Title:	Calculation of all pair-wise hetero-dimerization free energies of 52k 25-mers.
DNr:	SNIC 2016/1-268
Project Type:	SNIC Medium Compute
Principal Investigator:	Magda Bienko <magda.bienko@ki.se>
Affiliation:	Karolinska Institutet
Duration:	2016-05-31 – 2016-07-01
Classification:	10604
Keywords:

Abstract

In 2009, Xu et al. (Xu, PNAS 2009) published a list of 240000 25mer DNA barcode probes orthogonal to mammalian genomes. These barcodes can be used in a variety of applications, one of which is the selection of subsets of oligonucleotides from array-synthesized oligonucleotide pools. To perform such operation, each oligonucleotide is originally designed with two barcodes at its extremities, and sub-pools of oligonucleotides are selectively amplified via PCR by using a set of forward/reverse primers complementary to the aforementioned barcodes. The barcodes used to specifically amplify a sub-pool of oligonucleotides by PCR must not interact with themselves, or with other primers or their reverse-complement, to avoid unwanted amplifications. We already implemented both self-dimerization and hetero-dimerization free energy calculation in R, and one of these operations takes approximately 30ms to compute. Given that of the original 240k 25-mers list only ~52k do not self dimerize (dG >= -5 kcal/mol), we want to calculate the pair-wise hetero-dimerization free energy of all the remaining 52k 25-mers.