Harvard-Lipper Center for Computational Genetics
Oligonucleotide Sequences for Human and Mouse RNA Assays
We have designed a potentially shareable set of oligonucleotides for use in a variety of microarray and/or PCR measures of DNA and/or RNA. This consists of a simple list of one 70-mer per "gene" (i.e. dominant RNA.) Subsequent separate pages will have two or more oligos per RNA (often more than one RNA per gene.)
We expect to maintain this as an archival list with version-tracking and connections to NCBI resources for each RNA. The longer lists will contain the shorter list as a subset as much as possible.
We chose "unique" 70-mers on the assumption that smaller overlapping unique oligomers could be chosen from these as needed and still be referenced to a "standard" region. Seventy bases is also the maximum length seen for human oligos in various commercially available comprehensive oligo sets.
The criteria we use are listed below
Uniqueness: evaluated by BLAST alignment (bit score < 50)
Uniformity: Tm between 72.5 and 83.5 (same range used by Operon)
Sequence Complexity: compressibility score below 35 (described in documentation)
Secondary Structure: Gibbs energy of secondary structure formation (using RNAfold – described in documentation)