12 research outputs found
Length-Independent Charge Transport in Chimeric Molecular Wires
Advanced molecular electronic components remain vital for the next generation of miniaturized integrated circuits. Thus, much research effort has been devoted to the discovery of lossless molecular wires, for which the charge transport rate or conductivity is not attenuated with length in the tunneling regime. Herein, we report the synthesis and electrochemical interrogation of DNA-like molecular wires. We determine that the rate of electron transfer through these constructs is independent of their length and propose a plausible mechanism to explain our findings. The reported approach holds relevance for the development of high-performance molecular electronic components and the fundamental study of charge transport phenomena in organic semiconductors
Effects of Concentration and Temperature on DNA Hybridization by Two Closely Related Sequences via Large-Scale Coarse-Grained Simulations
A newly developed coarse-grained
model called BioModi is utilized
to elucidate the effects of temperature and concentration on DNA hybridization
in self-assembly. Large-scale simulations demonstrate that complementary
strands of either the tetrablock sequence or randomized sequence with
equivalent number of cytosine or guanine nucleotides can form completely
hybridized double helices. Even though the end states are the same
for the two sequences, there exist multiple kinetic pathways that
are populated with a wider range of transient aggregates of different
sizes in the system of random sequences compared to that of the tetrablock
sequence. The ability of these aggregates to undergo the strand displacement
mechanism to form only double helices depends upon the temperature
and DNA concentration. On one hand, low temperatures and high concentrations
drive the formation and enhance stability of large aggregating species.
On the other hand, high temperatures destabilize base-pair interactions
and large aggregates. There exists an optimal range of moderate temperatures
and low concentrations that allow minimization of large aggregate
formation and maximization of fully hybridized dimers. Such investigation
on structural dynamics of aggregating species by two closely related
sequences during the self-assembly process demonstrates the importance
of sequence design in avoiding the formation of metastable species.
Finally, from kinetic modeling of self-assembly dynamics, the activation
energy for the formation of double helices was found to be in agreement
with experimental results. The framework developed in this work can
be applied to the future design of DNA nanostructures in both fields
of structural DNA nanotechnology and dynamic DNA nanotechnology wherein
equilibrium end states and nonequilibrium dynamics are equally important
requiring investigation in cooperation
Coarse-Grained Simulation Study of Sequence Effects on DNA Hybridization in a Concentrated Environment
A novel
coarse-grained model is developed to elucidate thermodynamics
and kinetic mechanisms of DNA self-assembly. It accounts for sequence
and solvent conditions to capture key experimental results such as
sequence-dependent thermal property and salt-dependent persistence
length of ssDNA and dsDNA. Moreover, constant-temperature simulations
on two single strands of a homogeneous sequence show two main mechanisms
of hybridization: a slow slithering mechanism and a one-order faster
zippering mechanism. Furthermore, large-scale simulations at a high
DNA strand concentration demonstrate that DNA self-assembly is a robust
and enthalpically driven process in which the formation of double
helices is deciphered to occur via multiple self-assembly pathways
including the strand displacement mechanism. However, sequence plays
an important role in shifting the majority of one pathway over the
others and controlling size distribution of self-assembled aggregates.
This study yields a complex picture on the role of sequence on programmable
self-assembly and demonstrates a promising simulation tool that is
suitable for studies in DNA nanotechnology
Coarse-Grained Simulation Study of Sequence Effects on DNA Hybridization in a Concentrated Environment
A novel
coarse-grained model is developed to elucidate thermodynamics
and kinetic mechanisms of DNA self-assembly. It accounts for sequence
and solvent conditions to capture key experimental results such as
sequence-dependent thermal property and salt-dependent persistence
length of ssDNA and dsDNA. Moreover, constant-temperature simulations
on two single strands of a homogeneous sequence show two main mechanisms
of hybridization: a slow slithering mechanism and a one-order faster
zippering mechanism. Furthermore, large-scale simulations at a high
DNA strand concentration demonstrate that DNA self-assembly is a robust
and enthalpically driven process in which the formation of double
helices is deciphered to occur via multiple self-assembly pathways
including the strand displacement mechanism. However, sequence plays
an important role in shifting the majority of one pathway over the
others and controlling size distribution of self-assembled aggregates.
This study yields a complex picture on the role of sequence on programmable
self-assembly and demonstrates a promising simulation tool that is
suitable for studies in DNA nanotechnology
Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations
Using a novel coarse-grained model,
large-scale molecular dynamics
simulations were performed to examine self-assembly of 800 peptide
amphiphiles (sequence palmitoyl-V<sub>3</sub>A<sub>3</sub>E<sub>3</sub>). Under suitable physiological conditions, these molecules readily
assemble into nanofibers leading to hydrogel construction as observed
in experiments. Our simulations capture this spontaneous self-assembly
process, including formation of secondary structure, to identify
morphological transitions of distinctive nanostructures. As the hydrophobic
interaction is increased, progression from open networks of secondary
structures toward closed cylindrical nanostructures containing either
β-sheets or random coils are observed. Moreover, temperature
effects are also determined to play an important role in regulating
formation of secondary structures within those nanostructures. These
understandings of the molecular interactions involved and the role
of environmental factors on hydrogel formation provide useful insight
for development of innovative smart biomaterials for biomedical applications
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Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates.
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks
A Tail of Two Peptide Amphiphiles: Effect of Conjugation with Hydrophobic Polymer on Folding of Peptide Sequences
Peptide amphiphiles (PA) offer the
potential of incorporating biological
function into synthetic materials for tissue engineering in regenerative
medicine. These hybrid conjugates are known to undergo self-assembly
starting from single molecules to nanofibers before turning into hydrogel
scaffoldsî—¸such a process involves conformational changes in
secondary structures of peptides. Therefore, insights on the ability
of peptide amphiphiles to form secondary structure as single molecules
are useful for understanding self-assembly behavior. We report here
a molecular simulation study of peptide folding by two PA sequences,
each contains an alkyl tail and short peptide segment. The alkyl tail
is observed to play two opposing roles in modulating sequence-dependent
folding kinetics and thermodynamics. On one hand, it restricts conformational
freedom reducing the entropic cost of folding, which is thus promoted.
On the other hand, it acts as an interaction site with nonpolar peptide
residues, blocking the peptide from helix nucleation, which reduces
folding
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates
Perylene-3,4,9,10-tetracarboxylic diimides (PTCDIs) are a well-known class of organic materials. Recently, these molecules have been incorporated within DNA as base surrogates, finding ready applications as probes of DNA structure and function. However, the assembly dynamics and kinetics of PTCDI DNA base surrogates have received little attention to date. Herein, we employ constant temperature molecular dynamics simulations to gain an improved understanding of the assembly of PTCDI dimers and trimers. We also use replica-exchange molecular dynamics simulations to elucidate the energetic landscape dictating the formation of stacked PTCDI structures. Our studies provide insight into the equilibrium configurations of multimeric PTCDIs and hold implications for the construction of DNA-inspired systems from perylene-derived organic semiconductor building blocks