Physical Sciences and Mathematics Commons^™

A New Algorithm For Primer Design, Debanjan Guha Roy

Electronic Thesis and Dissertation Repository

The Polymerase Chain Reaction (PCR) technology is widely used to create DNA copies. It has impacted many diverse fields including genetics, forensics, molecular paleontology, medical applications and environmental microbiology.

The main object in PCR is a primer, a short single strand of DNA, about 18-25 bases long, that serves as the starting point of DNA synthesis. Primers are essential for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA. The PCR starts at the 3’-end of the primer and copies the opposite strand.Designing good primers is essential …

Oligonucleotide Design For Whole Genome Tiling Arrays, Qin Dong

Electronic Thesis and Dissertation Repository

Oligonucleotides are short, single-stranded fragments of DNA or RNA, designed to readily bind with a unique part in the target sequence. They have many important applications including PCR (polymerase chain reaction) amplification, microarrays, or FISH (fluorescence in situ hybridization) probes. While traditional microarrays are commonly used for measuring gene expression levels by probing for sequences of known and predicted genes, high-density, whole genome tiling arrays probe intensively for sequences that are known to exist in a contiguous region. Current programs for designing oligonucleotides for tiling arrays are not able to produce results that are close to optimal since they allow …