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Simulation of the efficiency of gene-capture probes
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Liu, Jingqian. Simulation of the efficiency of gene-capture probes. Retrieved from https://doi.org/doi:10.7282/t3-57fa-bs98

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TitleSimulation of the efficiency of gene-capture probes
NameLiu, Jingqian (author); Parekkadan, Biju (chair); Olson, Wilma K. (internal member); Nanda, Vikas (internal member); Rutgers University; School of Graduate Studies
Date Created2019
Other Date2019-05 (degree)
SubjectLASSO probe, Biomedical Engineering, DNA probes -- Computer simulation
Extent1 online resource (vii, 39 pages) : illustrations
DescriptionThe multiplexed cloning of long DNA sequences can be of great value for biotechnology applications such as long-read genome sequencing or the creation of libraries of open reading frames (ORFs) from genomes for expression screening. Long adapter single-stranded oligonucleotide (LASSO) probes have shown promise as a tool to enable the capture and cloning of long DNA fragments by engineering an adapter region of user-defined length flanked by PCR primer regions, ultimately creating a long probe to bind long DNA regions. The success of LASSO in cloning target ORFs relies on the design of its long adapter sequence to be non-specific to a genomic region while also providing an optimal length for flexibility of a stable probe-target complex for downstream processing. The reason behind the adapter-length depend capture enrichment was explored in this thesis. Herein, we proposed two hypotheses, which are respectively related to the probes’ secondary structures as well as probe-target interaction free energy. Mfold, a tool for secondary structure prediction and Monte Carlo simulation based on a coarse-grained DNA model were applied to verify the two hypotheses. According to the computational predictions, the latter explanation, which was associated with the probe-target interaction free energy, was considered to account for the capture enrichment efficiency. Our results suggest that the length of the adapter is a factor that contributes to the free energy of target-probe interaction, thereby determines the efficiency of capture. The results also reveal different preferences to various adapter lengths when the target shifts from 400bp to 1500bp. For long target genes, longer adapters are more favorable, as simulations and experiments show.
NoteM.S.
NoteIncludes bibliographical references
Genretheses, ETD graduate
Persistent URLhttps://doi.org/doi:10.7282/t3-57fa-bs98
LanguageEnglish
CollectionSchool of Graduate Studies Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.
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