Oligo Modifications

Oligo Modifications

BOC RNA can customize a full range of high-quality oligonucleotide modification and obtain artificial modifications including backbones, bases, sugars, and internucleotide bonds oligonucleotides.

Using our synthesis platform can reduce experiment costs for our customers by improving coupling efficiency. We can meet the needs of various synthesis scales, purification options, and modifications and allow large-scale production in a short time.

Modification options

  • Backbone modification
  • Modified oligonucleotides not only can enhance affinity but also increase the resistance to endonuclease and exonuclease, thereby having high stability in vitro and in vivo.

ModificationsNuclease ResistanceRNase H Activation
Bridged Nucleic Acids (BNA)
2' Fluoro RNA
2' O-Methyl RNA (2'OMe)
Phosphorothioate DNA
Phosphorothioate RNA
Phosphonoacetate (PACE)
Methylphosphonate linkages
ZNA Spermine
  • Modified bases

    We have many useful modified base analogs to be incorporated during oligonucleotide synthesis. The use of modified bases can increase the melting temperature, thereby improving specificity and sensitivity, and is suitable for detecting small or highly similar DNA or RNA targets.

    Base modifications are divided into the following categories:

    • 2'-Deoxyribonucleoside pyrimidines and analogs
    • 2'-Deoxyribonucleoside purine and analogs
    • Ribonucleoside analogs
    • 2'-Deoxyribonucleoside purine and analogs
    • Ribonucleoside analogs
    • 2'O-Methyl ribonucleoside analogs
    • Sugar modified analogs
  • Inverted bases
  • Oligonucleotides containing reverse base RNA or DNA linkages can be used for antisense research or for synthesizing oligonucleotide fragments with the opposite meaning to normal synthesis for structural research. BOC RNA synthesizes base inversion oligonucleotides, which can be used to produce oligonucleotides with 5'-5' or 3'-3' linkages or to combine them in the same oligonucleotide.

    It is recommended to purify anti-base modified oligonucleotides. The quality of each synthesized oligonucleotide can be strictly controlled through mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis.

  • Oligo modified linker attachment chemistry

    According to the position where the modification is introduced, the linker and the chemical modification of the oligonucleotide can be divided into three categories

    • 5'modification
    • Internal modification
    • 3'modify
  • Spacer modification
  • BOC RNA provides a variety of spacer modified oligonucleotides. These spacers have different atomic numbers. They are usually used between the functional part of the oligonucleotide and the hybridization region as the steric hindrance.

Modification typeCode5'Internal3'Function
C3 SpacerSpC3Introduce linker arm, prevent enzymatic degradation, a DNA abasic site, an effective chain terminator
C6 SpacerSpC6Introduce linker arm
C12 SpacerSpC12Introduce linker arm
Spacer 9Sp9Introduce linker arm, hydrophilic spacer
Spacer 18 (hexaethyleneglycol)Sp18 Introduce linker arm, hydrophilic spacer
dSpacer (Abasic furan)dSpDNA abasic site, prevent enzymatic degradation
ribospacer rSpacerrSpRNA abasic site, prevent enzymatic degradation
Photocleavable PC SpacerPLCphotocleavable spacer
  • Fluorescent labeling
  • Fluorescence labeled oligonucleotides can be used as hybridization probes for various in vivo and in vitro research/diagnostic applications, as well as structural and functional studies of DNA, RNA, and protein-oligonucleotide complexes. Contact BOC RNA for a spacer fluorescently labeled oligonucleotide synthesis service.

6-FAM (NHS ester) 496/516Yellow-green
6-FAM (Fluorescein) 495/520Yellow-green
Fluorescein dT495/520Yellow-green
TAMRA  559/583Yellow-orange
JOE (NHS ester) 529/555Yellow
TAMRA (NHS ester)559/583Yellow-orange
MAX (NHS ester) 531/556Yellow
TET  522/539Yellow-green
Cy5.5 685/706Red
ROX (NHS ester) 588/608Orange
TYE 563 549/563Yellow-orange
HEX  538/555Yellow
TEX 615 596/613Red
TYE 665 645/665Red
TYE 705  686/686Red
SUN  538/554Yellow
  • Phosphorylated modification

    3'and 5'-phosphorylated oligonucleotides can be used for further chemical modification or as substrates in DNA repair research. 5'phosphorylated oligonucleotides can be directly connected to the vector without using T4 polynucleotide kinase in advance. 3'phosphorylation can inhibit the degradation of some 3'-exonucleases. In addition, chemical phosphorylation allows a large number of labeling and is more reproducible than enzymatic methods.

    BOC RNA provides phosphorylated oligonucleotide synthesis of various scales and purity to meet different needs.

    • 2' Phosphate oligonucleotide modification
    • 2' Thiophosphate oligonucleotide modification
    • 3' Phosphate oligonucleotide modification
    • 3' Thiophosphate oligonucleotide modification
    • 5' Phosphate oligonucleotide modification
    • 5' Thiophosphate oligonucleotide modification
    • Diphosphosphate oligonucleotide modification


  • Modified oligonucleotides help to understand the mechanism of many biochemical reactions and processes.
  • Modified oligonucleotides have been used as probes in various diagnostic and therapeutic applications.
  • Used in drug discovery and disease treatment (nucleic acid vaccines and nucleic acid drugs) research.

Services process

Oligo Modifications

Our ability

  • Flexible production scale: 20 nmol, 50 nmol, 100 nmol, 200 nmol, 1 µmol, 5 µmol, and 10 µmol. Bulk orders can be provided upon request.
  • Purity: Desalted, PAGE, HPLC, dual HPLC purification process is adopted, which is 3%~5% higher than the industry average.
  • Physical isolation of synthesis, ammonolysis, purification, and concentration to prevent cross-contamination.
  • Complete variety: BOC RNA provides comprehensive modified oligonucleotide synthesis services. You might be interested in our DNA/RNA modifications services.

Contact us now to get technical advice and more information. Our technical support team will respond to your questions or provide a quotation as soon as possible.

* Only for research. Not suitable for any diagnostic or therapeutic use.
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