Description

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.

Description

Desthiobiotin allows capture by streptavidin and can be displaced simply by adding biotin.^1-3

Notes

Description

Desthiobiotin allows capture by streptavidin and can be displaced simply by adding biotin.^1-3

Notes

Description

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.

Notes

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

Description

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-workers^1-3 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.

Notes

Alternate Name(s):

3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N²-(dimethylaminomethylidene)-2'-deoxypseudoisocytidine

Ψ-iso-dC CEP, pidC CEP

Description

Fluorescent cytidine analog. Download a brief overview here.

Notes

Alternate Name(s):

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

Description

Oligonucleotides containing 8-aza-7-deaza-dA residues exhibit higher T_m's due to stronger base stacking interactions.¹

Notes

Alternate Name(s):

8-Aza-7-deaza-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N⁶-[(dimethylamino)methylidene]-2'-deoxyadenosine

PPA CEP

Description

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.

Notes

Alternate Name(s):

8-Aza-7-deaza-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N²-(dimethylaminomethylidine)-2'-deoxyguanosine

PPG CEP

Description

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

Notes

Alternate Name(s):

PC

Description

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.

Alternate Name(s):

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

Description

For additional information, download a Product Information sheet here.

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):

3'-O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N²-methyl-2'-deoxyguanosine

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

Description

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.

Notes

Alternate Name(s):

6-FAM II

Description

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).

Notes

Alternate Name(s):

^4HC CEP

2'-O-t-Butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-2(1H)-pyrimidinone-1-β-D-riboside

Description

Description

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.

Alternate Name(s):

8-Allyloxy-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-N²-(dimethylaminomethylidine)-2'-deoxyguanosine

Description

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.

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

Notes

Alternate Name(s):

O-[(Diisopropylamino)(2-cyanoethoxy)phosphino]-12-(4,4'-dimethoxytrityl)aminododecan-1-ol

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 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.

Notes

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

Alternate Name(s):

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

Description

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.

Notes

Alternate Name(s):

1-[2'-O-t-Butyldimethylsilyl-3'-O-[(diisopropylamino)(2-cyanoethoxy)phosphino]-5'-O-(4,4'-dimethoxytrityl)-β-D-ribofuranosyl]-2(1H)-pyridinone

Description

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 residues^2b,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.

Notes

Alternate Name(s):

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

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.

Notes

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

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.

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) 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

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