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Epigenetic Research

Modified base oligonucleotide synthesis epigenetic cancer research

Scientific interest in the study of epigenetic pathways that regulate gene expression without changing the genomic DNA has grown into one of the most exciting and dynamic fields in biology and cancer research. Post translational modifications such as DNA methylation, histone modification, as well as small regulatory RNAs are the hallmark of these epigenetic events. Of those, DNA methylation is the best recognized modification found in CpG sequence motifs. 5-methylcytosine (5mC) is a well-known epigenetic marker which regulates transcription of the genome. Since 2009 several modified TET-enzyme generated nucleobases such as 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) have been detected in the mammalian genome and were recently found to be key players in epigenetic pathways.

Bio-Synthesis offers several modified RNA and DNA oligos for epigenetic cancer research. We are one of the few manufacturers which offer the newly discovered and difficult to synthesize epigenetically modified bases such as N4-Me-dC, N4-Me-rC, N1-Me-dA, N2-Me-dG. In addition, we also offer many nucleoside triphosphates which can be incorporated into long RNAs either enzymatically or chemically.

Please contact us more information and for assistance in finding your desired modification.

Our Advantages

  • Wide selection of modified RNA, DNA bases beyond 5-Methyl C
  • Flexibility in oligo length and synthesis scale
  • Oligonucleotides are delivered as deprotected, desalted and/or purified
  • Quality checked by MALDI-TOF/LC-MS, analytical HPLC, PAGE
  • Specialize in producing newly-discovered and difficult-to-make modified bases

Modified Base for Epigenetic Research

Name 5' Prime Internal 3' Prime
N6-Methyl-deoxyadenosine Y Y Y

Important role in post-replicative DNA mis-match repair, chromosome compaction and regulation of gene expression. Essential for the viability or virulence of pathological bacterial strains.

N1-Methyl-deoxyadenosine Y Y Y

Important role in post-replicative DNA mis-match repair, chromosome compaction and regulation of gene expression. Essential for the viability or virulence of pathological bacterial strains.

N2-Methyl dG Y Y Y

N2-methyl dG modified oligos are primarily used in study of DNA damage and repair mechanisms related to alkylation damage and exposure to eposide carcinogens.

N3-Methyl deoxycytosine Y Y Y

N3-methyl dC modified oligos are primarily used in study of DNA damage and repair mechanisms related to alkylation damage.

N4-Methyl dC   Y Y Y

A methylation in bacterial DNA. Important role in the regulation of virulence and the control of many bacterial DNA functions.

5-methyl deoxycytosine Y Y Y

Predominantly in CpG islands of promoters. Modified oligos can be used in study of epigenetic effect of DNA methylation in tumorigenesis and effects of cocaine on fetal heart development.

8-Oxo-dA Y Y Y

A mutagenic lessions caused by 2-nitropropane. It is significant in mutagenesis and ultimately carcinogenesis. Modified oligos are use for DNA damage and repair resarch.

8-Oxo-dG, Y Y Y

A mutagenic lessions caused by 2-nitropropane. It is significant in mutagenesis and ultimately carcinogenesis. Modified oligos are use for DNA damage and repair resarch.

8-OMe-dG, Y Y Y

Cause by oxidative damage to G residues in biological systems. The predominant product of G damage. 8-OMe-dG modified oligo often use for DNA damage and repair studies.

5-OH-dC, Y Y Y

This is a free-radically induced DNA damage, this oxidataive damaged lessions are observed in liver, kidney and brain DNA. 5-OH-dC modfied oligo often use in DNA damage and repair studies.

8-OMe-dG, Y Y Y

Cause by oxidative damage to G residues in biological systems. The predominant product of G damage. 8-OMe-dG modified oligo often use for DNA damage and repair studies.

5-OH-dU, Y Y Y

This is a free-radically induced DNA damage, this oxidataive damaged lessions are observed in liver, kidney and brain DNA. 5-OH-dU modfied oligo often use in DNA damage and repair studies.

5-Hydroxymethyl deoxyuridine Y Y Y

Occurs by either oxidative attack via peroxide radicals, or ionizing radiation. 5-hm-dU modified oligos are used in the study of DNA base excision repair pathways.

5-Hydroxymethyl cytosine Y Y Y

TET-enzyme generated bases, also known as "fifth base", a intermediate in oxidative demethylation pathways.

5-Hydroxymethyl deoxyuridine Y Y Y

Occurs by either oxidative attack via peroxide radicals, or ionizing radiation. 5-hm-dU modified oligos are used in the study of DNA base excision repair pathways.

5-Carboxy-dC (cadC) Y Y Y

TET-enzyme generated bases, important role as an intermediate in a active oexidative demethylation pathway for conversion of 5-Me-dC to dC.

5-Formyl-dC (fdC) Y Y Y

A demethylation of 5-Me-dC, it plays a key role in cellular reprogramming, embryogenesis, establishment of maternal and paternal methylation patterns in the genome.

5.6-Dihydro-dU Y Y Y

A major base damage by oxidation and alkylation from free radicals, ultraviolet and ionizing radiation.Modified oligo are used in studies of irradiative DNA damage and repair mechanisms.

5.6-Dihydro-dT Y Y Y

Lessions are formed by gamma irradiation of deoxythymine under anoxic conditions. Modified oligo are used for studies of irradiative DNA damage and repair mechanisms.

Thymidine glycol Y Y Y

formed when thymine is subjected to oxidative stress, including ionizing radiation. Thymidine glycol modified oligo are often used in studies of DNA damage and repair.

Abasic II Site Y Y Y

Cause by the hydrolysis of DNA leaving just sugar-phosphate backbone, a spontaneous purination, depyrimidination event by UV ionizing radiation. Abasic modified oligo use for DNA damage and repair study

Cys-syn Thymidine dimer Y Y Y

This is a DNA damage induced by UV light on DNA that are dimerized of adjacent pyrimidine bases which leading to cyclobutane dimers. Cys-syn thymidine dimer modified oligo are use for DNA damage and repair study.

5’,8-Cyclo-dA Y Y Y

Oxidative damage in DNA by UV un light. Cyclo purine cause significant distortionof the regular DNA helix. This modification is used for DNA damage and repair study.

8-Oxo-rG Y Y Y

Oxidative damaged in RNA. This RNA damage is related to series of neurodegenerative diseases. 8-Oxo-rG modified oligo are use for the studies of DNA damage and repair resarch.

N1-Methyl riboadenosine Y Y Y

Methylated RNA used for the study of tRNA folding. A natural occuring post-transcriptional modification.

N6-methyl-riboadenosine Y Y Y

Abundant in mRNA of most eukaryotes; also observedin rRNA, rRNA snRNA and non-coding RNA. N6-methyl-rA levels in mRNA have significant effects on subsequent gene expression.

N6-dimethyl-riboadenosine Y Y Y

A minor RNA modification, primary found in rRNA, in Mycobacterium tRNA. It plays a structural role in rRNA

N4-Methyl rC Y Y Y

A methylation in bacterial DNA. Important role in the regulation of virulence and the control of many bacterial DNA functions i.e. replication, repair, expression and transposition of DNA.

5-methyl rC Y Y Y

Plays an important role in post-transcriptional control of cellular RNA that are critical for the cell to support various states of growth and differentiation.

N3-Methyl rU Y Y Y

N3-methyl rC modified oligos are primarily used in study of DNA damage and repair mechanisms related to alkylation damage.

N3-Methyl rT Y Y Y

N3-methyl rT modified oligos are primarily used in study of DNA damage and repair mechanisms related to alkylation damage.

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