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Engineering a Robust DNA Circuit for the Direct Detection of Biomolecular Interactions

Part of the Springer Theses Book Series

DOI: 10.1007/978-981-13-2188-7

ISBN: 978-981-13-2187-0

Publisher: Springer Singapore - Springer Journals

Sep 22, 2018

1 - 9 of 9 Chapters

LitStream

Chapter 1Introduction

Yan Shan, Ang

Pages: 1 –4

[DNA circuit is a highly programmable toolbox based on the dynamic interactions between logic gates driven by a series of hybridization events known as toehold-mediated strand displacements. Since the circuit design is modular and based primarily on the well-studied Watson-Crick base pairing, it...
LitStream

Chapter 2Literature Review

Yan Shan, Ang

Pages: 5 –46

[The field of DNA circuitry started with the aim of developing DNA molecular machine for autonomous molecular computation. However, the field has since recognized that the speed and scale of DNA computation can never surpass that of silicon-based microelectronics (Regalado in MIT Technology...
LitStream

Chapter 3Materials and Methods

Yan Shan, Ang

Pages: 47 –61

[This chapter details the experimental materials and methods used for all the experiments in this thesis. These includes the parameters for NUPACK simulation, assay kinetics study, detailed methods for analyzing different biomolecular systems and interpretation of the data collected.]
LitStream

Chapter 4Modular Framework for Engineering a Self-contained DNA Circuit

Yan Shan, Ang

Pages: 63 –77

[Biomolecular interactions have important cellular implications, however, a simple method for the sensing of such proximal events is lacking in the current molecular toolbox. We designed a dynamic DNA circuit capable of recognizing targets in close proximity to initiate a pre-programmed signal...
LitStream

Chapter 5Designing Hybridization Chain Reaction Monomers for Robust Signal Amplification

Yan Shan, Ang

Pages: 79 –99

[Methods to amplify the signal of biomolecular recognition events are essential for the detection of low target count encountered in applications such as early disease diagnosis. Hybridization chain reaction (HCR) is an attractive isothermal, enzyme-free amplification scheme involving the...
LitStream

Chapter 6Design Concepts in Association Toehold for Robust Signal Transduction

Yan Shan, Ang

Pages: 101 –119

[The experimental implementation of in silico DNA circuit designs has been hindered by the problem of circuit leakage. Here, we systematically analyzed the sources and characteristics of various types of leakage in a split proximity circuit which was engineered to spatially probe for target...
LitStream

Chapter 7DNA Split Proximity Circuit as a General Platform for Interrogating Biomolecular Events

Yan Shan, Ang

Pages: 121 –141

[The design aspects of the individual circuit modules have been conceptualized, validated and discussed in the previous chapters. The aim of this chapter is to integrate the different modules into an overall circuit, termed “split proxity circuit”, for detecting biomolecules and biomolecular...
LitStream

Chapter 8DNA Split Proximity Circuit for Visualizing Cell Surface Receptor Clustering—A Case Study Using Human Epidermal Growth Factor Receptor Family

Yan Shan, Ang

Pages: 143 –156

[Cell surface receptors play an important role in mediating cell communication and are used as disease biomarkers and therapeutic targets. We present a one-pot molecular toolbox, termed the split proximity circuit (SPC), for the autonomous detection and visualization of cell surface receptor...
LitStream

Chapter 9Conclusion and Future Outlooks

Yan Shan, Ang

Pages: 157 –164

[This doctoral work culminated in a circuit design capable of detecting bi-molecular proximity events, which we named “split proximity circuit (SPC)”. The circuit assembles dynamically on the target recognition sites in a self-contained manner to execute localized strand displacement. A recurring...

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