic acids continues to be an active area of investigation. Non-enzymatic approaches involving fluorescence changes are attractive alternatives to enzyme-based methods such as PCR. Autoligation probes involve two short oligonucleotides, each of which bears a reactive functional group on one end. The two probes are designed such that they hybridize to the appropriate target sequence in an end-to-end fashion to place the two reactive functional groups in close proximity, thus promoting the formation of a covalent bond. Recent work by Kool and co-workers describes an imaginative autoligation strategy that results in the appearance of a fluorescence signal upon template-promoted ligation.¹ Two probes are used, one bearing a 3'-phosphorothioate and the other a 5'-dabsylate and an internal fluorophore. The fluorophore of the second probe is quenched by the nearby dabsyl quencher and is thus dark. The two probes bear additional nucleotides and may bind to the correct sequence (if present) to place the sulfur nucleophile close to the 5'-O-dabsylate. A substitution reaction then occurs, displacing the dabsylate quencher and thus unquenching the fluorophore, resulting in a fluorescence signal. These "quenched autoligation probes" (QUAL probes) are more sensitive to single-nucleotide differences than most hybridization-based approaches. Further, the fluorescence change is permanent and is not subject to buffer or temperature. We now offer 5'-O-Dabsyl-T CEP for the synthesis of 5'-O-dabsylate QUAL probes. Download Product Information. (1) (a) Sando, S.; Kool, E. T. J. Am. Chem. Soc. 2002, 124, 2096-2097. (b) Review: Silverman, A. P.; Kool, E. T. Trends in Biochem. 2005, 23, 225-230. (c) Review: Silverman, A. P.; Kool, E. T. Chem. Rev. 2006, 106, 3775-3789.
2'-Deoxypseudoguanosine CEP >> 2'-Deoxypseudoguanosine (Pseudo-dG) is related to dG by transposition of the nitrogen atom at position 3 and the C-NH₂ group at position 2 of the nucleobase, providing a novel hydrogen bond donor/acceptor pattern. The transposition of atoms or groups in the purine nucleobase of G/dG provides isomers that have altered base-pairing capabilities. We offer a family of guanosine isomers in nucleoside and phosphoramidite forms. Pseudo-dG CEP (BA 0312) may be used to incorporate Pseudo-dG nucleotides into DNA. It is based on the nucleoside 2'-Deoxypseudoguanosine (Pseudo-dG, synthesized by Hosmane and co-workers¹), which is also available (PRA 10103). Pseudo-dG CEP and Pseudo-dG are part of a family that includes Guanosine (PR 3703), 2'-Deoxyguanosine (PR 3452), the isomeric nucleosides Isoguanosine (Iso-G, PR 3735), 2'-Deoxyisoguanosine (Iso-dG, PR 3465), 2'-Deoxypseudoisoguanosine (Pseudoiso-dG, PRA 10104), and the phosphoramidite Pseudoiso-dG CEP (BA 0314). Learn more about these novel compounds and their use by downloading a Product Information sheet for our family of guanosine isomers. Note: Pseudo-dG CEP (BA 0312) is from our Experimental Grab Bag. The compounds in this unique collection have met all Berry and Associates' purity standards, but have not been validated for any particular purpose. We hope that you may find them interesting, but please be aware that their purchase and use is at your own risk. 1. Ujjinamatada, R. K.; Paulman, R. L.; Ptak, R. G.; Hosmane, R. S. Bioorg. Med. Chem. 2006, 14, 6359-6367. See also: Ujjinamatada, R. K.; Phatak, P.; Burger, A. M.; Hosmane, R. S. J. Med. Chem. 2008, 51, 694-698.				2'-Deoxyxanthosine CEP (dX CEP) >> 2'-Deoxyxanthosine CEP (dX CEP) is useful for the installation of 2'-deoxyxanthosine (dX) nucleotides into oligonucleotides. Xanthosine (X) and 2'-deoxyxanthosine (dX), the products of deamination of G and dG, have been incorporated into oligonucleotides,^1-8 imparting a variety of properties to these nucleic acids. The pKa of the proton at N3 of dX is 5.5-5.7,^2,8 therefore dX is present as a mono-anion to the extent of about 95% at neutral pH. dX residues have the same hydrogen-bond donor/acceptor pattern as thymidine, thus allowing base-pairing with dA.⁸ This leads to a distortion of the helix, since two purines are paired. Stronger base stacking interactions are apparent. Duplex stability variations as a function of the opposing base pair have been studied.^4,8 dX is susceptible to depurination under acidic conditions, forming abasic sites.^2,8 At pH 4, dX depurinates more quickly than dG by a factor of about 1000. At neutral pH, dX has about the same stability as dG. The recognition and excision of dX by base excision repair enzymes has been studied.² dX has been considered to be a promiscuous or universal nucleoside.^1,8 dX may expand the genetic code when paired to a pyrimidine-2,4-diamine C-nucleoside.⁶ Studies of polymerase-mediated incorporation of various nucleotides opposite dX have been carried out.^2,4 The presence of dX residues may lead to triplexes, quartets, and other G-stranded structures.⁸ We now offer the phosphoramidite 2'-Deoxyxanthosine CEP (BA 0313), featuring 2-(4-nitrophenyl)ethyl (NPE) protecting groups at O² and O⁶.^1,2 Download a Product Information Sheet for BA 0313 for more information on the use of this monomer. 1. Jurczyk, S. C.; Horlacher, J.; Devined, K. G.; Benner, S. A.; Battersby, T. R. Helv. Chim. Acta 2000, 83, 1517-1524. 2. Weunschell, G. E.; O'Connor, T. R.; Termini, J. Biochemistry, 2003, 42, 3608-3616. 3. Tuschl, T.; Ng, M. M. P.; Pieken, W.; Benseler, F.; Eckstein, F. Biochemistry 1993, 32, 11658-11668. 4. Eritja, R.; Horowitz, D. M.; Walker, P. A.; Ziehler-Martin, J. P.; Boosalis, M. S.; Goodman, M. F.; Itakura, K.; Kaplan, B. E. Nucleic Acids Res. 1986, 14, 8135-8153. 5. Van Aerschot, A.; Mag, M.; Herdewijn, P.; Vanderhaeghe, H. Nucleosides Nucleotides Nucleic Acids 1989, 8, 159-178. 6. Lutz, M. J.; Held, H. A.; Hottiger, M.; Hubscher, U.; Benner, S. A. Nucleic Acids Res. 1996, 24, 1308-1313. 7. Groebke, K.; Hunziker, J.; Fraser, W.; Peng, L.; Diederichsen, U.; Zimmermann, K.; Holzner, A.; Leumann, C.; Eschenmoser, A. Helv. Chim. Acta 1998, 81, 375. 8. Seela, F.; Shaikh, K. I. Helv. Chim. Acta 2006, 89, 2794-2814.
3'-BBQ-650 CPG >> Dark quencher of long-wavelength fluorescence. Standard phosphoramidites and synthesis protocols may be employed with 3'-BBQ-650 CPG. Nucleobase deprotection may be performed using standard protocols with ammonium hydroxide or AMA without degradation of the quencher, e.g., 12 h, 55 ^oC. For quantification, the following extinction coefficients may be useful, which were determined using a simple BBQ chromophore (i.e., no oligonucleotide): At 598 nm in methanol, 40,667 M^-1cm^-1. At 260 nm in methanol, 15,077 M^-1cm^-1. Download a product information sheet for BL 2010 here. Download a brief overview of BlackBerry Quenchers here.				Diazaindacene NHS Ester >> A new fluorophore exhibiting an emission maxiumum at 530-535 nm, a large Stokes shift, and a high quantum yield.
7-O-Amino-4-methylumbelliferone >> Coumarin derivatives such as 7-O-Amino-4-methylumbelliferone have been shown to be useful in a simple spectroscopic assay for aldehydes in biologically relevant media.¹ Condensation of this compound with aldehydes (e.g., formaldehyde) forms aldimines that are susceptible to elimination with Lewis bases such as bovine serum albumin (BSA), forming blue-fluorescent 4-methylumbelliferone (4-MU). The excitation and emission maxima for 4-MU are the same at pH 7.0 (water) and pH 10.3 (0.15 M glycine buffer).² Maximum fluorescence was observed at 445 nm when excited at 365 nm, and the fluorescence intensity is 100 times as intense at pH 10.3 than at pH 7.0. 5 mg = 26.2 micromoles; 25 mg = 131 micromoles. Download a Product Information Sheet for HC 9070 here. 1. Salahuddin, S.; Renaudet, O.; Reymond, J.-L. Org. Biomol. Chem. 2004, 2, 1471-1475. 2. Strachan, R.; Wood, J.; Hirschmann, R. J. Org. Chem. 1962, 27, 1074-1075.				T-IP₅ >> T-IP₅ is a novel chromophoric substrate analog of phytic acid that allows the measurement of phytase activity.¹ Cleavage of phosphate ester bonds by phytase leads to dephosphorylated T-phosphatidylinositol intermediates that may be quantified using reversed phase chromatography with UV detection. 1. Berry, D. F.; Berry, D. A. Tethered phytic acid as a probe for measuring phytase activity. Bioorg. Med. Chem. Lett. 2005, 15(12), 3157-61.