Article
Computer Science, Theory & Methods
Shankai Yan, Ka-Chun Wong
Summary: DNA computing is still in its early stages, with high data storage density and efficient random data access. However, its popularity is limited by accessibility, despite its potential for high-throughput parallel computing due to its natural double-helix structure. Its underlying rationale differs from existing electronic computing devices.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2021)
Article
Chemistry, Analytical
Tao Li, Wei Xing, Fengshan Yu, Ziwei Xue, Xingdong Yang, Guizheng Zou, Ye Zhu
Summary: This study proposed a dynamic DNA nanosystem-integrated ratiometric electrochemical biosensor for highly sensitive and selective detection of HIV-DNA. The synergistic effect of the target recycling unit and multipedal DNA walker unit enabled ultrasensitive detection of HIV-DNA.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Yufeng Pei, Tianyuan Bian, Yonglin Liu, Yan Liu, Yujie Xie, Jie Song
Summary: This study developed a real-time, label-free, and force-controlled single-molecule DNA computing method. By using stretching forces and tracking real-time signals, Boolean logic computing was achieved at the single-molecule level with output determined at a single base-pair resolution.
Article
Chemistry, Multidisciplinary
Xiao Rui Liu, Xinpeng Hu, Iong Ying Loh, Zhisong Wang
Summary: The study demonstrates a novel strategy for transforming chemical nanomotors into optical nanomotors, achieving high directional fidelity through optomechanical control while retaining high efficiency performance similar to chemical nanomotors.
Article
Chemistry, Multidisciplinary
Liquan Liu, Qingyi Hu, Wenkai Zhang, Wenhao Li, Wei Zhang, Zhihao Ming, Longjie Li, Na Chen, Hongbo Wang, Xianjin Xiao
Summary: The development of the Clip tool expands the functionality of DNA strand displacement-based nanodevices, achieving multiple regulatory functions such as fine adjustment of reaction rates, allosteric strand displacement, selective activation, and reaction resetting. DNA walking machines constructed using this tool demonstrate controllable walking, concatenation, and programmable pathways, showcasing the versatility of the Clip-toehold-based DNA nanodevices.
Article
Biochemical Research Methods
Helena Hall-Thomsen, Shavier Small, Momcilo Gavrilov, Taekjip Ha, Rebecca Schulman, Pepijn Gerben Moerman
Summary: DNA strand displacement circuits have the potential to replicate the complex regulatory functions of biological reaction networks, but often lack crucial properties. This study introduces an engineered DNA helicase, Rep-X, that can provide energy in a controlled manner to strand displacement networks, allowing the strands to participate in downstream reactions. These findings can guide the design of active DNA strand displacement regulatory networks.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Enqiang Zhu, Xianhang Luo, Chanjuan Liu, Congzhou Chen
Summary: DNA encryption is a new method that enhances information security in DNA nanotechnology. This paper proposes a DNA-strand-displacement-based encryption framework with three main strategies: tri-phase conversion, development of DNA strand displacement molecular modules, and cyclic-shift-based operation. The feasibility of the scheme is validated through simulations and biological experiments.
Article
Biochemistry & Molecular Biology
Shuming Zhang, Xue Xiao, Jingwei Kong, Ke Lu, Shuo-Xing Dou, Peng-Ye Wang, Lu Ma, Yuru Liu, Guohong Li, Wei Li, Huidong Zhang
Summary: Strand displacement DNA synthesis (SDDS) is a crucial step in DNA replication with complex kinetics. Experiments with magnetic tweezers show that the rate and processivity of SDDS are influenced by force and dNTP concentration. Moreover, GC content has a significant impact on the processivity and rate of SDDS and exonuclease activity.
Article
Chemistry, Physical
Louie Slocombe, Max Winokan, Jim Al-Khalili, Marco Sacchi
Summary: This work uses first principles quantum chemistry calculations coupled with an open quantum systems master equation to model wobble mispairing and error incorporation rates in DNA replication. The calculated genetic error formation rates are in excellent agreement with experimental observations. Additionally, the quantum mechanics/molecular mechanics model predicts the presence of a short-lived tunnelling ready configuration in the polymerase active site, significantly increasing the rate of proton transfer.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Automation & Control Systems
Junwei Sun, Haoping Ji, Yanfeng Wang
Summary: The emergence of DNA strand displacement has led to the development of chaotic synchronization techniques. Previous research mainly focused on the synchronization of two three-dimensional chaotic systems using DNA strand displacement. This article introduces the use of four-dimensional chaotic systems and loop controllers to achieve loop synchronization of three 4-D chaotic systems. The results show that strand displacement reactions can realize loop synchronization and the method has robustness when one loop controller is not functioning. This work provides a reference for investigating chaotic synchronization using DNA techniques.
IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS
(2023)
Article
Chemistry, Multidisciplinary
Qiuyan Huang, Jiyeon Kim, Kun Wang, Simon Vecchioni, Yoel P. Ohayon, Nadrian C. Seeman, Natasa Jonoska, Ruojie Sha
Summary: The use of DNA triplex association, combined with toehold-mediated strand displacement, allows for the reconfiguration of dynamic DNA nanostructures through pH alteration. This study demonstrates that pH changes can enable a DNA duplex, with toehold assistance, to displace TFOs from another DNA duplex. The dependence of this process on toehold length is examined, and oscillatory conformational changes between two molecular formations are observed.
Article
Chemistry, Multidisciplinary
Zhi Weng, Hongyan Yu, Wang Luo, Yongcan Guo, Qian Liu, Li Zhang, Zhang Zhang, Ting Wang, Ling Dai, Xi Zhou, Xiaole Han, Luojia Wang, Junjie Li, Yujun Yang, Guoming Xie
Summary: In this study, a regulatory tool called cooperative branch migration (CBM) is introduced to flexibly control DNA strand displacement by regulating the complementarity of branch migration domains. CBM exhibits multifunctional regulatory abilities, including rate fine-tuning and continuous dynamic regulation.
Article
Chemistry, Multidisciplinary
Yunlong Qin, Yu Ouyang, Jianbang Wang, Xinghua Chen, Yang Sung Sohn, Itamar Willner
Summary: The article reports a functional bioreactor hybrid composed of glucose oxidase-loaded ZIF-90 metal-organic framework nanoparticles conjugated to hemin-G-quadruplexes, which can perform transient dissipative biocatalytic cascaded transformations. One system involves the temporal formation and depletion of the bioreactor conjugate operating the nickase-guided transient biocatalytic cascades, while the other demonstrates the transient operation of the two biocatalytic cascades dictated by exonuclease III.
Article
Chemistry, Physical
Hao Hu, Liquan Liu, Lei Zhang, Wei Zhang, Kejun Dong, Bei Yan, Yaoqin Mu, Mengdi Shi, Longjie Li, Xianjin Xiao
Summary: In this study, we constructed DNA circuits with low leakage by using locked nucleic acids (LNA) to inhibit the breathing effect. Various low-leakage DNA circuits were successfully built, and our strategy did not affect the desired main reactions.
Article
Biochemical Research Methods
Boya Wang, Chris Thachuk, David Soloveichik
Summary: Molecular control circuits embedded within chemical systems have transformative applications in synthetic biology, medicine, and other fields, but understanding the collective behavior of components is challenging due to combinatorial complexity. DNA strand displacement reactions have been used to construct large molecular systems, but they are susceptible to undesired interactions. We systematize the properties of enthalpy-neutral strand displacement cascades and develop a taxonomy for desired and undesired properties, guiding the engineering of efficient molecular algorithms.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kamaludin Dingle, Fatme Ghaddar, Petr Sulc, Ard A. Louis
Summary: Developmental bias is the primary explanation for the occupation of the RNA secondary structure morphospace, with only the most frequent structures appearing in nature and a small number of random sequences needed to produce all observed RNA secondary structures. These patterns are accurately predicted by the likelihood of structures appearing upon a uniform random sampling of sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Wilber Lim, Ferdinando Randisi, Jonathan P. K. Doye, Ard A. Louis
Summary: Thymine dimers are found to affect the supercoiling of DNA, causing changes in the occurrence of plectonemes and bubbles. The presence of thymine dimers increases the probability of localized tip-bubbles, facilitating repair enzyme binding and damage repair. The interplay between supercoiling and local defects plays an important role in DNA damage repair systems.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Iain G. Johnston, Kamaludin Dingle, Sam F. Greenbury, Chico Q. Camargo, Jonathan P. K. Doye, Sebastian E. Ahnert, Ard A. Louis
Summary: Engineers design modular and symmetric systems to increase robustness and facilitate alterations. Similarly, biological structures also exhibit modularity and symmetry, but the origin of these trends is not well understood. This study introduces a nonadaptive hypothesis based on an algorithmic perspective, suggesting that the preference for symmetric structures is not only driven by natural selection, but also by the lower information complexity required to encode them. Extensive biological data support this hypothesis, showing an exponential bias towards simpler and more symmetric phenotypes in protein complexes, RNA secondary structures, and gene regulatory networks. Lower descriptional complexity also correlates with higher mutational robustness.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Letter
Multidisciplinary Sciences
Iain G. Johnston, Kamaludin Dingle, Sam F. Greenbury, Chico Q. Camargo, Jonathan P. K. Doye, Sebastian E. Ahnert, Ard A. Louis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis, Petr Sulc
Summary: We explored the design space for self-assembled multicomponent objects, ranging from unique building blocks to minimum number of distinct building blocks defining the target structure. By using patchy particle simulations, we analyzed the assembly dynamics of different solutions and their influence on the kinetics and yield of the target assembly. Our findings show that resource-saving solutions with minimum distinct blocks can perform just as well or faster than designs with unique building blocks. We also designed multifarious structures by sharing building blocks between different targets, and investigated the realization of multicomponent shapes using DNA nanostructures as building blocks through coarse-grained DNA simulations.
Article
Chemistry, Physical
Benjamin Qureshi, Jordan Juritz, Jenny M. Poulton, Adrian Beersing-Vasquez, Thomas E. Ouldridge
Summary: Copolymers play a vital role in both living and synthetic systems. We have developed a general method for analyzing copolymerization processes, which can be used to derive thermodynamic, kinetic, and statistical quantities from the model definition.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Tomislav Plesa, Alexander Dack, Thomas E. Ouldridge
Summary: A central goal of synthetic biology is to design molecular controllers that can manipulate intracellular networks. Integral-feedback controllers (IFCs) have been proposed to control molecular abundances in the absence of detailed knowledge about intracellular networks. These controllers can maintain accuracy despite the uncertainties in the networks, but stability is also crucial.
JOURNAL OF MATHEMATICAL CHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Christina Jayachandran, Arindam Ghosh, Meenakshi Prabhune, Jonathan Bath, Andrew J. J. Turberfield, Lara Hauke, Jorg Enderlein, Florian Rehfeldt, Christoph F. F. Schmidt
Summary: Mechanical forces play a critical role in various biological processes, including wound healing, tumor formation, cell migration, and differentiation. This study presents a FRET-based DNA-protein tension sensor designed to measure transient forces in actin networks. The sensor utilizes two actin-binding motifs with a fast off-rate attached to a central DNA hairpin loop. The conformational state of the sensor is determined using fluorescence lifetime imaging, enabling robust measurements even with intensity variations. The sensor's potential is demonstrated through confocal microscopy and monitoring of crosslinking activity in vitro using bulk rheology.
ACS APPLIED NANO MATERIALS
(2023)
Article
Physics, Fluids & Plasmas
Ian Seet, Thomas E. Ouldridge, Jonathan P. K. Doye
Summary: Landauer's principle sets a lower limit on the work required for logically irreversible operations, which can be overcome by using logically reversible gates. This paper presents the design and simulation of molecular mechanical logic gates that approach the limits of thermodynamic reversibility, even in the presence of thermal noise. The study demonstrates the feasibility of constructing and simulating arbitrary combinatorial reversible circuits with these gates.
Article
Multidisciplinary Sciences
Vaibhav Mohanty, Sam F. Greenbury, Tasmin Sarkany, Shyam Narayanan, Kamaludin Dingle, Sebastian E. Ahnert, Ard A. Louis
Summary: Phenotype robustness is crucial for the neutral exploration of novel phenotypic variation. The maximal phenotype robustness occurs when genotypes are organized as bricklayer's graphs. The RNA secondary structure and the hydrophobic-polar (HP) model for protein folding can exhibit the maximum phenotype robustness.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Physics, Fluids & Plasmas
Vaibhav Mohanty, Ard A. Louis
Summary: Investigated the robustness of spin glasses in the glassy phase, finding high robustness and topological properties that scale similarly to other systems.
Article
Biochemical Research Methods
Alicia Climent-Catala, Ivan Casas-Rodrigo, Suhasini Iyer, Rodrigo Ledesma-Amaro, Thomas E. Ouldridge
Summary: This study investigates the performance of RNA light-up aptamers as transcriptional fluorescent reporters and compares them to protein-based reporters. The researchers found that RNA light-up aptamers exhibit suitable characteristics as transcriptional reporters over time and at the single-cell level, with higher variability in a population compared to protein-based reporters. Additionally, these RNA aptamers may offer faster dynamics compared to fluorescent proteins in E. coli. The implementation of these transcriptional reporters can facilitate transcription-based studies and expand the use of RNA-based circuits in bacterial cells.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Thomas E. Ouldridge, David H. Wolpert
Summary: This paper investigates the operational constraints of real-world computers that result in nonzero entropy production. The author first derives the nonzero entropy production caused by the locality and periodicity constraints in deterministic finite automata (DFA). The author then classifies the languages recognized by DFA into two categories based on the presence or absence of nonzero entropy production. The paper also demonstrates the thermodynamic advantages of implementing a DFA with a physical process that is agnostic about the inputs it processes.
NEW JOURNAL OF PHYSICS
(2023)
Article
Multidisciplinary Sciences
Kamaludin Dingle, Javor K. Novev, Sebastian E. Ahnert, Ard A. Louis
Summary: This study presents an application of algorithmic information theory and Kolmogorov complexity in the analysis of genotype-phenotype maps. The authors derive a simplicity bias in these maps and provide an upper bound on the probability of phenotype transition. They demonstrate the practical applicability of their findings in predicting phenotype transition probabilities in RNA and protein simulations. This research contributes to a better understanding of genotype-phenotype maps and has potential implications for predicting transitions solely based on phenotype information.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)