國立虎尾科技大學 |

Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy.

Record Type:	Language materials, manuscript : Monograph/item
Title/Author:	Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy./
Author:	Shah, Neel Arvind.
Description:	1 online resource (66 pages)
Notes:	Source: Masters Abstracts International, Volume: 82-09.
Contained By:	Masters Abstracts International82-09.
Subject:	Bioengineering. -
Online resource:	click for full text (PQDT)
ISBN:	9798569996629

Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy.
Shah, Neel Arvind.

Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy. - 1 online resource (66 pages)

Source: Masters Abstracts International, Volume: 82-09.

Thesis (Master's)--University of Washington, 2020.

Includes bibliographical references

Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are selected in vitro from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). In vitro selected RNA aptamers can be assembled into programmable biosensors for a broad range of synthetic biology applications requiring the detection and quantification of small molecule metabolites. Aptamers have been around for three decades now, however, sensors that work in proof-of-concept studies, mainly performed in academia, do not necessarily match the conditions, the statistical relevance, the compatibility with routine equipment found in e.g., clinical diagnostic departments, and the scale required for an industrial and/or clinical application. A major obstacle to the broader development of aptamer metabolite biosensors as tools for industrial biotechnology and translational medicine stems from uncertainty in the outcomes of in vitro selection and the aptamer-ligand binding affinities that can be obtained. We present, to our knowledge, the first approach for a priori estimation of RNA aptamer binding affinities and a virtual screening tool against small molecule targets. We illustrate the generalizability of this tool to identify in silico metabolites and biomarkers that could be targeted with aptamer biosensing. Further, we outline an RNA Capture-SELEX strategy to generate in vitro structure switching aptamers which could be incorporated into genetic switches for regulating gene expression; since in classical SELEX only binding and not conformational changes are selected which is an important property of 'sensing-actuation' devices that represent an important class of genetic devices which can detect, report on and act on environmental and intracellular signals, including small molecules and proteins, to study and control cellular functions.

Electronic reproduction.
Ann Arbor, Mich. :
ProQuest,
2024

Mode of access: World Wide Web

ISBN: 9798569996629Subjects--Topical Terms:

598252
Bioengineering.
Subjects--Index Terms:

In vitro selectionIndex Terms--Genre/Form:

554714
Electronic books.

Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy.
LDR:03389ntm a22003737 4500 001 1147935
005 20240916065942.5
006 m o d
007 cr bn ---uuuuu
008 250605s2020 xx obm 000 0 eng d
020 $a 9798569996629
035 $a (MiAaPQ)AAI28264954
035 $a AAI28264954
040 $a MiAaPQ $b eng $c MiAaPQ $d NTU
100 1 $a Shah, Neel Arvind. $3 1473784
245 1 0 $a Development of RNA Aptamers Through Supervised Learning and Capture-Selex Strategy.
264 0 $c 2020
300 $a 1 online resource (66 pages)
336 $a text $b txt $2 rdacontent
337 $a computer $b c $2 rdamedia
338 $a online resource $b cr $2 rdacarrier
500 $a Source: Masters Abstracts International, Volume: 82-09.
500 $a Advisor: Carothers, James M.
502 $a Thesis (Master's)--University of Washington, 2020.
504 $a Includes bibliographical references
520 $a Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are selected in vitro from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). In vitro selected RNA aptamers can be assembled into programmable biosensors for a broad range of synthetic biology applications requiring the detection and quantification of small molecule metabolites. Aptamers have been around for three decades now, however, sensors that work in proof-of-concept studies, mainly performed in academia, do not necessarily match the conditions, the statistical relevance, the compatibility with routine equipment found in e.g., clinical diagnostic departments, and the scale required for an industrial and/or clinical application. A major obstacle to the broader development of aptamer metabolite biosensors as tools for industrial biotechnology and translational medicine stems from uncertainty in the outcomes of in vitro selection and the aptamer-ligand binding affinities that can be obtained. We present, to our knowledge, the first approach for a priori estimation of RNA aptamer binding affinities and a virtual screening tool against small molecule targets. We illustrate the generalizability of this tool to identify in silico metabolites and biomarkers that could be targeted with aptamer biosensing. Further, we outline an RNA Capture-SELEX strategy to generate in vitro structure switching aptamers which could be incorporated into genetic switches for regulating gene expression; since in classical SELEX only binding and not conformational changes are selected which is an important property of 'sensing-actuation' devices that represent an important class of genetic devices which can detect, report on and act on environmental and intracellular signals, including small molecules and proteins, to study and control cellular functions.
533 $a Electronic reproduction. $b Ann Arbor, Mich. : $c ProQuest, $d 2024
538 $a Mode of access: World Wide Web
650 4 $a Bioengineering. $3 598252
653 $a In vitro selection
653 $a Medical diagnostics
653 $a Metabolic engineering
653 $a RNA aptamer biosensors
653 $a Supervised learning
655 7 $a Electronic books. $2 local $3 554714
690 $a 0202
710 2 $a ProQuest Information and Learning Co. $3 1178819
710 2 $a University of Washington. $b Chemical Engineering. $3 1182409
773 0 $t Masters Abstracts International $g 82-09.
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28264954 $z click for full text (PQDT)