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Full-Text Articles in Physical Sciences and Mathematics
A New Algorithm For Primer Design, Debanjan Guha Roy
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
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 …
A New Algorithm For De Novo Genome Assembly, Md. Bahlul Haider
A New Algorithm For De Novo Genome Assembly, Md. Bahlul Haider
Electronic Thesis and Dissertation Repository
The enormous amount of short reads produced by next generation sequencing (NGS) techniques such as Roche/454, Illumina/Solexa and SOLiD sequencing opened the possibility of de novo genome assembly. Some of the de novo genome assemblers (e.g., Edena, SGA) use an overlap graph approach to assemble a genome, while others (e.g., ABySS and SOAPdenovo) use a de Bruijn graph approach. Currently, the approaches based on the de Bruijn graph are the most successful, yet their performance is far from being able to assemble entire genomic sequences. We developed a new overlap graph based genome assembler called Paired-End Genome ASsembly Using Short-sequences …
Design And Syntheses Of Fluorescent Cytosine Analogues, David W. Dodd
Design And Syntheses Of Fluorescent Cytosine Analogues, David W. Dodd
Electronic Thesis and Dissertation Repository
The avid hybridization of peptide nucleic acid (PNA) to DNA and RNA along with the molecule’s biological stability has led it to be used in both antisense and antigene capacities. PNA acts against translation via a steric blockade mechanism. It is therefore reasonable to assume that increased heteroduplex stability could lead to increased potency. Two ways of doing this were explored. I) N-Terminal attachment of a platinous chloride chelating moiety to PNA complementary to Xenopus noggin was synthesized with the objective of selective, covalent platination of the target transcript in vivo. Phenotypes consistent with knockdown of the selected …