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SNP Microarrays

Design your own LNA™-enhanced microarray capture probes or let us design them for you. These arrays are ideal for detection of single nucleotide polymorphism (SNP).

  • Detect targets as short as 16 nucleotides in length with unmatched specificity
  • Tm-normalized capture probes allow multiplexed SNP detection
  • Superior sensitivity for successful detection of difficult targets

Features

LNA™-enhanced expression microarrays feature short capture probes and can be used without sacrificing the sensitivity or the specificity of the array. These arrays are ideal for the detection of short or highly similar targets. Use them for expression analysis of splice variants, single nucleotide polymorphisms (SNPs), small RNAs and even normal mRNA expression analysis.

Another advantage of using LNA™ is that the capture probes can be T m-normalized. Just vary the LNA™ content and positioning within the probes to get similar melting temperatures.

Coverage

Design your own LNA™-enhanced microarray capture probes using the design guidelines presented below. Alternatively, let Exiqon’s in-house LNA™ experts help you design the optimal LNA™ oligonucleotides for your targets. We deliver the LNA™-enhanced oligonucleotides you need for custom array spotting. You can choose to spot the arrays yourself or let us provide you with high-quality spotted arrays.

Please contact us to receive a quote for LNA™-enhanced capture probes for microarrays.

Design guidelines

LNA™-incorporation has a strong effect on the properties of oligonucleotides and great care must be taken to find the right design for your application. While you will want to take advantage of the properties of LNA™ in order to achieve high target specificity, it is important not to use too much LNA™ since this can result in a very “sticky” oligonucleotide.

By varying the length and LNA™-content of the sequence, it is possible to design an oligonucleotide with excellent mismatch discrimination and binding specificity, while avoiding unacceptable secondary structure and self-complementarity.

Please follow these design guidelines for optimal LNA™ capture probe design:
  • Capture probes should be approximately 16-22 nucleotides in length.
  • For SNP detection, 2-3 LNA™ bases should be positioned at the SNP site and the adjacent nucleotides.
  • Avoid stretches of 3 or more Gs or Cs.
  • Avoid stretches of more than 4 LNA™ bases. LNA™ hybridizes very tightly when several consecutive nucleotides are substituted with LNA™ bases.
  • Avoid LNA™ self-complementarity. LNA™ hybridizes very tightly to other LNA™ residues. Check your design using these tools.
  • Keep the GC-content between 30-60 %.
  • A T m of approximately 75 °C is recommended. Calculate T m using these tools.
  • No LNA™ bases should be placed in palindromes (G-C base pairs are more critical than A-T base pairs).
  • When designing probes for SNP detection, vary the length and LNA™ positioning to obtain similar T m for the alleles, while keeping the difference in T m of the perfect match and mismatch binding as high as possible.



 
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