Backbone Modifications

Chemically modified nucleotides are widely used to increase the stability of oligonucleotides or oligonucleotide conjugates. Many modifications of oligonucleotide backbones have been used as antisense reagents or for synthesis of siRNAs to control gene expression. BOC RNA offers a wide range of DNA/RNA modification services, including backbone modifications.

Chemical Modification of Phosphate Backbone

Natural oligonucleotides are formed by phosphodiester bonds between them. The internucleotide phosphodiester bond (pKa=2) of DNA and RNA is negatively charged at physiological pH and is a sensitive site for nuclease binding, which can be cut by nucleases in serum and endonucleases in mammalian cells Enzymes and exonucleases cut efficiently. Chemical modification of the phosphate backbone is a modification of the phosphodiester between nucleotides. Chemical modification of the phosphate backbone is able to

  • Improve the stability of antisense nucleic acids in the cell.
  • Improve the permeability to the cell membrane and affinity to mRNA.


Oligonucleotides containing phosphorothioate (PS) modifications differ from natural nucleic acids in that a non-bridging phosphate oxygen atom is replaced by a sulfur atom. PS modification has the following advantages:

  • Can greatly improve resistance to nuclease degradation and can make oligonucleotides sufficiently stable in plasma, tissues and cells to avoid complete metabolism before reaching the target RNA.
  • It can be combined with some other modifications to improve the binding affinity of the PS-modified antisense nucleic acid.
  • PS-modified oligonucleotides are also able to improve the penetration of cell membranes.


N3′phosphoramidate (NP) modification adopts the North conformation, which is a good natural RNA substitute. NP-containing oligonucleotide strands lack the ability to activate RNaseH-mediated cleavage mechanisms, but have good binding affinity for target sequences and high nuclease resistance, NP-modified oligonucleotides can be used as efficient RNaseH-independent Antisense oligonucleotides. The binding affinity to target RNA can be further enhanced by combining 2′-F functional groups with NP-modified oligonucleotide strands.

Morpholino Phosphoramidates

Morpholino phosphoramidate oligomers replace the sugar ring-phosphate backbone with phosphoramidate, resulting in uncharged oligonucleotides. These Morpholino-modified oligonucleotide chains have similar or even better binding affinity for the target mRNA than the natural oligonucleotide chains and can be used as translation inhibitors to block the mRNA from exercising its translation function.

Peptide Nucleic Acid

Peptide nucleic acid (PNA), which has a neutrally charged backbone consisting of N-(2-aminoethyl)-glycine, exhibits significant nuclease and protease resistance and has a higher binding affinity than DNA or RNA, while PNA obeys the rules of base complementary pairing. PNA does not activate the RNaseH-mediated cleavage mechanism, but can achieve gene silencing through the translation arrest mechanism.


Phosphonoacetate (PACE) bond-modified oligonucleotides retain the electronegativity characteristics of unmodified DNA (pKa=3.8), and this modification enhances nuclease resistance and activates RNaseH activity by adopting an A-type double-stranded body when bound to the RNA target. PACE modification reduces the binding affinity for the RNA complementary strand, with a decrease in Tm value of about 1.3°C for each phosphonoacetate bond introduced. An additional feature of interest is that the PACE-modified oligonucleotides can be taken up directly by the cells.

Chemical modification of phosphate backboneFig. 1 Chemical modification of phosphate backbone

We Provide the Following Backbone Modifications

Backbone ModificationsShort CodePrice
Peptide Nucleic AcidPNAInquiry


  • Our extensive experience in oligonucleotide chemical synthesis, exclusive equipment, reagents, and expertise ensure the high quality of each oligonucleotide.
  • We specialize in providing a wide range of custom oligonucleotide modification services.
  • We can synthesize oligonucleotides at scales of 10, 20, and 50 nmol. If you are unsure of the amount or need a specific amount, we can advise you on the best synthesis scale.
  • We offer industry-wide competitive pricing, so please contact us.
* Only for research. Not suitable for any diagnostic or therapeutic use.
Online Inquiry
Verification code
Event information
Inquiry Basket