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Thomas F. Knight, Jr. Che, Austin, 1979- Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science. Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science 2005-05-17T14:41:25Z 2005-05-17T14:41:25Z 2003 2004 http://hdl.handle.net/1721.1/16618 55693371 Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2004. Includes bibliographical references (p. 87-100). This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate. by Austin Che. S.M. 100 p. 2370513 bytes 2372070 bytes application/pdf application/pdf eng Massachusetts Institute of Technology M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 Electrical Engineering and Computer Science. Fluorescence assay for polymerase arrival rates Thesis application/pdf false Publication unknown unknown <Publication xmlns="https://www.openaire.eu/cerif-profile/1.1/" id="17dc5942-6048-42d6-9f59-0774c17db7f7"> <Type xmlns="https://www.openaire.eu/cerif-profile/vocab/COAR_Publication_Types">http://purl.org/coar/resource_type/c_1843</Type> <Language>eng</Language> <Title>Fluorescence assay for polymerase arrival rates</Title> <PublishedIn> <Publication> </Publication> </PublishedIn> <PublicationDate>2004</PublicationDate> <Authors> <Author> <DisplayName>Che, Austin, 1979-</DisplayName> <Affiliation> <OrgUnit> </OrgUnit> </Affiliation> </Author> </Authors> <Editors> </Editors> <Publishers> <Publisher> <DisplayName>Massachusetts Institute of Technology</DisplayName> <OrgUnit /> </Publisher> </Publishers> <License>http://dspace.mit.edu/handle/1721.1/7582</License> <Keyword>Electrical Engineering and Computer Science.</Keyword> <Abstract>To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.</Abstract> <Access xmlns="http://purl.org/coar/access_right" > </Access> </Publication>