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BNA PNA, LNA, DNA Comparison

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12/20/2005

BNA PNA, LNA, DNA Comparison

Comparison of various nucleic acid analogs: BNA, LNA, PNA and DNA

Criteria BNA LNA PNA DNA
Hybridization affinity with DNA 1-3 °C higher Tm per base 2-3 °C higher Tm per base At least 1 ℃ higher Tm per Tm -
Salt concentration for hybridization Dependent Dependent Independent Dependent
Tm for each single mismatch Ca. 4 ℃ Ca. 3-4 ℃ Lowering 1 - 5℃ Lowering 1℃
Chemical stability Stable to moderately stable Stable to moderately stable Stable Unstable or moderately stable
Biological stability Very stable Stable Stable to nuclease and protease Degradation by nuclease
Thermal stability Excellent Good Good Moderate
Water solubility Excellent Good to Excellent Soluble Soluble
Probe length for diagnostic use 10-25 10-25 13 - 18 bases 20-30 bases
PCR compatible Yes Yes No Yes
Ability to introduce other nucleic acids in oligonucleotide Yes Yes No Yes
Body clearance ability Yes Yes No Yes
Inhibition of RNAse H Yes Yes No Yes
Triplex formation Yes Yes Yes Yes
Hepatotoxicity No Moderate Moderate No
Nephrotoxicity No Very low High No
Innate immunity stimulation No No Yes Yes
Gene Silencing Yes Yes Yes na
Triplex Formation Ability Excellent Moderate Good Yes
RNA/DNA binding selectivity Excellent Good No preference na
Hybridization affinity with RNA 5-6 °C higher Tm per base 5-6 °C higher Tm per base At least 1 °C higher Tm per base na
Nuclease Resistance Yes Yes Yes No
SNP detection Yes Yes Yes na
Quantitativereal-time PCR applications Yes Yes Yes na
genotyping experiments Yes Yes Yes na
Telomere FISH Probes Yes Yes Yes na
Other FISH Probes Yes Yes Yes na
Design of shorter fluorescent probes Excellent Good Good no
Improved mismatch discrimination. Excellent Good Good no
Increases the window of annealing temperatures for accurate genotyping Excellent Good Good no
Various formats of detection Excellent Good Good no
Dection with dual-labeled probes, Excellent Good Good no