LNA™-based oligonucleotides are the best solution for highly sensitive and specific analysis of short RNA and DNA targets.
Tm normalization – robust detection regardless of GC content
m of a nucleotide duplex can be controlled by varying the LNA™ content. This feature can be used to normalize the T
m across a population of short sequences with varying GC-content. For AT-rich nucleotides, which give low melting temperatures, more LNA™ is incorporated into the LNA™ oligonucleotide to raise the T
m of the duplex. This enables the design of LNA™ oligonucleotides with a narrow Tm range which is beneficial in many research applications such as microarray, PCR and other applications where sensitive and specific binding to many different targets must occur under the same conditions simultaneously. The power of T
m-normalization is demonstrated by the comparison of DNA and LNA™ probes for detection of microRNA targets with a range of CG content (Figure 1). “LNA™-enhanced oligonucleotides can be designed to have a similar affinity towards all types of sequences regardless of the GC-content” Figure 1 The power of Tm normalization. (Click to learn more)
Superior single nucleotide discrimination
Intelligent placement of LNA™ monomers can also ensure excellent discrimination between closely related sequences down to as little as one nucleotide difference. The difference in Tm between a perfectly matched and a mismatched target is described as the delta Tm. Incorporation of LNA™ in oligonucleotides can increase the delta Tm between perfect match and mismatch binding by up to 8 °C. The increase in delta Tm enables better discrimination between closely related sequences such as members of microRNA families.
The affinity-enhancing effects of LNA™ give LNA™ oligonucleotides strand invasion properties making LNA™ excellent for in vivo
applications. Incorporation of LNA™ into oligonucleotides further increases resistance to endo- and exonucleases which leads to high in vitro
and in vivo
Since the physical properties (e.g. water solubility) of these sequences are very similar to those of RNA and DNA, conventional experimental protocols can easily be adjusted to their use.
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Superior results from challenging clinical samplesThe increase in sensitivity and specificity of LNA™-enhanced oligonucleotides makes them ideal for challenging applications where the target is present at low levels.
For example, LNA™-enhanced PCR primers are superior for quantifying short RNAs in small amounts of biofluids such as serum and plasma1 and LNA™-enhanced capture probes offer excellent sensitivity and signal-to-noise ratios in FFPE samples, where short RNA targets such as microRNAs are present in a background of highly degraded RNA.
1) Jensen et al. BMC Genomics 2011