Article
Chemistry, Multidisciplinary
Jialun Liang, Jiaxi Li, Zhensheng Zhong, Thitima Rujiralai, Jie Ma
Summary: The study quantitatively evaluated the hydrodynamic drag of DNA using the tethered-bead assay and demonstrated a linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system in a wide force range (0-110 pN). This research provides insights into the force in flow-cell based single-molecule stretching experiments and establishes flow-cells as a flexible and precise tool for single-molecule force measurements.
Article
Biochemistry & Molecular Biology
Wonje Heo, Jeonghwan Seo, Yoonhee Lee, Yoori Kim
Summary: This paper reviews the advances in single-molecule tools for imaging long genomic DNA and studying dynamic protein interactions. It focuses on three representative techniques: molecular combing, nanochannel confinement, and DNA curtain assays, which elongate individual DNA using fluid-driven force. The paper provides an integrated perspective and direction for future use in dissecting protein function.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Zilong Guo, Haiyan Hong, Hao Sun, Xiaofeng Zhang, Chen-Xu Wu, Bing Li, Yi Cao, Hu Chen
Summary: Single molecule force spectroscopy is a powerful tool for studying protein folding dynamics and other mechanobiological processes, but high force precision does not guarantee high force accuracy. The challenge in magnetic tweezers lies in accurately determining applied forces due to calibration uncertainties.
Article
Chemistry, Multidisciplinary
Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, Guillermo P. Acuna
Summary: This study demonstrates a controlled orientation of single molecules in DNA origami by linking them to oligonucleotide strands and leaving unpaired bases. The number of unpaired bases affects the stretching and orientation of the fluorophore linkers. These findings expand the application of DNA origami in the fabrication of nanodevices involving orientation-dependent molecular interactions.
Article
Physics, Multidisciplinary
Xiaoya Song, Chao Yang, Yuyu Feng, Hu Chen, Yanhui Liu
Summary: Three single-molecule experiments were conducted to investigate the effects of DNA mismatch on DNA hairpin stability, and it was found that DNA mismatch significantly reduced the critical forces of DNA hairpins. The establishment of a phase diagram provided a common rule for the relationship between the position of DNA mismatch and the intermediate state, which not only clarified the non-consensus between the experiments but also guided the design of future single-molecule experiments.
COMMUNICATIONS IN THEORETICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Sung Hyun Kim, Hyunwoo Kim, Hawoong Jeong, Tae-Young Yoon
Summary: The study demonstrates the use of single-molecule FRET technology to encode virtual signals in DNA barcodes, allowing for precise measurement of FRET efficiency for each binding event and differentiation of six DNA barcodes.
Review
Biochemistry & Molecular Biology
Longfu Xu, Matthew T. J. Halma, Gijs J. L. Wuite
Summary: Single-stranded DNA-binding proteins (SSBs) are essential for DNA metabolism and play crucial roles in maintaining genome integrity and coordinating with other proteins involved in DNA replication, recombination, and repair. Recent advances in single-molecule techniques and structural methods have greatly improved our understanding of the binding dynamics and interaction of SSBs with ssDNA and other protein partners. We highlight the central coordination role of SSBs in directly modulating the activities of other proteins and discuss the various modes of interaction between SSBs and their protein partners, providing a comprehensive view of the interaction network shaped by SSBs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Borja Cirera, Martin Wolf, Takashi Kumagai
Summary: The research demonstrates the direct observation of vibrational heating in a single C60 molecule using TERS, revealing qualitatively different heating mechanisms in distinct electron transport regimes. Strong Joule heating occurs in the SMPC regime, while optical heating is predominant in the tunneling regime.
Article
Optics
Shengzhe Pan, Chenxi Hu, Wenbin Zhang, Zhaohan Zhang, Lianrong Zhou, Chenxu Lu, Peifen Lu, Hongcheng Ni, Jian Wu, Feng He
Summary: In this study, we investigate the bond-length-dependent Rabi oscillations in the strong-laser-field dissociation of H-2(+). The coupling of the bond stretching and Rabi oscillations leads to different kinetic energies of the nuclei, while the electron absorbs and emits photons. The resulting proton kinetic energy spectra exhibit rich structures beyond theoretical predictions and provide insights into the bond-breaking mechanism.
LIGHT-SCIENCE & APPLICATIONS
(2023)
Review
Chemistry, Multidisciplinary
William Bro-Jorgensen, Joseph M. Hamill, Rasmus Bro, Gemma C. Solomon
Summary: This tutorial review describes the crucial aspects of applying machine learning to help users avoid common pitfalls. Examples based on single-molecule electron transport experiments demonstrate the application of machine learning and highlight the importance of careful application. The concepts explored are also applicable in other fields with similar data.
CHEMICAL SOCIETY REVIEWS
(2022)
Article
Biophysics
Marvin Freitag, Sigrun Jaklin, Francesco Padovani, Ecaterina Radzichevici, Sarah Zernia, Kurt M. Schmoller, Johannes Stigler
Summary: The conformational changes of coiled-coil domains in structural maintenance of chromosome complexes play a crucial role in their diverse functions. The elbow of the coiled-coil is shown to be a flexible and potentially non-structured feature, which divides the coiled-coil into segments and facilitates large-scale conformational changes. Manipulation of the elbow results in impaired complex function, highlighting the importance of the coiled-coil architecture.
BIOPHYSICAL JOURNAL
(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
Optics
Philippa-Kate Andrew, Allan Raudsepp, Daniel Fan, Urs Staufer, Martin A. K. Williams, Ebubekir Avci
Summary: Optical microrobotics has the potential to improve upon current optical tweezer studies by limiting exposure of biological molecules to laser radiation and overcoming limitations of low forces and unwanted interactions. This research successfully developed two types of microlevers for the first lever-assisted stretches of double-stranded DNA, providing a proof of concept for using optical micromachines in single molecule studies.
Article
Chemistry, Multidisciplinary
Jacob Bauer, Gabriel Zoldak
Summary: Single-molecule force spectroscopy experiments explore protein folding and unfolding using mechanical force. While steered molecular dynamics simulations are informative for understanding the structural aspects, they are computationally expensive. Normal mode analysis, a cheaper alternative, can provide insights that complement MD simulations for protein structural analysis in single-molecule force experiments.
Article
Electrochemistry
Christoph Schiel, Philipp Rahe, Philipp Maass
Summary: We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions. Explicit results are derived for an harmonic attractive and repulsive tip-molecule interaction. Applications of the theory allows one to estimate the type and strength of interactions between the STM tip and the molecule.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
P. S. Alves, O. N. Mesquita, M. S. Rocha
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Optics
T. A. Moura, U. M. S. Andrade, J. B. S. Mendes, M. S. Rocha
Article
Biochemistry & Molecular Biology
J. A. D. Batista, L. Oliveira, T. A. Moura, V. C. dos Anjos, M. J. Bell, M. S. Rocha
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2020)
Article
Optics
U. M. S. Andrade, A. M. Garcia, M. S. Rocha
Summary: The study introduces a Bessel beam optical tweezers setup that can stably trap superparamagnetic beads, with trap stiffness practically independent of beam radius and bead height. Despite the absorption coefficient of the beads, trap stiffness linearly increases with laser power. A geometric optics model accurately predicts optical forces and trap stiffness, advancing the field of optical trapping of absorbing magnetic particles.
Article
Chemistry, Physical
Rayane M. de Oliveira, Tiago A. Moura, Marcio S. Rocha
Summary: This study demonstrates that caffeine enhances the anticancer effects of cisplatin and other platinum-based drugs not only at the cellular level, but also at the molecular level. It acts as an allosteric catalyst, increasing the binding constant between DNA and platinum drugs and interfering with the binding reactions' cooperativity. This research provides new insights into the use of caffeine for chemotherapeutic applications.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Ethe A. Costa, Amanda P. Goncalves, Josiane A. D. Batista, Raniella F. Bazoni, Anesia A. Santos, Marcio S. Rocha
Summary: This study investigates the molecular mechanism of action of the drug chloroquine (CLQ) in its interaction with double-stranded DNA at the single-molecule level, and reveals that the ionic strength of the surrounding medium strongly influences this interaction. Furthermore, the cytotoxicity of CLQ against different cell lines is evaluated and compared to the closely related compound hydroxychloroquine (HCLQ).
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biochemistry & Molecular Biology
U. M. S. Andrade, A. S. B. Castro, P. H. F. Oliveira, L. H. M. da Silva, M. S. Rocha
Summary: We conducted a comprehensive characterization of the molecular interactions between DNA and two imidazolium-based ionic liquids (ILs), and identified DNA compaction at high IL concentrations as a result. By using various techniques, we obtained the changes in mechanical properties of DNA complexes formed with ILs and determined the thermodynamic characteristics and driving forces of the interactions. Our findings provide important insights into the interaction between DNA and imidazolium-based ionic liquids.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Microbiology
Lorena Souza Castro Altoe, Ethe de Araujo Costa, Gabriella Peterlini Tavares, Marcio Santos Rocha, Jose Humberto de Queiroz, Juliana Barbosa Coitinho Goncalves, Suely Gomes de Figueiredo, Jackson Victor de Araujo
Summary: The use of force spectroscopy with optical tweezers is valuable in studying the physical chemistry of DNA interactions with ligands. This study focuses on the poorly understood interactions between helminthophagous fungi enzymes and nucleic acids. The experimental assays show that the fungal protease strongly binds to dsDNA, forming aggregates and altering the DNA's properties. The findings provide molecular-level insights into the pathogenicity of these proteins when applied to target specimens.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Materials Science, Multidisciplinary
Kairon M. Oliveira, Tiago A. Moura, Janaisa L. C. Lucas, Alvaro V. N. C. Teixeira, Marcio S. Rocha, Joaquim B. S. Mendes
Summary: This paper proposes the use of PANI as handles in optical tweezers experiments. The stable trapping and manipulation of PANI beads using optical tweezers are demonstrated for the first time. The results suggest the potential of using semiconductor polymeric materials in optical manipulation and open up new possibilities for related applications.
ACS APPLIED POLYMER MATERIALS
(2023)
Article
Optics
T. A. Moura, U. M. S. Andrade, J. B. S. Mendes, M. S. Rocha
Summary: We demonstrate that optical trapping and manipulation of spherical-shaped semiconductor (germanium) particles can be effectively controlled using optical tweezers based on a highly focused Bessel beam. The behavior of the trapped germanium beads, including stable trapping, oscillatory dynamics, and repulsion, can be modulated by adjusting laser power, beam radius, and trap focal height. The versatility of Bessel beam optical tweezers opens up new possibilities for applications in various fields.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Jefferson V. P. B. Baeta, Ulisses M. S. Andrade, Rayane M. Oliveira, Leandro Oliveira, Anesia A. Santos, Gaspar Diaz-Munoz, Marcio S. Rocha, Marisa A. N. Diaz
Summary: The study found that DPAP has cytotoxic effects on B16F10 melanoma cells and interacts with DNA, causing a bending deformation of the polymer chain and reducing its persistence length. Each DPAP molecule likely occupies a single base pair upon binding to the double helix.
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Physical
R. F. Bazoni, T. A. Moura, M. S. Rocha
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2020)
Article
Physics, Fluids & Plasmas
E. F. Silva, U. M. S. Andrade, K. M. de Oliveira, A. V. N. C. Teixeira, M. S. Rocha
Article
Physics, Fluids & Plasmas
L. Oliveira, J. M. Caquito Jr, M. S. Rocha
Article
Physics, Multidisciplinary
W. H. Campos, T. A. Moura, O. J. B. J. Marques, J. M. Fonseca, W. A. Moura-Melo, M. S. Rocha, J. B. S. Mendes
PHYSICAL REVIEW RESEARCH
(2019)
