Longmers and their applications
Oligonucleotide microarrays and probe length
Oligonucleotide microarrays are valuable tools for genomic analyses with their probe length being one of the key considerations when designing a microarray experiment. When dealing with the complexities of probe set design and probe specific signal interpretation, the influence of probe sequences and length on bias and random measurement noise have to be observed1.
Depending on the application, the use of shortmers that are about 25 bp in length can be advantageous as they are viewed as high-specificity probes.
Longmer benefits
- Longmers of up to 60mers however are believed to be more sensitive, due to the longer sequence stretch available for hybridization.
- Longmers are also more tolerant of sequence mismatches, simplifying the analysis of highly polymorphic regions. As sequence knowledge grows at an increasing pace, the advantages of longmers become more and more substantial.
Longmer synthesis sets
The use of the longmer synthesis set enables the generation of up to 60mers within the Geniom biochip, with array design and capture probe setup being easily adapted to any kind of application. The careful design and selection of the probes give improved experimental control of hybridization properties, and systematic targeting of specific gene sub-sequences allows for better discrimination of highly similar targets such as splice variants or gene families2.
Geniom longmer applications
Geniom offers the flexibility to choose either ready-to-go microarray designs or the freedom to switch to creating dedicated custom arrays. It now also offers the possibility to adjust probe length for new applications and even higher levels of specificity. 60mer probes can be designed to specifically hybridize with unique genomic DNA, which would be impossible with shorter oligonucleotides.
Applications like genomic hybridization, the analysis of dsDNA-protein interactions, chIP-on chip approaches and the determination of DNA copy number variations (CNVs) that depend on longer probes can now easily be performed on the Geniom platform.