Description

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.

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.

Notes

Alternate Name(s):

Pseudo-dG CEP

Description

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

Notes

Alternate Name(s):

3'-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2,6-di-O-[2-(4-nitrophenyl)ethyl]-2'-deoxyxanthosine

dX CEP

Description

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.

Pseudoiso-dG CEP (BA 0314) may be used to incorporate Pseudoiso-dG nucleotides into DNA. It is based on the nucleoside 2'-Deoxypseudoisoguanosine (Pseudoiso-dG, originally synthesized by Hosmane and co-workers¹), which is also available (PRA 10104).

Pseudoiso-dG CEP and Pseudoiso-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'-Deoxypseudoguanosine (Pseudo-dG, PRA 10103), and the phosphoramidite Pseudo-dG CEP (BA 0312) .

Learn more about these novel compounds and their use by downloading a Product Information sheet for our family of guanosine isomers .

Notes

Alternate Name(s):

Pseudoiso-dG CEP

Description

Notes

Alternate Name(s):

3-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-1-O-(4,4'-dimethoxytrityl)-1,3-di-(2-nitrophenyl)-1,3-propanediol

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)^1-4 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. Alkynyl-modifier-C6-dT CEP (BA 0316) is an analogous reagent with a slightly longer alkyne appendage that we have introduced as an alternative for oligo click ligations.

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

Notes

Alternate Name(s):

3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-
5-[N-(hex-5-ynyl)-3-(E)-acrylamido]-2'-deoxyuridine

Description

Many strategies have surfaced for the caging of oligonucleotides using photochemically labile groups. Caging the nucleobase is particularly attractive.^1,2 One of the most promising strategies for doing so involves the use of the 6-nitropiperonyloxymethyl (NPOM) group, installed at N1 of thymidine, as developed by Deiters and co-workers at North Carolina State University.^3-5 Thus, NPOM-Caged-dT CEP (BA 0317) was incorporated it into oligonucleotides using standard automated DNA synthesis protocols, resins, and reagents.^3,4 The bulky NPOM group was found to effectively block hydrogen-bond formation in duplexes, blocking DNAzyme activity, DNA/RNA hybridization, and allowing the control of PCR amplification. The caged thymidine is stable to a wide range of chemical and physiological conditions, but the NPOM caging group is removed within minutes by irradiation with 365 nm UV light, restoring normal biological function in all cases. This can be achieved using a standard fluorescent microscope, UV LED fiberoptic instruments, or even with a simple hand-held 25 watt UVA lamp. This wavelength is long enough to avoid damage to the oligonucleotides or cells.

Notes

Alternate Name(s):

3'-O-[(Diisopropylamino)-(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N³-[[1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]methyl]thymidine

Description

Cross-coupler-C6-dT CEP (BA 0321) allows the incorporation of a nucleotide containing an aryl bromide for post-synthetic modification via transition metal-mediated cross-coupling, e.g., using a Sonogashira coupling. A longer tether is employed in order to remove the sterically-demanding palladium chemistry further from the oligonucleotide. For more information, download a Product Information sheet.

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.

Notes

Description

Cross-coupler CEP (BA 0322) allows the incorporation of a nucleotide containing an aryl bromide for post-synthetic modification via transition metal-mediated cross-coupling, e.g., using a Sonogashira coupling. A longer tether is employed in order to remove the sterically-demanding palladium chemistry further from the oligonucleotide. For more information, download Product Information.

Cross-Coupler CEP (BA 0322) 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.

Notes

Description

G-Rich regions in nucleic acids often display disrupted Watson-Crick base-pairing due to the ability of dG and G residues to enter into non-Watson-Crick inter- and intramolecular hydrogen bonding. A solution to this problem is to replace the N⁷ nitrogen atom on the guanine nucleobase with a CH group, obviating the possibility of hydrogen bonding at that position. ¹We have long offered 7-Deaza-dG CEP (BA 0008), and now also offer 7-Deaza-G CEP (BA 0323) for oligoribonucleotide synthesis.

For more information, download a Product Information sheet.

(1) Seela, F.; Driller, H. Nucleic Acids Res. 1989, 17(3), 901-910.

Notes

Description

N-protecting groups for 5’-amino-modifiers be problematic in automated synthesis. DMT protection is frequently too labile for the amino group. MMT is usually preferred for its greater stability as an N-protecting group, however, it has two practical disadvantages: (1) It requires a custom deprotection protocol since NH-MMT is slightly more robust than O-DMT. (2) Automated synthesizers are designed to quantify DMT cleavage, not MMT cleavage. While the aforementioned Fmoc protected 5’-amino-modifiers offer one potential solution to these disadvantages, sometimes it is preferable to have acid-labile N-protection. BA 0324 has a novel N-protecting group that is based upon colorimetric-oxycarbonyl (Cmoc). In essence, the Cmoc group is an O-DMT that is tethered to an N-bis(4-chlorophenyl)-methoxycarbonyl protecting group. Both protecting groups are acid labile, but only the DMT cation generates a colorimetric signal because the tether quenches the bis(4-chlorophenyl)-methyl-carbocation in an intra-molecular fashion, affording a neutral tetrahydrofuran derivative. The acid lability of the Cmoc group allows the choice between on-column deprotection, and off column deprotection. Being more lipophilic than a traditional DMT group, the Cmoc protecting group does a superb job in facilitating SPE purification of full length oligos. If you like the DMT-on purification strategy, you will similarly like the Cmoc-on purification strategy.

Notes

Description

8,5’-Cyclodeoxyadenosine (cyclo-dA) is a naturally occurring free-radical-induced DNA lesion. This bulky lesion has been shown to be present in human cells.¹ Cyclo-dA is a strong block to gene expression in both CHO and human cells but can be repaired via nucleoside excision repair mechanisms, but not by base excision repair mechanisms.² Our (5'S)-8,5’-Cyclodeoxyadenosine CEP can be used for efficient incorporation of cyclo-dA into oligonucleotides.

(2) Brooks, P.J.; Wise, D.S.; Berry, D.A.; Kosmoski, J.V.; Smerdon, M.J.; Somers, R.L.; Mackie, H.; Spoonde, A.Y.; Ackerman, E.J.; Coleman, K.; Tarone, R.E.; Robbins, J.H. J. Biol. Chem. 2000, 275 , 22355-22362.

Notes

Description

Description

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. Fluorescein II CEP ("6-FAM II", BA 0253), which features the same tether length as 6-FAM, but includes a DMT group.¹ We now offer Fluorescein III CEP ("6-FAM III",BA 0334) which also includes the DMT group, but with a 1,3-diol framework. This extended framework serves two functions. First, the one carbon extension disfavors cyclic phosphate formation when the DMT group is removed, thereby minimizing label loss. Second, the 1,3-diol framework maintains the natural 3-carbon atom internucleotide phosphate distance, which diminishes duplex destabilization.² The DMT may also be used to facilitate cartridge purification with on-column detritylation, e.g. with Fluoro-Pak columns.

2. Nelson, P.S.; Kent, M.; Muthini, S. Nucleic Acids Res. 1992, 20 , 6253-6259.

Notes

Alternate Name(s):

6-FAM III

Description

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. Our new Fmoc-amino Modifier III (BA 0335) contains a 1,3,5-triol framework which serves two functions. First, extended framework disfavors cyclic phosphate formation when the DMT group is removed, thereby minimizing loss of the amine modification. Second, the 1,3,5-triol framework maintains the natural 3-carbon atom internucleotide phosphate distance. ¹

We also offer 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 (500 Å CPG) and BA 0307 (1000 Å CPG). It features a 7-atom spacer between the amino group and the O-DMT group.

1. Nelson, P. S.; Kent, M.; Muthini, S. Nucl. Acids Res. 1992, 20, 6253-6259.

Notes

Description

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.

Notes

Alternate Name(s):

N²-Benzyl-deoxyguanosine CEP

Description

The Sasaki labs have identified a variation of Matteucci’s cytosine analog “G-Clamp”¹ that is specific for 8-oxoG. This fluorescent phenoxazine analog 8-oxoG Clamp CEP (BA 0339) appears to be highly specific for pairing with 8-oxoG.² When incorporated into an oligonucleotide, the duplex stabilization was lowered only slightly, and 8-oxoG was selectively detected by fluorescence quenching the 8-oxoG Clamp.³

For more information, download a Product Information Sheet for BA 0339 here..

1. Lin, K.-Y.; Jones, R.J.; Matteucci, M. J. Am. Chem. Soc., 1995, 117, 3873-3874.

2. Nakagawa, O.; Ono, S.; Li, Z.; Tsujimoto, A.; Sasaki, S. Angew. Chem. Int. Ed., 2007, 46, 4500-4503.

3. Nasr, T.; Li, Z.; Nakagawa, O.; Taniguchi, Y.; Ono, S.; Sasaki, S. Bioorg. & Med. Chem. Lett. 2009, 19, 727-730.

Notes

Alternate Name(s):

8-Oxo-dG Clamp CEP

Description

Electrochemical detection is a less expensive alternative to common optical methods in DNA biosensors and chips. Hocek and coworkers¹ have shown that when aminophenyl (BA 0342) and nitrophenyl (BA 0355) substituted 2’-deoxyribonucleosides are incorporated into oligonucleotides, they exhibit excellent electrochemical label properties. Both types of markers in the same oligonucleotide can be easily detected and differentiated since the aminophenyl tag is irreversibly oxidized, and the nitophenyl tag is irreversibly reduced.

Notes

Description

The dNaM (BA 0343) and d5SICS (BA 0344) matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.^1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction. For more information, download a Product Information Sheet for BA 0343 here.

1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7.

2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52.

3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400.

4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63.

5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9.

6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82.

7. Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43.

Notes

Alternate Name(s):

3-(3-O-[(Diisopropylamino)(2-cyano-ethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-2-methoxy napthalene

Description

The dNaM (BA 0343) and d5SICS (BA 0344)matched pair appears to be a very interesting novel base pair, achieving pair recognition through hydrophobic interactions that rivals the A-T and G-C pairing in the natural genetic alphabet.^1-7 In addition, they have been shown to be well-replicated by DNA polymerases under steady-state conditions, regardless of sequence. The fidelity and efficiency of dNaM and d5SICS replication approach those of natural synthesis. Both dNaM and d5SICS are also efficiently transcribed by T7 RNA polymerase in either direction. For more information, download a Product Information Sheet for BA 0344 here.

1. Seo, Y.J.; Matsuda, S.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 5046-7.

2. Seo, Y.J.; Hwang, G.T.; Ordoukhanian, P.; Romesberg, F.E. J. Am. Chem. Soc., 2009, 131, 3246-52.

3. Seo, Y.J.; Romesberg, F.E. ChemBioChem, 2009, 10, 2394-2400.

4. Hwang, G.T.; Hari, Y.; Romesberg, F.E. Nucleic Acids Res., 2009, 37, 4757-63.

5. Hari, Y.; Hwang, G.T.; Leconte, A.M.; Joubert, N.; Hocek, M.; Romesberg, F.E. ChemBioChem, 2008, 9, 2796-9.

6. Hwang, G.T.; Romesberg, F.E. J. Am. Chem. Soc., 2008, 130, 14872-82.

7. Leconte, A.M.; Hwang, G.T.; Matsuda, S.; Capek, P.; Hari, Y.; Romesberg, F.E J. Am. Chem. Soc., 2008, 130, 2336-43.

Notes

Alternate Name(s):

3-(3-O-[(Diisopropylamino)(2-cyano-ethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyribofuranosyl)-6-methyl-1(2H)-isoquinolinethione

Description

Template-directed DNA ligation has multiple potential biotechnological applications.^1-4 The research of Fujimoto, Saito and coworkers have illustrated the utility of 5-vinyldeoxyuridine^5a and a carbazole-tethered 5-carboxyvinyldeoxyuridine^5b for photo induced non-enzymatic chemical DNA ligation. This carbazole-tethered analog (BA 0345) gives a photo ligation system where ligation and splitting (at 366 nm) can be repeated without damage to the normal DNA. Data suggests that the carbazole group intercalates in the duplex formed when photo ligation takes place in the presence of template DNA. This intercalation prevents photo induced splitting when in the duplex form, allowing control of the ligation/splitting based on the presence or absence of the template DNA strand. Our Carbazole dT CEP (BA 0345) provides an efficient way to form carbazole-tethered vinyl dU containing oligonucleotides.

For more information, download a Product Information Sheet for BA 0345 here.

Note: This product is from our Experimental Grab Bag. The compounds in this unique collection meet all of Berry & Associates' purity standards, but have not been proven in oligonucleotide synthesis. We hope that you may find them interesting and useful for your research.

References

1. (a) Silverman, A.P.; Kool. E.T. Chem. Rev., 2006, 106, 3775-3789. (b) Gartner, Z.J.; Kanan, M.W.; Liu, D.R. J. Am. Chem. Soc. 2002, 124, 10304-10306.

2. (a) Gothelf, K.V.; Brown, R.S. Chem. Eur. J. 2005, 11, 1062-1069. (b) Shih, W.M.; Quispe, Erben, C.M.; Berry, R.M.; Schmidt, C.F.; Turberfield, A.J. Science 2005, 310, 1661-1665.

3. (a) Su, X.; Smith, L.M. Nucleic Acids Res. 2004, 32, 3115-3123. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647. (b) Weizmann, Y.; Elnathan, R.; Lioubashevski, O.; Willner, I. J. Am. Chem. Soc. 2005, 127, 12666-12672.

4. (a) Shin, J.-S.; Pierce, N.A.; Nano Lett., 2004, 4, 905-909. (b) Le, J.D.; Pinto, Y.; Seeman, N.C.; Musier-Forsyth, K.; Taton, T.A.; Kiehl, R.A Nano Lett., 2004, 4, 2343-2347.

5. (a) Fujimoto, K.; Yoshino, H.; Ami, T. Yoshimura, Y.; Saito, I. Org. Lett., 2008, 10(3), 397-400. (b) Fujimoto, K.; Matsuda, S.; Takahashi, N.; Saito, I. J. Am. Chem. Soc. 2000, 122, 5646-5647.

Notes

Alternate Name(s):

5'-O-(4,4'-Dimethoxytrityl)-3'-O-[2-cyanoethoxy-(N,N-diisopropylamino)-phosphino]-5-(,em>E)-(2-(6-(2-carbazol-9-yl-acetylamiono)-hexylamino)-carbonylvinyl)-2'-deoxyuridine

Description

BA 0346 is a phosphoramidite of a small, fluorescent nucleoside that is an isosteric mimic of thymidine.^1,2 This probe has been shown to pair with adenine to form a stable duplex. DNA probes constructed to contain BA 0346 at a selected sequence position show a significant emission enhancement when hybridization results in an opposing abasic residue as compared to an opposing adenine residue.¹ This property makes BA 0346 useful for the preparation of probes that are designed to detect sequence-specific depurination and depyrimidination.

For more information, download a Product Information Sheet for BA 0346 here.

1) Greco, N.J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785.

2) Greco, N.J.; Tor, Y. Nature Protocols, 2007, 2, 305-316.

Notes

Description

Tor and co-workers have reported on the preparation and photophysical characteristics of a number of small, fluorescent isosteric nucleosides that are capable of normal Watson-Crick base paring in unaltered duplexes.^1-6 These probes are useful tools for studying nucleic acid sequence, structure, dynamics and recognition. BA 0347 is the phosphoramidite of one such nucleoside.^1,2 This probe is a minimally disruptive fluorescent dC analog that can be used in vitro for analysis of oxidative damage caused by reactive oxygen species.⁶ When incorporated into an oligonucleotide and hybridized, BA 0347 can photophysically distinguish between G, 8-oxoG, or T on the complementary strand. When paired with 8-oxoG, which is the major mutagenic product of oxidative damage, significant emission quenching is observed. When paired with T, the transversion mutation resulting from failure to repair the oxidation, enhanced emission is observed from BA 0347.

For more information, download a Product Information Sheet for BA 0347 here.

1) Greco, N.J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785.

2) Greco, N.J.; Tor, Y. Nature Protocols, 2007, 2, 305-316.

3) Greco, N.J.; Tor, Y. Tetrahedron, 2007, 63, 3515-3527.

4) Sinkeldam, R.W.; Greco, N.J.; Tor, Y. ChemBioChem. 2008, 9, 706-709.

5) Srivastan, S.G.; Tor, Y. Tetrahedron, 2007, 63, 3601-3607.

6) Greco, N.J.; Sinkeldam, R.W.; Tor, Y. Org. Lett. 2009, 11, 1115-1118.

Notes

Alternate Name(s):

N⁴-Benzoyl-5-(furan-2-yl)-dC CEP

4-Benzoyl-5-(2-furyl)-dC CEP