4 research outputs found
Multiplexed Optical Detection of Plasma Porphyrins Using DNA Aptamer-Functionalized Carbon Nanotubes
A novel
optical platform based on DNA aptamer-functionalized SWCNTs
(a-SWCNTs) is developed for multiplexed detection of plasma porphyrins.
We have investigated the interactions of a-SWCNTs with heme (FePP),
protoporphyrin (PP), coproporphyrin (CP), and uroporphyrin (UP). Two
interaction mechanisms, specific binding, and nonspecific adsorption
between porphyrins and a-SWCNTs are proposed based on observed optical
signal modulations. The optical transduction signals are used to formulate
a multiplexed detection strategy for the four porphyrin species without
a laborious separation process. The detection scheme is sensitive,
selective, and can readily be used for porphyrin detection in plasma
samples when combined with a solvent extraction method. Our optical
platform offers novel analytical tools for probing the surface chemistry
at the porphyrin/a-SWCNTs interface, showing great promise for both
research and clinical applications
Understanding the Mechanical Properties of DNA Origami Tiles and Controlling the Kinetics of Their Folding and Unfolding Reconfiguration
DNA origami represents
a class of highly programmable macromolecules
that can go through conformational changes in response to external
signals. Here we show that a two-dimensional origami rectangle can
be effectively folded into a short, cylindrical tube by connecting
the two opposite edges through the hybridization of linker strands
and that this process can be efficiently reversed via toehold-mediated
strand displacement. The reconfiguration kinetics was experimentally
studied as a function of incubation temperature, initial origami concentration,
missing staples, and origami geometry. A kinetic model was developed
by introducing the <i>j</i> factor to describe the reaction
rates in the cyclization process. We found that the cyclization efficiency
(<i>j</i> factor) increases sharply with temperature and
depends strongly on the structural flexibility and geometry. A simple
mechanical model was used to correlate the observed cyclization efficiency
with origami structure details. The mechanical analysis suggests two
sources of the energy barrier for DNA origami folding: overcoming
global twisting and bending the structure into a circular conformation.
It also provides the first semiquantitative estimation of the rigidity
of DNA interhelix crossovers, an essential element in structural DNA
nanotechnology. This work demonstrates efficient DNA origami reconfiguration,
advances our understanding of the dynamics and mechanical properties
of self-assembled DNA structures, and should be valuable to the field
of DNA nanotechnology
Design Principles of DNA Enzyme-Based Walkers: Translocation Kinetics and Photoregulation
Dynamic DNA enzyme-based walkers
complete their stepwise movements
along the prescribed track through a series of reactions, including
hybridization, enzymatic cleavage, and strand displacement; however,
their overall translocation kinetics is not well understood. Here,
we perform mechanistic studies to elucidate several key parameters
that govern the kinetics and processivity of DNA enzyme-based walkers.
These parameters include DNA enzyme core type and structure, upper
and lower recognition arm lengths, and divalent metal cation species
and concentration. A theoretical model is developed within the framework
of single-molecule kinetics to describe overall translocation kinetics
as well as each reaction step. A better understanding of kinetics
and design parameters enables us to demonstrate a walker movement
near 5 μm at an average speed of ∼1 nm s<sup>–1</sup>. We also show that the translocation kinetics of DNA walkers can
be effectively controlled by external light stimuli using photoisomerizable
azobenzene moieties. A 2-fold increase in the cleavage reaction is
observed when the hairpin stems of enzyme catalytic cores are open
under UV irradiation. This study provides general design guidelines
to construct highly processive, autonomous DNA walker systems and
to regulate their translocation kinetics, which would facilitate the
development of functional DNA walkers
Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts
DNA origami has received enormous
attention for its ability to
program complex nanostructures with a few nanometer precision. Dynamic
origami structures that change conformation in response to environmental
cues or external signals hold great promises in sensing and actuation
at the nanoscale. The reconfiguration mechanism of existing dynamic
origami structures is mostly limited to single-stranded hinges and
relies almost exclusively on DNA hybridization or strand displacement.
Here, we show an alternative approach by demonstrating on-demand conformation
changes with DNA-binding molecules, which intercalate between base
pairs and unwind DNA double helices. The unwinding effect modulates
the helicity mismatch in DNA origami, which significantly influences
the internal stress and the global conformation of the origami structure.
We demonstrate the switching of a polymerized origami nanoribbon between
different twisting states and a well-constrained torsional deformation
in a monomeric origami shaft. The structural transformation is shown
to be reversible, and binding isotherms confirm the reconfiguration
mechanism. This approach provides a rapid and reversible means to
change DNA origami conformation, which can be used for dynamic and
progressive control at the nanoscale