The Bridged Nucleic Acid 2',4'-BNANC (2'-O,4'-aminoethylene bridged nucleic acid) is a molecule that contains a six-membered bridged structure with an N-O linkage. This novel nucleic acid analog can be synthesized and easily incorporated into oligonucleotides.
When compared to the earlier generations of bridged nucleic acids (e.g., LNA, ENA), BNA was found to possess:
Higher binding affinity to an RNA complement.
Excellent single-mismatch discrimination.
Enhanced binding selectivity to RNA.
Stronger and more sequence selective triplex-forming characteristics.
Stronger nuclease resistance to endo and exo-nucleases, even higher than S(p)-phosphorothioate analogs.
Based on the above observations, BNA has shown great promise for applications in antisense and antigene technologies. BNAs, or bridged nucleic acids, are well suited for the following applications:
Antisense oligonucleotides (ASOs)
Gapmer ASOs
Blocking ASOs
Affinity capture probes
Real-Time PCR probes
PCR Clamping
In situ hybridization probes
Primers for single, multiplex and allele-specific PCR
Capture probes for SNP genotyping
Capture probes for expression analysis
Probes to monitor exon skipping
Also, BNAs are useful tools for hybridization assays that require high specificity and/or reproducibility.
The BNA modification is perfectly suited for SNP detection.
Reduction in probe size maximises the impact of mismatch in the stability of the probe/target duplex.
BNA modifications increase the specificity of the probe and also its power of discrimination.
Advantages
Affinity
BNA increases the thermal stability of duplexes due to its RNA-like structure.
BNA-BNA duplex formation creates a very stable Watson-Crick base pairing system
Tm modulation
Depending on their position along the sequence, BNA bases allow reaching the desired Tm level without losing specificity.
The introduction of BNA allows for shorter probes while maintaining the same Tm.
Ease of use
BNA enhances hybridization performance relative to native DNA, RNA or phosphorothioate.
BNA lowers experimental error rates due to better mismatch discrimination.
BNA improves the signal-to-noise ratio.
Enzyme compatibility
BNA exhibits increased resistance to certain exo- and endonucleases with a high biostability.
DNA-BNA gapmers readily activate RNAse H.
BNA acts as a substrate for standard molecular biology enzymes: T4 PNK, T4 DNA ligase, DNA polymerases.
Simplicity
BNA behaves like DNA. Therefore it is easily transferable to DNA-based assays.
BNA is highly soluble in water.
BNA can be used in oligonucleotide synthesis and analysis methods (QC, purification, etc.).
BNA exhibits the same salt dependence as DNA and RNA.
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