Fluorescence assay for polymerase arrival rates
Author(s)Che, Austin, 1979-
Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Thomas F. Knight, Jr.
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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.
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.
DepartmentMassachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.
Massachusetts Institute of Technology
Electrical Engineering and Computer Science.