LNA™ longRNA GapmeR

LNA™ gapmers are potent antisense oligonucleotides used for highly efficient inhibition of mRNA and lncRNA function. Designed using advanced algorithms, the RNase H-activating LNA™ gapmers offer excellent performance and high success rate.

Marie-Louise Lunn, Ph.D., Product Manager

High affinity and high stability LNA™ GapmeRs
Low toxicity and superior potency
Less off-target effects and increased ease-of-use with short, single stranded antisense oligonucleotides (ASO)
High flexibility – target mRNAs and nuclear lncRNAs in vitro or in vivo
Save time and effort – sophisticated design algorithms ensure high efficacy

Features

LNA™ longRNA GapmeRs are antisense oligonucleotides (ASOs) used for functional analysis of mRNA and long non-coding RNA. They contain a central stretch (gap) of DNA monomers flanked by blocks of LNA™ modified nucleotides (Figure 1). The LNA™ blocks increase the target affinity and nuclease resistance of the oligo and the DNA gap activates RNase H cleavage of the target RNA upon binding. The gapmers are 14-16 nucleotides in length and fully phosphorothioated.

Design process

All the LNA™ longRNA GapmeRs are designed using Exiqon’s advanced design algorithms to identify the most potent gapmers. The software evaluates more than 100,000 designs based on over 30 design criteria. The process ensures a high success rate and minimal off-target effects.

The design criteria include:

Optimization of length, sequence and LNA™ content, resulting in high-affinity binding and minimal self-hybridization.
Calculation of target sequence accessibility for increased potency of the LNA™ gapmer
Sequence database searches to ensure highly specific LNA™ gapmers and reduced potential non-specific targets into account, leading to high success rates and minimal off-target effects.
Designs are optimized to include only nucleotides and LNA™ pattern known to work well for RNase H dependent silencing

Table 1

Workflow for LNA™ longRNA GapmeRs. (Click to learn more)

Coverage

LNA™ longRNA GapmeRs can be designed for any RNA target > 80 nucleotides and are available in four different categories depending on application (see also Tables 1 & 2):

LNA™ longRNA GapmeR in vitro Standard: Cost effective alternative for initial screening of multiple designs using standard cell-lines.

LNA™ longRNA GapmeR in vitro Premium: HPLC-purified gapmers with guaranteed purity suitable for most cell assays, also available with 5’or 3’ fluorescent labels.

LNA™ longRNA GapmeR in vivo Ready: High quality, animal-grade gapmers recommended for any projects that have in vivo testing as the ultimate goal. Also recommended for hard-to-transfect cell-lines such as B-cells, T-cells, primary cell lines, cells in suspension etc.

Custom LNA™ longRNA GapmeR in vivo Large Scale: The same high quality and purity as the in vivo Ready GapmeRs available with custom large scale yields.

Table 2

Overview of LNA™ longRNA GapmeR products. (Click to learn more)

Figure 1

Structure and function of the LNA™ longRNA GapmeRs. (Click to learn more)

Efficient RNase H mediated silencing

RNase H activation by gapmer ASO has proven to be a powerful method in inhibition of gene function and is emerging as a popular approach for antisense therapeutics. RNase H is a ubiquitous enzyme found both in the nucleus and the cytoplasm of all cells. It hydrolyzes the RNA of the RNA-DNA heteroduplexes formed after sequence-specific binding of ASOs to their target mRNA (or lncRNA). Upon cleavage by RNase H, the degraded mRNA will not be translated into the corresponding protein and will result in down-regulation of the targeted protein (Figure 2).

Advantages of LNA™ GapmeRs over siRNA

The use of single stranded RNase H-activating LNA™ gapmers has several advantages over traditional siRNA approaches both in vitro and in vivo:

Fewer off-target effects due to the lack of a passenger strand (Kole et al., 2012) and no issues with saturation of the RISC complex (Khan et al., 2009) .
Potent inhibition of nuclear targets. RNase H-activating ASOs are also able to efficiently target RNAs in the nucleus which makes them more suitable for studying the function of nuclear lncRNA (Lee et al., 2012).
No need for transfection agent. Besides the conventional methods of delivery, it has been demonstrated recently that LNA™ gapmer ASOs can be taken up in the cell unassisted ( Gupta et al., 2010, Stein et al.,2010, Zhang et al.,2011). The term ‘gymnosis’ was coined for this process, which denotes naked delivery. Gymnosis can be used to deliver LNA™ gapmers to cell-lines that are difficult to transfect. Please consult the LNA™ longRNA GapmeR Manual for more information.

LNA™ GapmeRs in vivo

The advantages of using LNA™ longRNA GapmeRs in vivo include:

High biological stability. The incorporation of LNA™ increases the serum stability of the ASO. LNA™ gapmer ASOs have also been shown to have high potential in penetrating the cell membrane barrier and successfully interact with the intracellular target site.
Easier workflow. Formulation, e.g., liposomes or cationic complexes, is not required for efficient delivery in vivo , making the workflow easier.
Lower concentrations needed. LNA™ longRNA GapmeRs offer superior potency and stability due to the incorporation of Locked Nucleic Acids (LNA™) as well as phosphorothioate (PS) modifications. The high binding affinity, allows the use of short oligonucleotides (14-16nt). The excellent pharmacokinetic and pharmacodynamic properties of LNA™ gapmers have been demonstrated in many different tissues and organs. In addition, short, high affinity LNA™ gapmers are active at lower concentrations compared to other antisense oligonucleotides (Straarup et al., 2012) .
Low toxicity. LNA™ antisense oligonucleotides are well tolerated and show low toxicity in vivo . Since the gapmers can be used in lower concentrations, any potential toxic effects are further reduced.

Figure 2

LNA™ longRNA GapmeRs mode of action. (Click to learn more)

Buy 4, Get 1 Free

Purchase 5 or more LNA™ longRNA GapmeRs and get a 20% discount. Offer valid world-wide for product no. 300600 when purchasing 5 or more designs for the same target.