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Simulation of the efficiency of gene-capture probes

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TitleInfo
Title
Simulation of the efficiency of gene-capture probes
Name (type = personal)
NamePart (type = family)
Liu
NamePart (type = given)
Jingqian
NamePart (type = date)
1993-
DisplayForm
Jingqian Liu
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Parekkadan
NamePart (type = given)
Biju
DisplayForm
Biju Parekkadan
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Olson
NamePart (type = given)
Wilma K.
DisplayForm
Wilma K. Olson
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Nanda
NamePart (type = given)
Vikas
DisplayForm
Vikas Nanda
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
School of Graduate Studies
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (encoding = w3cdtf); (keyDate = yes); (qualifier = exact)
2019
DateOther (encoding = w3cdtf); (qualifier = exact); (type = degree)
2019-05
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2019
Language
LanguageTerm (authority = ISO 639-3:2007); (type = text)
English
Abstract (type = abstract)
The 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.
Subject (authority = local)
Topic
LASSO probe
Subject (authority = RUETD)
Topic
Biomedical Engineering
Subject (authority = LCSH)
Topic
DNA probes -- Computer simulation
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_9870
PhysicalDescription
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application/pdf
InternetMediaType
text/xml
Extent
1 online resource (vii, 39 pages) : illustrations
Note (type = degree)
M.S.
Note (type = bibliography)
Includes bibliographical references
RelatedItem (type = host)
TitleInfo
Title
School of Graduate Studies Electronic Theses and Dissertations
Identifier (type = local)
rucore10001600001
Location
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NjNbRU
Identifier (type = doi)
doi:10.7282/t3-57fa-bs98
Genre (authority = ExL-Esploro)
ETD graduate
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Liu
GivenName
Jingqian
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2019-04-15 15:15:16
AssociatedEntity
Name
Jingqian Liu
Role
Copyright holder
Affiliation
Rutgers University. School of Graduate Studies
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical

RULTechMD (ID = TECHNICAL1)
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ETD
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windows xp
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1.4
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macOS 版本 10.14(版号 18A391) Quartz PDFContext
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2019-04-24T01:13:35
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2019-04-24T01:13:35
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