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DNA Damage and Repair

Bio-Synthesis provides 3' chain terminator or end blocker oligo modifications to block ligation at 5' terminus or preventing polymerase extension from the 3' terminus. These bases can also be used internally to create a 5'-2' phosphate linkage in the oligo. All four bases are available with the deoxyribose sugar blocked at the 3' position, to give 3'-deoxy terminator G, T, C, and A. Cordecypin is an alternative name for the 3'-deoxy A terminator. These modifiers are preferred in place of dideoxy modifications. 2',3'- dideoxy chain terminator are designed to be used with reverse 5' to 3' synthesis and support.

contact us Bio-Synthesis for Oligo Chain Termination Modification Services.

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

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O6-Methyl-2'-deoxyguanosine [O6-Me-dG] Y N Y

O6-Methyl-deoxyguanosine (O6-Me-dG) is classified as an O-alkyl purine, and O6-Me-dG-modified oligonucleotides are primarily used in studies of the role of DNA alkylating agents in mutagenesis and carcinogenesis, and in studies into possible enzymatic mechanisms involved in repair of DNA alkylation damage.

8-Oxo-2'-deoxyadenosine [8-oxo-dA] N N Y

8-Oxo-deoxyadenosine (8-Oxo-dA) is primarily used in studies of oxidative DNA damage and associated repair mechanisms. In the cell, 8-Oxo-dA DNA lesions are formed by reaction with reactive oxygen species (ROS) generated either via normal oxidative metabolic processes, UV ionizing radiation, or 2-nitropropane (an industrial solvent and component of tobacco smoke). 8-Oxo-dA can potentially mispair with G, but this potential is fairly limited. As a single-base lesion, 8-Oxo-dA is removed by the base excision repair (BER) mechanism and the native guanine base restored (3). In the cell, 8-Oxo-dA does not appear to be strongly mutagenic.

8-Oxo-2'-deoxyguanosine [8-oxo-dG] N N Y

8-Oxo-deoxyguanosine (8-Oxo-dG) is classified as an oxidized nucleotide, and is primarily used in studies of oxidative DNA damage and associated repair mechanisms. 8-Oxo-dG can potentially mispair with A (leading to G-to-T transversions) (2). As a single-base lesion, 8-Oxo-dG is removed by the base excision repair (BER) mechanism and the native guanine base restored.

5-Hydroxymethyl-2'-deoxyuridine [5-hme-dU] N N Y

5,6-Dihydro pyrimidines are naturally occurring compounds that are structural components of alanine transfer RNA. Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

5-Hydroxy-2'-deoxyuridine   [5-Hydroxy dU ] N N Y

Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

O4-Methylthymidine [O4-Me-dT] N N Y

Primerily used in studies of DNA alkylation in mutagenesis, carcinogenesis, and enymatic mechanism in the repair cause by DNA alkylation damage.

5-Hydroxy-2'-deoxycytidine [5-Hydroxy dC ] N N Y

Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

Thymidine Glycol (5,6-dihydroxy-5,6-dihydrothymine) [Thymidine Glycol] N N Y

Thymine glycol (5,6-dihydroxy-5,6-dihydrothymine) is formed when thymine is subjected to oxidative stress, including ionizing radiation. Oxidation of the 5,6 double bond of Thymidine generates two chiral centers at C5 and C6. The cis-5R,6S form is generated as the predominant product along with the other diastereomer, the cis-5S,6R form. The presence of thymidine glycol in DNA has significant biological consequences and many organisms possess specific repair enzymes for the excision of this lesion.

8-Amino-dG [8-Amino-dG] N N Y

Form by mutagenic lesions by 2-nitropropane in DNA damage. 8-Amino-dA and 8-amino-dG are useful in triplex formation due to the presence of the additional amino groups.

8-Amino-dA [8-Amino-dA] N N Y

Form by mutagenic lesions by 2-nitropropane in DNA damage. 8-Amino-dA and 8-amino-dG are useful in triplex formation due to the presence of the additional amino groups.

8,5'-cyclo-dA [8,5-Cyclo-dA] N N Y

DNA damage cause by UV light on DNA dimerization.

8,5'-cyclo-dG [8,5-Cyclo-dG] N N Y

DNA damage cause by UV light on DNA dimerization.

5,6-Dihydro-dT [5-6 DH-dT] N N Y

5,6-Dihydro pyrimidines are naturally occurring compounds that are structural components of alanine transfer RNA. Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation

5,6-Dihydro-dU [5-6 DH-dU] N N Y

5,6-Dihydro pyrimidines are naturally occurring compounds that are structural components of alanine transfer RNA. Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

2'-DeoxyXanthosine [dX] N N Y

Naturally occuring nucleoside derived from oxidative deamination of 2'-dG. dX has also interested researchers in the field of DNA damage and repair since it is a product of nitric oxide-induced mutagenesis.

Pyrrolidine [Pyrrolidine] N N Y

This modificationform stable complex with DNA glycosylase AlkA for study of base excision repair (BER) study

Abasic II [Abasic II] N N Y

Cause by the hydrolysis of dA site in DNA

Cis-Syn Thymidine Dimer [Cis-Syn TT] N N Y

induced by UV light on DNA is dimerization of adjacent pyrimidine bases leading to cyclobutane dimers (CPDs). The dimers formed in the most significant quantity are the cis-syn cyclobutane dimer of two thymine bases.

dSpacer [Ab] Y Y Y
5-Formyl dC III [Formyl dC III] Y Y Y
5-Formly dC [Formly dC] Y Y Y
5-Hydroxymethyl dC II [Hydroxymethyl dC II] Y Y Y
5-Carboxy dC [5-COOH-dC] Y Y Y
dU [dU] Y Y Y
dX [dX] Y Y Y
5-Hydroxy dC [5-OH-dC] Y Y Y
5-Hydroxy dU [5-OH-dU] Y Y Y
Etheno deoxyadenosine dA [Etheno dA] Y Y Y
N3-Methyl-dC [N3-Me-dC] Y Y Y
N6-Methyl dA [N6-Me-dA] Y Y Y
O6-Methyl dG [O6-Me-dG] Y Y Y
rAbasic [rAb] Y Y Y

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