eprintid: 25879
rev_number: 10
userid: 4945
dir: disk0/00/02/58/79
datestamp: 2015-09-28 01:01:44
lastmod: 2018-09-27 05:15:04
status_changed: 2015-09-28 01:01:44
type: thesis_degree
metadata_visibility: show
contact_email: aprokup@gmail.com
item_issues_count: 0
eprint_status: archive
creators_name: Prokup, Alexander
creators_email: aprokup@gmail.com
title: Engineering DNA Computation with Unnatural Nucleotides and Protein Function with Unnatural Amino Acids
ispublished: unpub
divisions: sch_as_chemistry
full_text_status: public
keywords: DNA computation, unnatural amino acid mutagenesis, DNA, protein, signal amplification
abstract: Synthetic engineering methods, such as DNA computation and unnatural amino acid mutagenesis, have provided a route to improve the control of DNA and proteins. DNA computation encompasses a broad field that attempts to build computational devices from DNA structures. Logic gates are a fundamental component of any larger computational network, and have been constructed from purely DNA frameworks. Operation is determined by strict rules, which allow for the predictable creation of complex circuits. Described herein are methods to alter DNA logic gates with photochemical caging groups, interface logic gates with protein output, and optically control DNA amplification cycles. These methods have enabled precise temporal and spatial control, as well as merged the interface between DNA circuits and biological systems. Unnatural amino acid mutagenesis enables the site specific alteration of protein residues, through the insertion of a non-canonical amino acid. Incorporation of these unnatural residues has greatly expanded the function of proteins, with the introduction of new chemical functionalities. These chemical handles have enabled applications such as the study of abasic bypass in DNA polymerases and protein-RNA crosslinking.
date: 2015-09-27
date_type: published
pages: 192
institution: University of Pittsburgh
refereed: TRUE
etdcommittee_type: committee_chair
etdcommittee_type: committee_member
etdcommittee_type: committee_member
etdcommittee_type: committee_member
etdcommittee_name: Deiters, Alexander
etdcommittee_name: Islam, Kabirul
etdcommittee_name: Horne, Seth
etdcommittee_name: Bruchez, Marcel
etdcommittee_email: alexdeiters@gmail.com
etdcommittee_email: kai27@pitt.edu
etdcommittee_email: horne@pitt.edu
etdcommittee_email: bruchez@cmu.edu
etdcommittee_id: 
etdcommittee_id: KAI27
etdcommittee_id: HORNE
etdcommittee_id: 
etd_defense_date: 2015-07-02
etd_approval_date: 2015-09-27
etd_submission_date: 2015-08-03
etd_release_date: 2015-09-27
etd_access_restriction: 3_year
etd_patent_pending: FALSE
thesis_type: dissertation
degree: PhD
citation:   Prokup, Alexander  (2015) Engineering DNA Computation with Unnatural Nucleotides and Protein Function with Unnatural Amino Acids.  Doctoral Dissertation, University of Pittsburgh.    (Unpublished)  
document_url: http://d-scholarship-dev.library.pitt.edu/25879/1/ProkupAM_etd2015.pdf