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Analysis of Interacting Nucleic Acids in Dilute Solutions


Bois, Justin S. (2007) Analysis of Interacting Nucleic Acids in Dilute Solutions. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/2JCJ-SX75.


Motivated by the growing demand for analysis tools for diverse natural and engineered DNA and RNA systems, we develop a general theory and set of computational algorithms to perform thermodynamic analysis of dilute reactive solutions and then apply these techniques to interacting nucleic acids. The theory correctly accounts for the effects of indistinguishability in partition function calculations for complexes of interacting strands. With partition functions in hand, the unique complex concentrations corresponding to thermodynamic equilibrium are obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables corresponding to experimentally measurable properties. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.

To make these analysis tools available to researchers worldwide, we present NUPACK, a web-based software suite for thermodynamic analysis of nucleic acids. Its efficacy is demonstrated in example calculations and the results are shown to be in agreement with experiment.

Finally, the thermodynamic properties of a DNA-based triggered self-assembly device [1] are analyzed using NUPACK and extensions of its tools. The computational results complement experimental studies, exposing novel properties about the system and dictating further research.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:base pair; convexity; dilute solution; distinguishability; DNA; duality; equilibrium; folding; multiple strands; nucleic acid; NUPACK; partition function; redundancy; RNA; secondary structure; symmetry; thermodynamics
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemical Engineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Pierce, Niles A.
Thesis Committee:
  • Wang, Zhen-Gang (chair)
  • Smolke, Christina D.
  • Winfree, Erik
  • Pierce, Niles A.
Defense Date:30 April 2007
Non-Caltech Author Email:bois (AT)
Record Number:CaltechETD:etd-05242007-211446
Persistent URL:
Bois, Justin S.0000-0001-7137-8746
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:2032
Deposited By: Imported from ETD-db
Deposited On:31 May 2007
Last Modified:08 Nov 2023 00:43

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