Oligo Base Modification

Oligo Base Modification

BOC Sciences has the expertise and capability to provide oligonucleotide modification services to clients worldwide. BOC Sciences' state-of-the-art facilities, advanced technology and experienced staff can provide you with a full range of modifications and labeling to meet your biological, diagnostic and drug discovery needs.


Base modifications can alter the quality and affect the structure of oligonucleotides, sometimes changing UV absorbance, molecular weight and melting temperature (Tm), base mismatch detection and oligonucleotide repair. Diverse base modifications provide many improvements for efficient, large-scale genome engineering and the application of nucleic acid therapeutics, such as antisense oligonucleotides (ASO), and small interfering RNA (siRNA).


  • 2,6-Diaminopurine-2'-deoxyriboside (DAPdR)

DAPdR oligonucleotides can be used to improve the ability of oligonucleotides to hybridize to their targets because the strength of the 2-amino-A-thymine (T) base pair is comparable to that of the guanine: thymine (G: T) base pair, and these modified DNA analogs are commonly used to replace adenine (A) bases to increase the stability of primer duplexes. And for each additional DAPdR residue, the Tm of the duplex increases by 3oC compared to the unmodified case. DAPdR oligonucleotides also destabilize the A-G wobble mismatch, thereby increasing specificity.

  • 2-Amino Purine deoxyribose and 2-Amino Purine ribose

The absence of the O6 carbonyl group of guanine produces 2-aminopurine (2-AP), a mildly fluorescent molecule that is an analogue of adenine and guanine and therefore can pair with thymine and cytosine bases.

  • 4-Thio-Uridine

4-Thio-Uridine (4SU) is a thiol-modified ribonucleoside that has the advantage of being incorporated into the RNA strand with minimal structural perturbation and similar base-pairing properties, reducing the possibility of substitution of RNA function. RNA pentamers modified with 4SU were used to investigate the role of this modification on the interaction of codons and tails at the tRNA wobble position.

  • 5-bromo deoxycytosine (Br dC)

5-Br-dC is classified as a halogenated nucleotide, which contributes to determination of DNA structure by X-ray crystallography. When incorporated into DNA strands, the multi-wavelength anomalous dispersion (MAD) technique can be applied to obtain the phase information necessary to correctly calculate the electron density of the cell of the molecule under study.

  • EDTA 2'- deoxythymidine

EDTA-C2-dT is a deoxythymidine conjugated to the triacetic acid derivative of EDTA at the C-5 position of the thymidine base. EDTA-C2-dT modified oligonucleotides are commonly used as artificial nucleases to cleave single- and double-stranded DNA.

  • N3-Methyl deoxy Cytidine

N3-methyldeoxycytosine (N3-Me-dC) is a methylated nucleoside base, which is mainly used to study the DNA damage and repair mechanism associated with alkylation damage.

  • 7-deaza-2'-deoxyguanosine

deoxyguanosine (deaza G (7-deaza)) is a deoxyribonucleoside in which the 7-nitrogen (N7) of the base is replaced by C-H, which leaves the 7-deoxypurine monomer lacking a group essential for hydrogen bonding.

  • 8-Oxo-Guanosine

Oxo-Guanosine, which contains an oxidized guanosine, has been used in intracellular oxidative RNA damage and related RNA repair mechanisms.

Our Oligo Base Modification Services Specification

Backbone ModificationModification codeChemical formulaMolecular weightPrice
2,6-Diaminopurine-2'-deoxyriboside (DAPdR)Inquiry
2-Amino Purine deoxyribose2APdRC10H12N5O5P313.21Inquiry
2-Amino Purine ribose2-APrC10H12N5O6P329.21Inquiry
5-bromo deoxycytosine (Br dC)5-Br-dCC9H11BrN3O6P366.08Inquiry
EDTA 2'- deoxythymidineEDTA-C2-dTC24H33N6O15P676.53Inquiry
N3-Methyl deoxy Cytidinem3dCC10H15N3O4241.24Inquiry

The role of base modification

  • Altering the quality of oligonucleotides
  • Sometimes changes UV absorbance, molecular weight and unchaining temperature (TM)


  • High-quality products
  • competitive price
  • Data analysis, detailed reporting including results and discussion
  • Guaranteed total yield per oligonucleotide is a fixed final yield of OD units
  • All samples are carefully monitored for stability and characterized to ensure batch-to-batch consistency


  1. Rublack, N; et al. Synthesis of specifically modified oligonucleotides for application in structural and functional analysis of RNA. J Nucleic Acids. 2011. 2011: p. 805253.
  2. Leiros, I; et al. Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA. EMBO J. 2007. 26(8): p. 2206-17.
  3. Ganguly, M; et al. A study of 7-deaza-2′-deoxyguanosine–2′-deoxycytidine base pairing in DNA. Nucleic Acids Research. 2007. 35(18): p. 6181-6195.
  4. Aubert, Y; et al. Synthesis and properties of triple helix-forming oligodeoxyribonucleotides containing 7-chloro-7-deaza-2′-deoxyguanosine. Bioorganic & Medicinal Chemistry. 2001. 9(6): p. 1617-1624.
  5. Wurtmann, E.J.; et al. RNA under attack: cellular handling of RNA damage. Crit Rev Biochem Mol Biol. 2009. 44(1): p. 34-49.
* Only for research. Not suitable for any diagnostic or therapeutic use.
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