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Full Catalog (page 5)
Product Number Product Name Molecular Formula Cas. No. Description Notes Alt. Name Alt. Name 2
BA 0194 8-Amino-dG CEP C46H59N10O7P  166092-91-7         
BA 0197 Propynyl-pyrrolo-dC CEP C45H52N5O7P  None found 

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 0198 Thymidine glycol CEP C52H79N4O10PSi2  318497-58-4         
BA 0200 N2-Neopentyl-dG
CEP		 C45H58N7O7P  204515-49-1  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.

N2-Neopentyl-dG CEP should behave in oligonucleotide synthesis in a manner similar to the other (known) N2-alkyl-dG CEPs, but this has not yet been proven.

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) 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 0201 5-Methyl-2'-deoxyzebularine CEP C40H49N4O7P  125258-62-0 

5-Methyl-2'-deoxyzebularine or m5K, is an intrinsically fluorescent nucleoside that, upon incorporation into oligonucleotides,1,2 allows the characterization of the assembly of RecA-ssDNA complexes that initiate DNA repair responses.2 Further, deletion of the C4 amino group of dC allows dissection of the roles of various hydrogen bonds, and the incorporation of 2-pyrimidinone residues into DNA allows the formation of abasic sites at selected positions after mild acid hydrolysis.3 See also a ribo version, Zebularine CEP (BA 0254).

1. Gildea, B.; McLaughlin, L. W. Nucleic Acids Res. 1989, 17(6), 2261-2281.
2. Singleton, S. F. et al., Organic Lett. 2001, 3, 3919-3922.
3. Iocono, J. A.; Gildea, B.; McLaughlin, L. W.,Tetrahedron Lett. 1990, 31, 175-178.
 		 A fluorescent nucleoside useful for probing the characterisitcs of DNA repair complexes.     
BA 0202 N2-(Fluorescein-TEG)-2-amino-
dA CEP		 C88H109N10O19P  None found 

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 0205 N6-Methyl-2-amino-dA
CEP		 C50H68N9O6P  None found 

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.

 		   2,6-Diaminopurine 2’-deoxyriboside, N6-methyl CEP   
BA 0206 N2-Methyl-2-amino-dA
CEP		 C44H56N9O6P  None found 

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.

 		   2,6-Diaminopurine 2’-deoxyriboside, N2-methyl CEP   
BA 0208 5-Methoxymethyl-dU CEP C41H51N4O9P  942271-36-5 

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 0209 N1-Methyl-dG
CEP		 C44H55N8O7P  220252-95-9 

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 0210 Desthiobiotin-TEG CEP C52H78N5O11P  None found  Desthiobiotin allows capture by streptavidin and can be displaced simply by adding biotin.1-3

1. Hirsch, J.D.; Eslamizar, L.; Filanoski, B.J.; Malekzadeh, N.; Haughland, R.P.; Beechem, J. M.; Haughland, R.P. Anal. Biochem. 2002, 308, 343-357.

2. (a) Hofmann, K.; Titus, G.; Montibeller, J.A.; Finn, F.M. Biochemistry, 1982, 21, 978-984. (b) Romovacek, H.; Finn, F.M.; Hofmann, K. Biochemistry, 1983, 22, 904-909. © Finn, F.M.; Titua, G.; Hofmann, K. Biochemistry, 1984, 23, 2554-2558.

3. Regarding association constants and kinetics: (a) Busse, S.; Scheumann, V.; Menges, B.; Mittler, S. Biosensors and Bioelectronics, 2002, 17, 704-710. (b) Yoon, H.C.; Hong, M.-Y.; Kim, H.-S. Langmuir, 2001, 17, 1234-1239.
 		 Allows affinity capture via the biotin-streptavidin interaction with the ability to recover the material.     
BA 0211 Desthiobiotin-TEG CPG N/A  N/A  Desthiobiotin allows capture by streptavidin and can be displaced simply by adding biotin.1-3

1. Hirsch, J.D.; Eslamizar, L.; Filanoski, B.J.; Malekzadeh, N.; Haughland, R.P.; Beechem, J. M.; Haughland, R.P. Anal. Biochem. 2002, 308, 343-357.

2. (a) Hofmann, K.; Titus, G.; Montibeller, J.A.; Finn, F.M. Biochemistry, 1982, 21, 978-984. (b) Romovacek, H.; Finn, F.M.; Hofmann, K. Biochemistry, 1983, 22, 904-909. (c) Finn, F.M.; Titua, G.; Hofmann, K. Biochemistry, 1984, 23, 2554-2558.

3. Regarding association constants and kinetics: (a) Busse, S.; Scheumann, V.; Menges, B.; Mittler, S. Biosensors and Bioelectronics, 2002, 17, 704-710. (b) Yoon, H.C.; Hong, M.-Y.; Kim, H.-S. Langmuir, 2001, 17, 1234-1239.
 		 Allows affinity capture via the biotin-streptavidin interaction with the ability to recover the material.     
BA 0212 3-Deaza-3-methyl-dA CEP C56H59N6O8P  1031750-37-4 

3-Deaza-3-methyl-adenine has been shown to be a stable analog of  N3-methyladenine (3MeA) which is the major cytotoxic lesion formed in DNA by methylating agents. 3-Deaza-3-methyl-dA CEP (BA 0212) can be used to incorporate this important, stable analog into synthetic oligonucleotides.1

3MeA is unstable and is converted to an abasic site which has made rigorous proof of its role in cytotoxicity elusive.The use of 3-deaza-3-methyl-dA in oligonucleotides for replication assays has provided the most direct evidence to date showing that 3MeA is a significant block to two of the main replicases in eukaryotes.1 These studies also showed that the Y-family polymerases are capable of bypassing the modified base in vitro.

Download a product information sheet here.

The nucleoside 3-deaza-3-methyl-2'-deoxyadenosine (CA reg. no. 515815-12-0), which is fixed in the anti conformation, is also known.2 

1. Plosky, B. S.; Frank, E. G.; Berry, D. A.; Vennall, G. P.; McDonald, J. P.; Woodgate, R.  Nucleic Acids Res. 2008, 36, 2152-2162.

2. Irani, R. J.; SantaLucia, J., Jr. Nucleosides, Nucleotides, and Nucleic Acids, 2002, 21, 737-751.

 

3-Deaza-3-methyl-dA is a stable analog of  N3-methyladenine (3MeA).  

    
BA 0224 3-Deaza-dA CEP C48H53N6O7P  666257-76-7         
BA 0232 6-Thio-G CEP C53H71N8O8PSSi  None found         
BA 0236 2'-Deoxypseudoisocytidine CEP C42H53N6O7P  307314-31-4  The C-nucleoside 2'-deoxypseudoisocytidine is an isostere of dC that offers an additional hydrogen-bond donor at N3. Interest in the incorporation of 2'-deoxypseudoisocytidine and related compounds into oligonucleotides has grown due to their success in improving triplex formation between oligonucleotides and duplex DNA.1-3 The C to GC pyrimidine-purine-pyrimidine binding motif requires acidic conditions in order to protonate N3 of cytosine in the Hoogsteen strand (i.e., C+ to GC). Unfortunately, this interaction is disrupted under the higher pH of physiological conditions. Improvements have been observed using 5-methyl-2'-deoxycytidine in place of dC, although protonation of N3 is still required.4 Kan and co-workers1-3 have examined the use of 2'-deoxypseudoisocytidine and 2'-O-methylpseudoisocytidine as neutral replacements for protonated cytidine. Indeed, oligonucleotides containing these cytidine replacements form improved triplexes under neutral conditions.

We offer 2'-Deoxypseudoisocytidine CEP3,5 for incorporation of 2'-deoxypseudoisocytidine into oligonucleotides, allowing researchers to explore the alternate hydrogen-bonding motif afforded by this interesting dC surrogate. For those interested in nucleosides, we also offer pseudoisocytidine hydrochloride (PYA 11060) and 2'-deoxypseudoisocytidine (PYA 11005).

Download a Product Information sheet.

(1) Ono, A.; Ts'o, P. O. P.; Kan, L. J. Org. Chem. 1992, 57, 3225-3230.

(2) Ono, A.; Ts'o, P. O. P.; Kan, L. J. Am. Chem. Soc. 1991, 113, 4032-4033.

(3) Chin, T.-M.; Lin, S.-B.; Lee, S.-Y.; Chang, M.-L.; Cheng, A. Y.-Y.; Chang, F.-C.; Pasternack, L.; Huang, D.-H.; Kan, L.-S. Biochemistry 2000, 39, 12457-12464.

(4) Singleton, D. F.; Dervan, P. B. Biochemistry 1992, 31, 10995-11003.

(5) For an alternate phosphoramidite for 2'-deoxypseudoisocytidine incorporation, see: Mayer, A.; Leumann, C. J. Nucleosides, Nucleotides & Nucleic Acids 2003, 22, 1919-1925.

 		 A C-nucleoside that is isosteric with deoxycytidine and has additional hydrogen-bonding ability.  3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-(dimethylaminomethylidene)-2'-deoxypseudoisocytidine  Ψ-iso-dC CEP, pidC CEP 
BA 0237 5,6-Dihydro-5-aza-dC CEP C41H54N7O7P  None found         
BA 0238 dF CEP C42H48N5O8P  162585-09-3  Fluorescent cytidine analog. Download a brief overview here.

The ribo version fluoresces at 385 nm (Bergstrom, D. E.; Inoue, H.; Reddy, P. A. J. Org. Chem., 1982, 47, 2174-2178; Bergstrom, D., et. al. Synlett, 1992, 179-188).

When incorporated into oligonucleotides, dF pairs with dG, resulting in a higher melting temperature (Inoue, H.; Imura, A.; Ohtsuka, E. Nucleic Acids Res., 1985, 13, 7119-7128). In triple helices, dF pairs well with dA (Staubli, A. B.; Dervan, P. B. Nucleic Acids Res. 1994, 22, 2637-2642). We offer the phosphoramidite version, which has been used for oligonucleotide synthesis (Durland, R. H.; Rao, T. S.; Jayaraman, K.; Revankar, G. R. Bioconjugate Chem., 1995, 6, 278-282), where it is known as "P", and serves as a fluorescent replacement of T in targeting AT base pairs during triplex formation.

We also offer the corresponding nucleoside (PYA 11100).
 		 Fluorescent cytidine analog.  3-[3-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5-O-(4,4'-dimethoxytrityl)-2-deoxy-β-D-erythro-pentofuranosyl]pyrido[2,3-d]pyrimidine-2,7(8H)-dione   
BA 0239 8-Aza-7-deaza-dA CEP C43H53N8O6P  None found  Oligonucleotides containing 8-aza-7-deaza-dA residues exhibit higher Tm's due to stronger base stacking interactions.1

Use: Employ acetonitrile diluent at the concentration recommended by the synthesizer manufacturer. Use standard coupling protocols; extended coupling is not required. Cleavage from the solid support and nucleobase deprotection with concentrated ammonium hydroxide may be carried out using standard protocols.

(1) Seela, F.; Kaiser, K. Helv. Chim. Acta 1988, 71, 1813-1823.

 		 The 8-aza-7-deazaadenine nucleobase is isosteric with adenine but offers a different pi-electron distribution and thus an altered dipole moment.  8-Aza-7-deaza-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N6-[(dimethylamino)methylidene]-2'-deoxyadenosine  PPA CEP 
BA 0242 8-Aza-7-deaza-dG CEP C43H53N8O7P  500891-26-9  For studies on alternating d(G-C)3 and d(C-G)3 hexanucleotides containing 8-aza-7-deaza-2'-deoxyguanosine or 7-deaza-dG CEP (see BA 0008) in place of dG, see: Seela, F.; Driller, H. Nucleic Acids Res. 1989, 17(3), 901-910.

Download a Product Information sheet here. 

 An isosteric analog of dG.  8-Aza-7-deaza-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-(dimethylaminomethylidine)-2'-deoxyguanosine  PPG CEP 
BA 0244 Amino-modifier-C6-dG
CEP		 C51H66F3N10O8P  None found      3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N2-[(dimethylamino)methylidene]-N8-[6-(trifluoroacetylamino)hexyl]-2'-deoxyguanosine   
BA 0245 2'-O-TBS-Pyrrolo-C CEP C48H64N5O8PSi  None found  Pyrrolo-C (PC) is a fluorescent analog of cytidine.1 It is highly fluorescent, the 2'-deoxy version exhibiting an emission maximum at 473 nm when incorporated into a 19-mer oligodeoxyribonucleotide, where it base-pairs normally with dG. Pyrrolo-C has proven to be useful for monitoring RNA secondary structure formation, where its fluorescence is reversibly quenched upon base-pairing.2 PC has been used to follow the kinetics of formation and dissociation of an RNA/DNA complex and has been used to monitor the thermal denaturation of the central segment of an RNA duplex.2 Most recently, PC has been incorporated into native and minimal hammerhead ribozymes at cleavage site position C17, where it was found to be capable of efficient photocrosslinking to G12, resulting in catalytically active RNA that was useful in structural studies.3

We also offer the 2'-O-Methyl phosphoramidite of Pyrrolo-C (BA 0356) as well as the 2'-deoxyribo version, Pyrrolo-dC CEP (BA 0170). BA 0245 and BA 0170 are also available from Glen Research (Pyrrolo-C CEP as the 2'-O-TOM version), our development partner for these products. Glen Research also offers the triphosphates of Pyrrolo-C and -dC. We offer the two nucleosides (PYA 11090 and PYA 11092) as well as the simple fluorescent pyrrolocytosine heterocycle (i.e., Pyrrolo-C aglycone (HC 9060). Thompson and co-workers have studied the photophysical properties of these fluorescent pyrrolopyrimidines.4

2'-O-TBS-Pyrrolo-C CEP should behave in oligonucleotide synthesis in a manner similar to the other modified 2'-O-TBS nucleoside CEPs, but this has not yet been proven. 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. Berry, D.A.; Jung, K.-Y.; Wise, D.S.; Sercel, A.D.; Pearson, W.H.; Mackie, H.; Randolph, J.B.; Somers, R.J. Tetrahedron Lett. 2004, 45 (11), 2457-2461).

2. Tinsley, R.A.; Walter, N.G. RNA, 2006, 12, 522-529.

3. Lambert, D.; Heckman, J. E.; Burke, J. M. Biochemistry, 2006, 45, 7140-7147.

4. Thompson, K. C.; Miyake, N., J. Phys. Chem. B, 2005, 109, 6012-6019.
 		 Pyrrolo-C (PC) is a fluorescent analog of cytidine.  PC   
BA 0246 5-Fluoro-dU CEP C39H46FN4O8P  142246-63-7         
BA 0247 Amino-modifier-C6-U CEP C56H76F3N6O11PSi  None found  Use standard RNA protocols for coupling. Download a Product Information sheet 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.

 		   2'-O-(tert-Butyldimethylsilyl)-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5-[E-2-[N-[6-(trifluoroacetamido)hexyl]carboxamido]vinyl]-5'-O-(4,4'-dimethoxytrityl)uridine   
BA 0248 rSpacer CEP C41H59N2O7PSi  159299-31-7  For additional information, download a Product Information sheet here.       
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