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Product Number Product Name Molecular Formula Cas. No.

BA 0266

2-Aminopurine riboside CEP

C50H68N7O8PSi 

151059-65-3 

Description

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.

Notes

Guanosine analog which lacks the O6 carbonyl resulting in a hydrogen bonding pattern isomeric with that of adenosine.

Alternate Name(s):

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 

None Assigned 

Description

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.

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).

Notes

8-Aza-7-deaza-a CEP features a nucleobase that is isosteric with adenine but offers a different pi-electron distribution.

Alternate Name(s):

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 

Description

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.

Notes

Useful for modification of base pairing and metal chelating characterisitcs of purine nucleosides through elimination of the N7 nitrogen.

Alternate Name(s):

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 

1269413-27-5 

Description

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.

Notes

Allows the introduction of a 5-aminoallyluridine residue into oligonucleotides for the purpose of post-synthetic labeling by acylation.

Alternate Name(s):

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 

Description

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.

Notes

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

Alternate Name(s):

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 

Description

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.

Notes

Useful for incorporation of fluorescent 8-vinyl-deoxyadenosine (8vdA) residues into oligonucleotides.

Alternate Name(s):

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 

Description

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.

Notes

The convertible nucleoside 2-Fluoro-I CEP allows the formation of N2-alkyl-G residues in RNA for structural studies.

Alternate Name(s):

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 

Description

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.

Notes

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.

Alternate Name(s):

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 Assigned 

Description

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.

Download Product Information.

Notes

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.

Alternate Name(s):

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 Assigned 

Description

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.

Notes

Useful for site-specific incorporation of 3-methyl-2'-deoxycytidine (m3C) into DNA.

BA 0283

5'-O-Dabsyl-T CEP

C33H44N7O8PS 

None Assigned 

Description

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.

Notes

We offer 5'-O-Dabsyl-T CEP for the synthesis of 5'-O-dabsylate "quenched autoligation probes" (QUAL probes).

Alternate Name(s):

5'-O-Dabsyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]thymidine

BA 0287

Fmoc-amino-modifier-C6-dT CEP

C63H73N6O11P 

None Assigned 

Description

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.

Notes

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 Assigned 

Description

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.

Alternate Name(s):

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 0290

5-Propynyl dC CEP

C44H52N5O8P 

945537-44-0 

Description

For information on the use of this product, download a Product Information Sheet for BA 0290.

Notes

Useful for the installation of 2'-deoxy-5-propynyl cytidine for stabilization of duplex and triplex nucleic acids.

Alternate Name(s):

N4-Acetyl-pdC CE Phosphoramidite

BA 0295

Fmoc-pyrrolidine CEP

C50H56N3O7P 

1221186-22-6 

Description

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.

Notes

Used to install (2R,3S)-2-hydroxymethyl-3-hydroxypyrrolidine (3-hydroxyprolinol) residues into DNA.

BA 0298

Amino-modifier-C6-G CEP

C57H80F3N10O9PSi 

None Assigned 

Description

Use standard RNA protocols with a 12 minute coupling. Download a Product Information sheet for BA 0298 here.

BA 0299

3'-Fmoc-amino-modifier CPG (500
Angstrom)

N/A 

None 

Description

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.

Notes

Enables the installation of an amino group at the 3'-terminus of an oligonucleotide.

BA 0300

Anthraquinone-pyrrolidine CEP

C50H52N3O8P 

1221186-23-7 

Description

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.

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.

Notes

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.

BA 0301

Formylindole-dT CEP

C59H70N7O11P 

None Assigned 

Description

Aldehydes are attractive electrophiles for bioconjugation, since they react with nucleophiles such as amines and hydrazines to form imines and hydrazones, respectively. For the incorporation of an aldehyde functional group into an oligonucleotide, its reactivity often necessitates carrying it through solid-phase synthesis in protected or otherwise masked form, thus requiring one or more post-synthetic unmasking transformations. Saito and co-workers1 reported that an aldehyde can be incorporated directly using a 3-formylindole nucleoside phosphoramidite via solid-phase nucleic acid synthesis. The electron-donating indole ring offered some stabilization of the aldehyde while retaining enough electrophilic character to allow conjugation with hydrazines and hydrazones. We now offer Formylindole-dT CEP which features a tether between the formylindole nucleus and the oligonucleotide strand. Internal and 5'-incorporation are possible.

Download a Product Information Sheet for BA 0301 here.

1. Okamoto, A.; Tainaka, K.; Saito, I. Tetrahedron Lett. 2002, 43, 4581-4583.

Notes

Formylindole-dT CEP features a tether between the formylindole nucleus and the oligonucleotide strand. Internal and 5'-incorporations are possible.

BA 0302

Anthraquinone-C2-dT CEP

C59H61N6O12P 

None Assigned 

Description

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. Anthraquinone-C2-dT CEP features an electronically insulating tether that places the anthraquinone at a significant distance from the oligonucleotide. Internal or 5'-installations are efficient.

Download a Product Information Sheet for BA 0302 here.

Notes

Anthraquinone-C2-dT CEP features an electronically insulating tether that places the anthraquinone at a significant distance from the oligonucleotide. Internal or 5'-installations are efficient.

BA 0303

6-Aza-dU CEP

C46H52N5O10P 

909782-90-7 

Description

As compared to dU residues, 6-aza-dU nucleotides are deprotonated at neutral pH, have enhanced 3'-exonuclease stability, and exhibit a high-anti glycosidic bond conformation and N-type sugar pucker. DNA duplexes containing 6-aza-dU-dA base pairs have been studied and are less stable than T-dA base pairs at neutral pH due to deprotonation of the N3 hydrogen on 6-aza-dU. However, at lower pH, duplex stability increases as N3 becomes protonated and therefore able to hydrogen bond to dA. Metal-DNA (M-DNA) complexes are formed at neutral pH rather than at higher pH as is the case for canonical DNA.

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

(1) Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.

Notes

6-Aza-dU CEP enables incorporation of an N3-o-anisoyl protected 6-aza-dU residue into oligonucleotides. The stability, conformation, and metal chelating characteristics of nucleotides containing 6-aza-dU residues differ from those with dU residues.

Alternate Name(s):

6-Aza-2'-deoxyuridine CEP

BA 0306

6-Azathymidine CEP

C39H48N5O8P 

142234-18-2 

Description

6-Azathymidine1 has a nitrogen atom in place of the methine group at position 6 of the thymine ring. This results in a significant lowering of the pKa of the N3 hydrogen (7.0)2 vs. that of thymidine (10.0). Hence, 6-azathymidine will be significantly deprotonated at neutral pH.

The phosphoramidite of this nucleoside, 6-Azathymidine CEP (BA 0306) has been incorporated into oligonucleotides,1 where it imparts nuclease resistance when installed at the 5'-position. Duplexes with DNA or RNA are only slightly destabilized, and heteroduplexes with RNA support RNase-H cleavage.

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

ALso available: The phosphoramidite 6-Aza-dU CEP and the nucleosides 6-Azathymidine and 6-Aza-2'-deoxyuridine.

(1) Sanghvi, Y.; Hoke, G. D.; Freier, S. M.; Zounes, M. C.; Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P. D. Nucleic Acids Res. 1993, 21, 3197-3203.

(2) Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.

Notes

6-Azathymidine has a nitrogen atom in place of the methine group at position 6 of the thymine ring. The phosphoramidite 6-Azathymidine CEP (BA 0306) can incorporated into oligonucleotides.

BA 0307

3'-Fmoc-amino-modifier CPG (1000
Angstrom)

N/A 

None 

Description

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.

Notes

Useful for the installation of an amino group at the 3'-terminus of an oligonucleotide.

BA 0308

5-Octadiynyl-dU CEP

C47H55N4O8P 

938186-76-6 

Description

An attractive strategy for nucleic acid conjugation involves the Cu(I)-catalyzed click reaction between terminal alkynes and azides. While 5-Ethynyl-dU in oligonucleotides has been reported to undergo the click reaction,1 the short rigid nature of the alkyne group severely limits its application for this purpose. 5-Octadiynyl-dU CEP (BA 0308)1-5 is a much superior reagent for the installation of an alkyne-bearing nucleoside into an oligonucleotide when click reactions are contemplated. The terminal alkyne is more flexible and extends farther away from thr pyrimidine ring, thereby allowing more efficient ligation via click chemistry, even when multiple ligations to a single oligo are desired. Interestingly, the 5-Octadiynyl-dU modification gives a slight stabilization of DNA duplexes, much like the well-known effect of propynyl-dU modification.3

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

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

(1) Gierlich, J.; Burley, G. A.; Gramlich, P. M. E.; Hammond, D. M.; Carell, T. Org. Lett. 2006, 8, 3639-3642.

(2) Seela, F.; Sirivolu, V. R. Chem. Biodiversity 2006, 3, 509-514. Gierlich, J.; Burley, G. A.; Gramlich, P. M. E.; Hammond, D. M.; Carell, T. Org. Lett. 2006, 8, 3639-3642.

(3) Seela, F.; Sirivolu, V. R. Helv. Chim. Acta 2007, 90, 535-552.

(4) Hammond, D. M.; Manetto, A.; Gierlich, J.; Azov, V. A.; Gramlich, P. M. E.; Burley, G. A.; Maul, M.; Carell, T. Angew. Chem. Int. Ed. 2007, 46, 4184-4187.

(5) Rozkiewicz, D. I.; Gierlich, J.; Burley, G. A.; Gutsmiedl, K.; Carell, T.; Ravoo, B. J.; Reinhoudt, D. N. ChemBioChem 2007, 8, 1997-2002.

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

Notes

Useful for the installation of an alkyne-bearing nucleoside into an oligonucleotide. The flexible tether allows for efficient elaboration via Click chemistry.

BA 0309

Anthraquinone-5-ethynyl-dU CEP

C55H53N4O10P 

None Assigned 

Description

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. Barton and co-workers1 have studied the importance of the tether in electronic coupling of the anthraquinone to the DNA. Connection of the anthraquinone moiety to the nucleobase of 2'-deoxyuridine via an ethynyl group provides an electronic coupling to the nucleobase pi-stack. Such nucleotides were made by incorporation of a 5-ethynyl-dU nucleotide using 5-Ethynyl-dU CEP (BA 0167) followed by a post-synthetic palladium-catalyzed Sonogashira coupling with 2-iodoanthraquinone.1 For the direct incorporation of an ethynyl-dU-linked anthraquinone into an oligonucleotide, Anthraquinone-5-ethynyl-dU CEP (BA 0309) may be used, avoiding post-synthetic palladium couplings.

Download a Product Information Sheet for BA 0309 here.

1. Gorodetsky, A. A.; Green, O.; Yavin, E.; Barton, J. K. Bioconjugate Chem. 2007, 18, 1434-1441.

Notes

For the direct incorporation of an ethynyl-dU-linked anthraquinone into an oligonucleotide, providing an electronic coupling to the nucleobase pi-stack.

BA 0311

5-Aminoallyl-dU CEP

C44H51F3N5O9P 

144253-90-7 

Description

Early work on the introduction of a 5-aminoallyl-dU amino modifier into oligonucleotides involved the methyl phosphoramidite.1 5-Aminoallyl-dU CEP, employing a 2-cyanoethyl phosphoramidite, was reported later.2,3

Williams and co-workers3 studied the incorporation of 5-aminoallyl-dU residues into triplex-forming oligonucleotides (TFOs), where a single incorporation did not change the stability of the triplex vs. unmodified TFOs. Multiple incorporations led to a lower triplex stability. The pKa of the protonated form of the amino group of 5-aminoallyl-dU is expected to be 9.7 based on studies on the free nucleoside. Conformational studies on the nucleoside were also carried out.

For information on the use of this product, download a Product Information Sheet for BA 0311.

1. Cook, A. F.; Vuocolo, E.; Brakel, C. L. Nucleic Acids Res. 1988, 16, 4077-4095.

2. Lermer, L.; Yoann, R.; Ting, R.; Perrin, D. M. J. Am. Chem. Soc. 2002, 124, 9960-9961. See especially the Supporting Information.

3. 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.

Notes

Allows the introduction of a 5-aminoallyl-dU residue into oligonucleotides for the purpose of post-synthetic labeling by acylation. Further, triplex-forming oligonucleotides (TFOs) containing this residue form triplexes that are similar in stability to those bearing unmodified residues.



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