Applications for circular oligonucleotides

Circularized or circular single-stranded deoxyribosnucleotides (ssDNAs), also often just called circular oligonucleotides, are more resistant to the attack by nucleases when compared to their linear oligonucleotides. These properties makes these circular oligonucleotides important tools for in vivo studies.

A closed-loop configuration formed from a linear nucleic oligonucleotide by an intramolecular covalent linkage of their two ends characterizes circular nucleic acids. 

Circular nucleic acids (CNAs) exist in nature as circular DNAs and RNAs that vary in size and function. Naturally occurring circular DNA exists as bacterial genomes, plasmids, mitochondrial DNA, chloroplast DNA, bacteriophage DNA, and eukaryotic viral DNA. Viroids, virusoids, spliced introns or exons of eukaryotes, bacteria, and archaea contain circular RNA.

In general, theta replication, rolling circle replication, or back-splicing produces CNAs. The fields of biotechnology, disease therapy and nanotechnology already utilize CNAs.

Circularized or circular single-stranded deoxyribosnucleotides (cssDNAs) are more resistant to the attack by nucleases than their linear oligonucleotides. These properties make these circular oligonucleotides important tools for in vivo studies.  

Circular DNAs have been investigated for their unique DNA binding properties, for example, as useful models in studying DNA structures such as hairpin motifs by NMR. Also, circular DNAs are used for diagnostic applications, such as padlock probes and the synthesis of concatemeric polypeptides. Also, circular ssDNA allows for both DNA and RNA amplification. CNAs can function as templates for both DNA and RNA polymerases. Additional examples are the use of plasmids in molecular cloning to study protein functions, the treatment of bacterial infections with circular lytic bacteriophages, the construction of “DNA origami” with circular phage DNA, and the use of circular RNA to regulate the transcription of microRNAs (miRNAs).

Use and applications for circular oligonucleotides are

  • Anti sense using circular oligonucleotides

  • Binding of duplex DNA

  • Delivery vectors for miRNAs

  • Diagnostics

  • DNA fragment assembly using a nicking enzyme system

  • DNA polymerase inhibition

  • DNA structure studies

  • Efficient templates for DNA and RNA polymerases

  • Hairpin motif design

  • Hairpin studies

  • Ligation-independent cloning (LIC)

  • Manipulating gene expression with caged circular oligonucleotides

  • Mutation detection

  • Padlock probes

  • Probing DNA-protein interactions

  • Quantitation of sequence-dependent DNA bending and flexibility

  • RNA polymerase inhibition

  • Rolling Circle Amplification (RCA)

  • Single molecule counting

  • Specific gene expression

  • Study of noncanonical DNA structural motifs

  • Synthesis of concatemeric polypeptides

  • Topologic modifications

  • Triple helix formation

  • Unique DNA recognition properties

  • Study of splicing events

  • Post-translational modifications


Diegelman, A. M. and Kool, E. T.; (2000) Chemical and enzymatic methods for preparing circular single-stranded DNAs. In Current Protocols in Nucleic Acid Chemistry, vol. 2 (Beaucage, S. et al., eds.). John Wiley, New York, Chapter 5.2. [PubMed]

Oligonucleotide synthesis: methods and applications in Methods in molecular biology ; 288.  Edited by Piet Herdewijn. ISBN 1-58829-233-9. [Springer]