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Product Name |
Molecular Structure |
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BA 0287
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Fmoc-Amino-Modifier-C6-dT CEP
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Notes: 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.
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BA 0289
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Amino-Modifier-15-dT CEP
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Notes: 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.
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BA 0295
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Fmoc-Pyrrolidine CEP
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Notes: 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.
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BA 0298
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Amino-modifier-C6-G CEP
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Notes: Use standard RNA protocols with a 12 minute coupling. Download a Product Information sheet for BA 0298 here. 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 interesting, but please be aware that their purchase and use is at your own risk. |
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BA 0300
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Anthraquinone-Pyrrolidine CEP
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Notes: 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.
Please also note: This product is from our Experimental Grab Bag. The compounds in this unique collection 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. (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.
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BA 0301
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Formylindole-dT CEP
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Notes: 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,2 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.
2. This new compound is from our Experimental Grab Bag. The compounds in this unique collection have not been validated for any particular oligonucleotide application. We hope that you may find them of interest, but please be aware that their purchase and use is at your own risk.
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BA 0302
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Anthraquinone-C2-dT CEP
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Notes: 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'-installation are efficient.
Download a Product Information Sheet for BA 0302 here.
Please note: This product is from our Experimental Grab Bag. The compounds in this unique collection 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.
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BA 0303
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6-Aza-dU CEP
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Notes: 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.
Also available: The phosphoramidite 6-Azathymidine CEP and the nucleosides 6-aza-2'-deoxyuridine PYA 11057 and 6-azathymidine PYA 11058.
(1) Seela, F.; Chittepu, P. J. Org. Chem. 2007, 72, 4358-4366.
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BA 0306
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6-Azathymidine CEP
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Notes: 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.
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BA 0307
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3'-Fmoc-amino-modifier CPG (1000
Angstrom)
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Notes: 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.
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