Handhold-mediated strand displacement: a mechanism for non-equilibrium and catalytic templating
File(s)
Author(s)
Cabello Garcia, Javier
Type
Thesis
Abstract
Polymer-templating copying processes – like RNA transcription and protein translation – are
of vital importance to the cell. Regardless of their complexity, all polymer-templating copying
processes are bound by the same physical first principles. A complete understanding of those
first principles will shed some light on the origins of life and offers the potential for engineering
new complex molecular systems and even synthetic life. However, the complexity and abundance
of components in extant cellular polymer-templating processes hinder the extraction of
their first principles. Creating a minimal system – composed only of a template and monomers
– capable of autonomously templating polymer copies would set the basis for the experimental
study of the first principles underlying biological templated-copying mechanisms.
In this thesis, I describe the first minimal mechanism that can underpin the catalytic templating
of DNA polymer copies of arbitrary length. This enzyme-free mechanism exploits a physical
DNA reaction introduced in this work: Handhold-mediated strand displacement (HMSD).
Firstly, I experimentally characterise and model HMSD kinetics. Then, I build a functional
HMSD-based mechanism for the catalytic templated-copying of DNA duplexes. Finally, I use
the mechanism to catalytically template out of equilibrium the formation of one specific DNA
duplex out of 9 alternative products.
The main achievement of this thesis is the thorough characterisation of HMSD, introducing a
new primitive DNA reaction that enables far-from-equilibrium templating for dynamic DNA
nanotechnology. In addition, I demonstrate a minimal templated-copying mechanism that can
autonomously detach the produced copies from their template, acting effectively as a catalyst.
Unlike the minimal mechanisms for templated-copying described so far, the HMSD-based
mechanism can be theoretically extended to produce arbitrary-length copies without relying
on external intervention or highly-evolved proteins. Besides its use as a minimal model for
templated-copying, the presented mechanism is potentially relevant for other complex functionalities
like chemical synthesis.
of vital importance to the cell. Regardless of their complexity, all polymer-templating copying
processes are bound by the same physical first principles. A complete understanding of those
first principles will shed some light on the origins of life and offers the potential for engineering
new complex molecular systems and even synthetic life. However, the complexity and abundance
of components in extant cellular polymer-templating processes hinder the extraction of
their first principles. Creating a minimal system – composed only of a template and monomers
– capable of autonomously templating polymer copies would set the basis for the experimental
study of the first principles underlying biological templated-copying mechanisms.
In this thesis, I describe the first minimal mechanism that can underpin the catalytic templating
of DNA polymer copies of arbitrary length. This enzyme-free mechanism exploits a physical
DNA reaction introduced in this work: Handhold-mediated strand displacement (HMSD).
Firstly, I experimentally characterise and model HMSD kinetics. Then, I build a functional
HMSD-based mechanism for the catalytic templated-copying of DNA duplexes. Finally, I use
the mechanism to catalytically template out of equilibrium the formation of one specific DNA
duplex out of 9 alternative products.
The main achievement of this thesis is the thorough characterisation of HMSD, introducing a
new primitive DNA reaction that enables far-from-equilibrium templating for dynamic DNA
nanotechnology. In addition, I demonstrate a minimal templated-copying mechanism that can
autonomously detach the produced copies from their template, acting effectively as a catalyst.
Unlike the minimal mechanisms for templated-copying described so far, the HMSD-based
mechanism can be theoretically extended to produce arbitrary-length copies without relying
on external intervention or highly-evolved proteins. Besides its use as a minimal model for
templated-copying, the presented mechanism is potentially relevant for other complex functionalities
like chemical synthesis.
Version
Open Access
Date Issued
2022-01
Date Awarded
2022-04
Copyright Statement
Creative Commons Attribution NonCommercial Licence
License URL
Advisor
Ouldridge, Thomas
Stan, Guy-Bart
Sponsor
Royal Society
Grant Number
RG160606
Publisher Department
Bioengineering
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)