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 may make these circular oligonucleotides important tools for in vivo studies.
In the past circular oligonucleotides have been investigated for their unique DNA binding properties and as useful models in studying DNA structures such as hairpin motifs by NMR. Currently, circular oligonucleotides are also being used for diagnostic applications, such as padlock probes, as well as the synthesis of concatemeric polypeptides. In addition, circular ssDNAs allow for both DNA and RNA amplification as these molecules are accepted as templates by both DNA and RNA polymerases.
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
References
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.
Oligonucleotide synthesis: methods and applications / edited by Piet Herdewijn. (Methods in molecular biology ; 288). ISBN 1-58829-233-9