There are numerous chemical modifications commonly done to synthetic oligonucleotides for a variety of reasons. Some of these reasons can be to increase stability of the phosphate backbone, adjust duplex stability, change the conformation of the oligo, or to increase its ability to penetrate a lipid bilayer. In recent years, it has become a common practice to incorporate a modified sugar moiety into an oligonucleotide. Changing the sugar moiety generally increases nuclease resistance and binding affinity to a complementary target. This article focuses on three popular DNA analogs:
LNA (Locked Nucleic Acids)
BNA (Bridged Nucleic Acids)
2’-F-RNA.
Locked Nucleic Acids (LNA) gained its notoriety in being used in probes and siRNA. Currently Bio-Synthesis does not offer LNA monomers and they are now only available from Exiqon. A common question is whether there are other modified monomers that could offer the same properties as LNA or be better. One modified monomer that has gained notoriety is 2’-F-RNA. When 2’-F-RNA is incorporated into oligonucleotides, it increases the Tm of the duplex by about 1 to 2 oC per substitution. Just like LNA and most other sugar modified bases, 2’-F-RNA substituted oligos are more resistant to degradation both in vitro and in vivo. LNA received its name due to its ability to lock a nucleotide into the 3’-endo (North) conformation which is often found in the A-Form duplexes. However, while 2’-F RNA nucleotides also prefer a C3’- endo/north conformation unlike LNA 2’-F RNA nucleotides have the ability to undergo pseudorotation of the ribose.
A third and new modification that can be done to oligonucleotides is the incorporation of Bridged Nucleic Acids (BNA) monomers. Currently Bio-Synthesis exclusively offers custom oligonucleotides modified with BNA. BNA is closely related to LNA and developed by Takeshi Imanishi in Japan. 2’,4’-BNA modified oligonucleotides perform as well as and even better than LNA modified oligonucleotides. BNA has a very high target affinity, similar to or even higher than that of LNA and can increase Tm per modification by 5 to 6oC when binding to complementary RNA. Additionally BNA shows enhanced triplex formation, improved resistance to nuclease depredation, and more use in antisense and probe applications than LNA or 2’-F RNA.
LNA (Locked Nucleic Acids)
BNA (Bridged Nucleic Acids)
2’-F-RNA.
Locked Nucleic Acids (LNA) gained its notoriety in being used in probes and siRNA. Currently Bio-Synthesis does not offer LNA monomers and they are now only available from Exiqon. A common question is whether there are other modified monomers that could offer the same properties as LNA or be better. One modified monomer that has gained notoriety is 2’-F-RNA. When 2’-F-RNA is incorporated into oligonucleotides, it increases the Tm of the duplex by about 1 to 2 oC per substitution. Just like LNA and most other sugar modified bases, 2’-F-RNA substituted oligos are more resistant to degradation both in vitro and in vivo. LNA received its name due to its ability to lock a nucleotide into the 3’-endo (North) conformation which is often found in the A-Form duplexes. However, while 2’-F RNA nucleotides also prefer a C3’- endo/north conformation unlike LNA 2’-F RNA nucleotides have the ability to undergo pseudorotation of the ribose.
Antisense and siRNA oligonucleotides are commonly found to have 2’-F-RNA substitutions due to its ability to enhance gene silencing and increase effectiveness of native siRNA, but its popularity is due to its lower cost compared to LNA. Biosynthesis offers 2’-F-RNA to suit your research needs.
A third and new modification that can be done to oligonucleotides is the incorporation of Bridged Nucleic Acids (BNA) monomers. Currently Bio-Synthesis exclusively offers custom oligonucleotides modified with BNA. BNA is closely related to LNA and developed by Takeshi Imanishi in Japan. 2’,4’-BNA modified oligonucleotides perform as well as and even better than LNA modified oligonucleotides. BNA has a very high target affinity, similar to or even higher than that of LNA and can increase Tm per modification by 5 to 6oC when binding to complementary RNA. Additionally BNA shows enhanced triplex formation, improved resistance to nuclease depredation, and more use in antisense and probe applications than LNA or 2’-F RNA.