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Full Catalog (page 6)
Product Number Product Name Molecular Formula Cas. No. Description Notes Alt. Name Alt. Name 2
BA 0249 N2-Methyl-dG
CEP		 C41H50N7O7P  808132-80-1  Guanine bases in DNA are susceptible to N-alkylation by various carcinogens, leading to miscoding and mutagenicity. Choi and Guengerich have prepared a series of N2-alkyl-2'-deoxyguanosine phosphoramidites where the alkyl group ranges in size from methyl to anthracenylmethyl for studies on the effect of the size of these groups on the catalytic efficiency and fidelity of various DNA polymerases.1 We offer the N2-methyl- (BA 0249), N2-ethyl- (BA 0076), and N2-isobutyl-dG (BA 0250) phosphoramidites1 as well as two additional bulkier choices, the N2-neopentyl version (BA 0200), and the N2-benzyl version (BA 0337) . Researchers may find this "steric tool box" useful for probing the steric requirements at N2 of dG in various applications.

Use: Add 1 part of anhydrous dichloromethane to dissolve the phosphoramidite, followed by 2 parts of anhydrous acetonitrile. Couple as recommended by instrument manufacturer. See Product Information.

(1) Choi, J.-Y.; Guengerich, F. P. J. Biol. Chem. 2004, 279 , 19217-19229.
 		 Smallest member of the "steric tool box" for probing the steric requirements at N2 of dG in various applications.  3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-methyl-2'-deoxyguanosine   
BA 0250 N2-Isobutyl-dG
CEP		 C44H56N7O7P  808132-82-3  Guanine bases in DNA are susceptible to N-alkylation by various carcinogens, leading to miscoding and mutagenicity. Choi and Guengerich have prepared a series of N2-alkyl-2'-deoxyguanosine phosphoramidites where the alkyl group ranges in size from methyl to anthracenylmethyl for studies on the effect of the size of these groups on the catalytic efficiency and fidelity of various DNA polymerases.1 We offer the N2-methyl- (BA 0249), N2-ethyl- (BA 0076), and N2-isobutyl-dG (BA 0250) phosphoramidites1 as well as two additional bulkier choices, the N2-neopentyl version (BA 0200), and the N2-benzyl version (BA 0337) . Researchers may find this "steric tool box" useful for probing the steric requirements at N2 of dG in various applications.

Use: Add 1 part of anhydrous dichloromethane to dissolve the phosphoramidite, followed by 4.5 parts of anhydrous acetonitrile. Couple as recommended by instrument manufacturer. See Product Information.

(1) Choi, J.-Y.; Guengerich, F. P. J. Biol. Chem. 2004, 279 , 19217-19229.
 		 Useful for probing the steric requirements at N2 of dG in various applications.      
BA 0253 Fluorescein II CEP C67H76N3O14P  1027512-13-5  For the installation of fluorescein internally or 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 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.

We also offer Fluorescein III CEP ("6-FAM III", BA 0334) with a DMT on a 1,3-diol framework.

Download Product Information for BA 0253 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.

 		 For the installation of fluorescein at the 5'-terminus of an oligonucleotide while allowing multiple additions or assaying the coupling step.  6-FAM II   
BA 0254 Zebularine CEP C45H61N4O8PSi  155831-90-6  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 (BA 0201).
 		 Zebularine is a des-methyl analog of cytidine useful for probing the hydrogen-bonding characterisitcs in oligonucleotides.  4HC CEP  2'-O-t-Butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2(1H)-pyrimidinone-1-β-D-riboside 
BA 0261 8-Allyloxy-dG CEP C46H57N8O8P  133783-15-0  Download a Product Information sheet for BA 0261 here.

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.

 		   8-Allyloxy-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-(dimethylaminomethylidine)-2'-deoxyguanosine   
BA 0262 5'-Amino-modifier-C12-DMT CEP C42H62N3O4P  1027512-19-1  The installation of an amino-modifier at the 5'-terminus of an oligonucleotide provides, via amide bond formation, a handle for the attachment of a variety of chemical species. If purification of the amine-modified oligonucleotide is desired, it is common to employ an MMT group on the amine. The lipophilicity of the MMT group aids in reversed-phase purification techniques and may also be useful for assaying the coupling yield. For applications where acid sensitivity is an issue, we offer 5'-Amino-modifier-C12-DMT CEP, which uses the more acid-labile DMT protecting group. Amine-modified oligonucleotides have been synthesized using closely related DMT-bearing amino-modifier phosphoramidites.1,2 Coupling: Use standard protocols; extended coupling times are not required.

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.

(1) Sinha, N. D.; Cook, R. M. Nucleic Acids Res.1988, 16, 2659-2669.
(2) Guar, R. K. Nucleosides & Nucleotides1991, 10, 895-909.

 		 An amino-modifier with an acid-labile DMT protecting group.  O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-12-(4,4'-dimethoxytrityl)aminododecan-1-ol   
BA 0263 O4-Chlorophenyl-U
CEP		 C51H64ClN4O9PSi  220382-28-5 

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 a Product Information Sheet.

Allerson, C. R.; Chen, S. L.; Verdine, G. L. J. Am. Chem. Soc. 1997, 119, 7423-7433.

 

The convertible nucleoside O4-Chlorophenyl-U CEP allows the formation of N4-alkyl-C residues in RNA for structural studies.

 		 2'-O-(tert-Butyldimethylsilyl)-O4-(4-chlorophenyl)-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)uridine  Convertible C CEP or ClφU CEP 
BA 0264 Pyridin-2-one riboside CEP C46H62N3O8PSi  179915-57-2  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 For more information, download a Product Information Sheet.

(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.
 		 Modified pyrimidine used for probing ribozyme catalytic activity.  1-[2'-O-t-Butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-β-D-ribofuranosyl]-2(1H)-pyridinone   
BA 0265 Nebularine CEP C46H61N6O7PSi  151132-95-5  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 residues2b,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. Biochemistry 1993, 32, 10629-10673.
(4) Wörner, K.; Strube, T.; Engels, J. W. Helv. Chim. Acta 1999, 82, 2094-2104.

 		 Nebularine (purine riboside) is an adenosine analog with the hydrogen bond donor deleted. This nucleobase scaffold offers an altered hydrogen bonding scheme while retaining base stacking ability.  9-[2-O-t-Butyldimethylsilyl-3-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5-O-(4,4'-dimethoxytrityl)-beta-D-ribofuranosyl]-9H-purine  Purine Riboside CEP, or P CEP 
BA 0266 2-Aminopurine riboside CEP C50H68N7O8PSi  151059-65-3  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. Biochemistry 1993, 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. Acta 1999, 82, 2094-2104.
(4) Zagorowska, I.; Adamiak, R. W. Biochemie 1996, 78, 123-130.
(5) Doudna, J. A.; Szostak, J. W.; Rich, A.; Usman, N. J. Org. Chem. 1990, 55, 5547-5549.
 		 Guanosine analog which lacks the O6 carbonyl resulting in a hydrogen bonding pattern isomeric with that of adenosine.  9-[2-O-t-Butyldimethylsilyl-3-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5-O-(4,4'-dimethoxytrityl)-β-D-ribofuranosyl]-2-isobutyrylamino-9H-purine  2-AP CEP 
BA 0267 8-Aza-7-deaza-A CEP C53H66N7O8PSi  104992-55-4  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.

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.

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).

 		 8-Aza-7-deaza-a CEP features a nucleobase that is isosteric with adenine but offers a different pi-electron distribution.  N6-Benzoyl-2'-O-t-butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-8-aza-7-deazaadenosine  PPA Riboside CEP 
BA 0268 7-Deaza-A CEP C54H67N6O8PSi  144994-95-6  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 (BA 0001), which was useful in showing that N7 of dA is an important hydrogen bond acceptor site for the endodeoxyribonuclease Eco RI. For RNA work, we offer 7-Deaza-A CEP (BA 0268), also known as Tubercidin CEP or C7A CEP. 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 a a Product Information sheet for more information.

(1) (a) Seela, F.; Kehne, A. Biochemistry 1987, 26, 2232-2238. (b) Seela, F.; Berg, H.; Rosemeyer, H. Biochemistry1989, 28, 6193-6198.
(2) Fu, D.-J.; McLaughlin, L. W. Biochemistry 1992, 31, 10941-10949.
(3) Grasby, J. A.; Mersmann, K.; Singh, M.; Gait, M. J. Biochemistry 1995, 34, 4068-4076. This work involves a related phosphoramidite using 2'-O-triisopropylsilyl and N6-(dimethylamino)methylidene protecting groups.  		 Useful for modification of base pairing and metal chelating characterisitcs of purine nucleosides through elimination of the N7 nitrogen.

 		 N6-Benzoyl-2'-O-t-butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-7-deazaadenosine  Tubercidin CEP or C7A CEP 
BA 0269 5-Aminoallyl-U CEP C50H65F3N5O10PSi  None found  To our knowledge, 5-Aminoallyl-U CEP does not appear in the literature. However, the 2'-deoxyribo version (5-Aminoallyl-dU CEP) is known1,2 and is also offered by Berry & Associates (see Product Number BA 0311). It should be noted that the 2'-deoxy version is useful not only in amine modification, but in triplex-forming oligonucleotides (TFOs) that are similar in stability to those bearing unmodified residues.2

For information on the use of this product, download a Product Information Sheet for BA 0269.

1. Early work on the introduction of a 5-aminoallyl-dU amino modifier into oligonucleotides involved the methyl phosphoramidite.1a 5-Aminoallyl-dU CEP (our BA 0311), employing a 2-cyanoethyl phosphoramidite, was reported later.1b See: (a) Cook, A. F.; Vuocolo, E.; Brakel, C. L. Nucleic Acids Res. 1988, 16, 4077-4095. (b) Lermer, L.; Yoann, R.; Ting, R.; Perrin, D. M. J. Am. Chem. Soc. 2002, 124, 9960-9961. See especially the Supporting Information.

2. Brazier, J. A.; Shibata, T.; Townsley, J.; Taylor, B. F.; Frary, E.; Williams, N. H.; Williams, D. M. Nucl. Acids Res. 2005, 33, 1362-1371.

 		 Allows the introduction of a 5-aminoallyluridine residue into oligonucleotides for the purpose of post-synthetic labeling by acylation.   2'-O-t-Butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-5-[E-3-(trifluoroacetamido)-1-propenyl]uridine   
BA 0272 O6-Chlorophenyl-I
CEP		 C52H64ClN6O8PSi  220382-26-3  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.

 

The convertible nucleoside O6-Chlorophenyl-I CEP allows the formation of N6-alkyl-A residues in RNA. 

 O6-(4-Chlorophenyl)-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-O-(tert-butyldimethylsilyl)inosine  Convertible A CEP or ClφI CEP 
BA 0278 8-Vinyl-dA CEP C45H55N8O6P  851228-42-7  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 details.

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.

 		 Useful for incorporation of fluorescent 8-vinyl-deoxyadenosine (8vdA) residues into oligonucleotides.  3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N6-(dimethylaminomethylidene)-8-vinyl-2'-deoxyadenosine   
BA 0279 2-Fluoro-I CEP C54H67FN7O10PSi  220382-27-4  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.

 		 The convertible nucleoside 2-Fluoro-I CEP allows the formation of N2-alkyl-G residues in RNA for structural studies.  3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2-fluoro-6-O-(4-nitrophenylethyl)-2'-O-(tert-butyldimethylsilyl)inosine  Convertible G CEP or NPE-FI CEP 
BA 0280 Pseudouridine CEP C45H61N4O9PSi  163496-23-9  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 version2,5 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 © Chui, H. M.-P.; Desaulniers, J.-P.; Scaringe, S. A.; Chow, C. S. J. Org. Chem. 2002, 67, 8847-8854.

 		 Enables incorporation of Pseudouridine (ψ) into RNA. Pseudouridine is a uracil nucleobase identical to uridine but is attached to the ribose ring via C5 giving a C-nucleoside.  ψ CEP  2'-O-(t-Butyldimethylsilyl)-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)pseudouridine 
BA 0281 2'-O-Aminolinker-U CEP C45H55F3N5O11P  None 

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. Coupling is accomplished 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 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.

Download Product Information.

 		 2'-O-Aminolinker-U CEP enables the incorporation of a uridine residue that allows tethering of a reporter group to the 2' oxygen of uridine via an amine.  3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-O-2-[2-(trifluoroacetamido)ethoxy]ethyluridine   
BA 0282 3-Methyl-dC CEP C47H54N5O8P  None  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. 

 Useful for site-specific incorporation of 3-methyl-2'-deoxycytidine (m3C) into DNA.    m3C CEP 
BA 0283 5'-O-Dabsyl-T CEP C33H44N7O8PS  None  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. 

 We offer 5'-O-Dabsyl-T CEP for the synthesis of 5'-O-dabsylate "quenched autoligation probes" (QUAL probes).   5'-O-Dabsyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]thymidine   
BA 0287 Fmoc-amino-modifier-C6-dT CEP C63H73N6O11P  None found  The (fluorenylmethyl)carbamoyl (Fmoc) group has been shown to be a useful amine protecting group for amine modification of oligonucleotides.1 It is removed during cleavage/deprotection with ammonium hydroxide. Alternatively, the Fmoc group can be removed before cleavage of the oligonucleotide from the solid support,2 e.g., with piperidine, simplifying the acylation process. After the acylation is complete, the labeled oligonucleotide can then be cleaved from the support and further deprotected with ammonium hydroxide.

For applications requiring a nucleobase-tethered amine at internal or 5' positions, we offer the new Fmoc-protected compound Fmoc-Amino-Modifier-C6-dT CEP (BA 0287), which offers the possibility of on-bead acylation as discussed above. It is an alternative to the venerable Amino-Modifier-C6-dT CEP (BA 0015), which bears a trifluoroacetyl (TFA) protecting group. The TFA group cannot be removed without cleavage of the oligonucleotide from the resin.

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

For 3'-amino-modification involving Fmoc-deprotection, see BA 0299 and BA 0307.

(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 incorporation of a nucleobase-tethered amine that can be deprotected prior to cleaving the oligonucleotide from the solid support.     
BA 0289 Amino-modifier-15-dT CEP C56H73F3N7O13P  None  Amino-modifier-15-dT CEP is similar to Amino-modifier-C6-dT CEP (BA 0015) except that it offers a longer tether that includes an amphipathic glycol ether region.

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

 		   3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-5-[E-2'-[N-[15-(trifluoroacetamido)-7-aza-10,13-dioxa-8-oxopentadecyl]carboxamido]vinyl]-2'-deoxyuridine   
BA 0295 Fmoc-pyrrolidine CEP C50H56N3O7P  1221186-22-6  Verdine and co-workers1 described the use of Fmoc-pyrrolidine CEP to install (2R,3S)-2-hydroxymethyl-3-hydroxypyrrolidine (3-hydroxyprolinol) residues into DNA. Such oligonucleotides were found to be potent and selective inhibitors of E. coli 3-methyladenine DNA glycosylase II (AlkA). The pyrrolidine ring, which should be protonated under experimental conditions, is proposed to mimic the charged intermediate encountered during glycosyl hydrolysis. Related 3-hydroxyprolinol-bearing oligonucleotides have been made and subjected to hybridization studies.2

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

(1) Scharer, O. D.; Ortholand, J.-Y.; Ganesan, A.; Ezaz-Nikpay, K.; Verdine, G. L. J. Am. Chem. Soc. 1995, 117, 6623-6624.

(2) Ceulemans, G.; Van Aerschot, A.; Rozenski, J. Herdewijn, P. Tetrahedron 1997, 53, 14957-14974.

 		 Used to install (2R,3S)-2-hydroxymethyl-3-hydroxypyrrolidine (3-hydroxyprolinol) residues into DNA.     
BA 0298 Amino-modifier-C6-G CEP C57H80F3N10O9PSi  None  Use standard RNA protocols with a 12 minute coupling. Download a Product Information sheet for BA 0298 here.

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 0299 3'-Fmoc-amino-modifier CPG (500
Angstrom)		 N/A  None  For the installation of an amino group at the 3'-terminus of an oligonucleotide, a solid-support-linked monomer with a protected amine and DMT-protected alcohol is required. The amine protecting group is typically removed and acylated with an appropriate NHS ester. The (fluorenylmethyl)carbamoyl (Fmoc) group has been shown to be useful as such an amine protecting group for amine modification of oligonucleotides.1 It is removed during cleavage/deprotection with ammonium hydroxide. Alternatively, the Fmoc group can be removed before cleavage of the oligonucleotide from the solid support, e.g., with piperidine, simplifying the acylation process. After the acylation is complete, the labeled oligonucleotide can then be cleaved from the support and further deprotected with ammonium hydroxide.2

Berry & Associates offers a version of such an Fmoc-protected amino-modifier for installation of an amino group at the 3'-terminus, i.e., 3'-Fmoc-amino-modifier CPG, in both higher- and lower-loaded versions, namely BA 0299 (ca. 70-80 µmol/g on 500 Angstrom CPG) and BA 0307 (ca. 35-45 µmol/g on 1000 Angstrom CPG). Both products feature a 7-atom spacer between the amino group and the O-DMT group.

If an Fmoc-protected amine modifier is required for internal or 5'-incorporation, please see Fmoc-amino-modifier-C6-dT CEP.

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) (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.

 		 Enables the installation of an amino group at the 3'-terminus of an oligonucleotide.     
BA 0300 Anthraquinone-pyrrolidine CEP C50H52N3O8P  1221186-23-7  Anthraquinones may be incorporated into oligonucleotides by a variety of methods using a host of different phosphoramidites. The anthraquinone moiety is useful for applications such as intercalation, duplex and triplex stabilization, photochemical immobilization, quenching of fluorescence, electrochemical detection, and charge transport through nucleic acids. Of the various anthraquinone phosphoramidites that have been explored, amide formation at the carboxyl group of anthraquinone-2-carboxylic acid is popular.1-8

Hydroxyprolinol has found use as a substitute for the sugar ring of nucleotides.9-10 We now offer Anthraquinone-pyrrolidine CEP, a 3-hydroxyprolinol analog bearing an anthraquinone amide at the pyrrolidine amino group. The anthraquinone pyrrolidine can be installed internally or at the 5'-terminus of an oligonucleotide.

Download a Product Information Sheet for BA 0300 here.

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.

1. (a) Gasper, S. M.; Schuster, G. B. J. Am. Chem. Soc. 1997, 119, 12762-12771. (b) Shao, F.; Augustyn, K.; Barton, J. K. J. Am. Chem. Soc. 2005, 127, 17445-17452.

2. Whittemore, N. A.; Mullenix, A. N.; Inamati, G. B.; Manoharan, M.; Cook, P. D.; Tuinman, A. A.; Baker, D. C.; Chambers, J. Q. Bioconj. Chem. 1999, 10, 261-270.

3. Tierney, M. T.; Grinstaff, M. W. Org. Lett. 2000, 2, 3413-3416.

4. Tierney, M. T.; Grinstaff, M. W. J. Org. Chem. 2000, 65, 5355-5359.

5. Koch, T.; Jacobsen, N.; Fensholdt, J.; Boas, U.; Fenger, M.; Jakobsen, M. H. Bioconj. Chem. 2000, 11, 474-483.

6. Al-Rawi, S.; Ahlborn, C.; Richert, C. Org. Lett. 2005, 7, 1569-1572.

7. Asanuma, H.; Hayashi, H.; Zhao, J.; Liang, X.; Yamazawa, A.; Kuramochi, T.; Matsunaga, D.; Aiba, Y.; Kashida, H.; Komiyama, M. Chem. Commun. 2006, 5062-5064.

8. Shibata, A.; Ueno, Y.; Shinbo, K.; Nakanishi, M.; Matsuda, A.; Kitade, Y. Bioorg. Med. Chem. Lett. 2006, 16, 1410-1413.

9. Ceulemans, G.; Van Aerschot, A.; Rozenski, J.; Herdewijn, P. Tetrahedron 1997, 53, 14957-14974.

10. Scharer, O. D.; Ortholand, J.-P.; Ganesan, A.; Ezaz-Nikpay, K.; Verdine, G. L. J. Am. Chem. Soc. 1995, 117, 6623-6624.

 		 Anthraquinone-Pyrrolidine CEP is a 3-hydroxyprolinol analog bearing an anthraquinone amide at the pyrrolidine amino group. The anthraquinone pyrrolidine can be installed internally or at the 5'-terminus of an oligonucleotide.