Article
Multidisciplinary Sciences
Chen Zhang, Fujia Tian, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang, Liang Dai
Summary: DNA deformations can occur upon environmental changes, and an increase in salt concentration leads to DNA overwinding. Our magnetic tweezers experiments and simulations demonstrate that the twist change induced by salt can be quantitatively explained by the screening of electrostatic repulsion and the coupling between twist and DNA diameter. We determine the coupling constant and predict the temperature dependence of DNA twist, finding that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.
Article
Physics, Multidisciplinary
Xiao-Wei Qiang, Chen Zhang, Hai-Long Dong, Fu-Jia Tian, Hang Fu, Ya-Jun Yang, Liang Dai, Xing-Hua Zhang, Zhi-Jie Tan
Summary: It has been discovered that both RNA and DNA can change their twist angles through twist-stretch coupling when stretched. The coupling is positive for RNA and negative for DNA. Magnetic tweezers experiments have shown that the coupling of RNA can be reversed from positive to negative by multivalent cations. Molecular dynamics simulations have provided a unified mechanism for the couplings of both RNA and DNA.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Minjung Kim, Sehui Bae, Inrok Oh, Jejoong Yoo, Jun Soo Kim
Summary: This study investigates the sequence-dependent coupling between DNA bending and its helical twist, identifying specific dinucleotide steps with strong twist-bend coupling during DNA minicircle formation. This work provides new insights into the structural responses of DNA to mechanical deformation, particularly in sharply bent DNA minicircles, for nanoscale applications.
Article
Chemistry, Analytical
Shu-Ying Ye, Chang-Gang Pan, Yu-Hua Dai, Guo-Xi Liang
Summary: An ultrasensitive biosensor for the detection of telomerase activity was constructed utilizing gold@Carbon dots nanohybrids (Au@CDs) as a high efficiency electrochemiluminescence (ECL) emitter and nicking enzyme assisted signal amplification (NESA) technology. By employing a dual signal amplification strategy, the biosensor showed excellent sensitivity and detection limit for telomerase activity.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Tamilselvan Rajasekaran, Graeme C. Freestone, Rodrigo Galindo-Murillo, Barbara Lugato, Lorena Rico, Juan C. Salinas, Hans Gaus, Michael T. Migawa, Eric E. Swayze, Thomas E. Cheatham, Stephen Hanessian, Punit P. Seth
Summary: The study investigates the impact of restricting rotation around the sugar-phosphate backbone on the hybridization kinetics of modified oligonucleotides. Experimental and molecular dynamics simulation results suggest that backbone-constrained compounds and conformationally preorganized LNA analogues contribute to improving the hybridization properties of modified oligonucleotides.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
Gaurav Goyal, Elina Ekedahl, My Nyblom, Jens Krog, Erik Frobrant, Magnus Brander, Tsegaye Sewunet, Teerawit Tangkoskul, Christian G. Giske, Linus Sandegren, Visanu Thamlikitkul, Tobias Ambjornsson, Fredrik Westerlund
Summary: Antimicrobial resistance is a growing threat to global health, and effective methods for detecting antimicrobial resistance genes on bacterial plasmids are necessary. In this study, researchers propose a simple and inexpensive assay based on CRISPR/Cas9 excision and DNA combing to detect these genes.
SCIENTIFIC REPORTS
(2022)
Article
Biophysics
Ming-Yue Wang, Wen-Jie Jing, Li-Juan Wang, Li-Ping Jia, Rong-Na Ma, Wei Zhang, Lei Shang, Xiao-Jian Li, Qing-Wang Xue, Huai-Sheng Wang
Summary: A new electrochemiluminescence biosensor was developed for sensitive detection of miRNA-21 using a three-dimensional DNA nanomachine and duplex-specific nuclease (DSN)-mediated target recycle amplification strategy. The biosensor demonstrated excellent performance with a wide linear range and low detection limit, benefiting from the dual amplification strategy. This work provides a new approach for the application of DNA walkers in the construction of various biosensors.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Chemistry, Multidisciplinary
Michael Penth, Kordula Schellnhuber, Roland Bennewitz, Johanna Blass
Summary: DNA has become a powerful platform for designing functional nanodevices with significant differences from native DNA. Through Flow Force Microscopy, high flexibility was observed in DNA origami constructs, contributing to understanding DNA nanomechanics and improving DNA nanodevice design.
Article
Chemistry, Multidisciplinary
Wenxiao Wang, Yu Shen, Fuan Wang, Ying Liu, Xiaoqing Liu
Summary: A versatile approach for fine control of DNA-based hierarchical assembly is developed using dual stimuli and two assembly strategies. By designing functional thrombin aptamer structures on the DNA nanoassembly, precise regulation of thrombin activity can be achieved.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Lohra M. Miller, Benjamin E. Draper, Lauren F. Barnes, Polycarp C. Ofoegbu, Martin F. Jarrold
Summary: Conventional mass spectrometry of nucleic acids is complicated by counter ions, limiting the analysis of DNA size. This study overcomes this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Different charge distributions are observed for DNA plasmids, with a low-charge population resembling compact DNA and a higher-charge population with a broad charge range. The high-charge population is attributed to supercoiled plasmids in random coil configuration, while the low-charge population is attributed to a condensed form of the plasmid.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Soumya P. Tripathy, Manvitha Ponnapati, Suhaas Bhat, Joseph Jacobson, Pranam Chatterjee
Summary: In this study, computational protein modeling tools were used to propose a molecular beacon architecture for high-sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain. By integrating these beacons on a miniaturized total internal reflection fluorescence microscope, the SARS-CoV-2 and pseudotyped SARS-CoV-2 could be detected with limits of detection in the femtomolar range.
Article
Biology
Takehiko Ichikawa, Dong Wang, Keisuke Miyazawa, Kazuki Miyata, Masanobu Oshima, Takeshi Fukuma
Summary: Chemical fixatives have been found to potentially affect the nanoscale structures of cell surfaces by inducing aggregation of membrane proteins. However, research in this area has been limited due to the lack of methods for observing cell surface structures at the nanoscale. In this study, a method using atomic force microscopy and a microporous silicon nitride membrane was developed to observe cell surfaces with high resolution. The results showed that commonly used fixatives increased the size of protrusions on the cell surface, indicating the aggregation of membrane proteins caused by the fixatives.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Swarnadeep Seth, Arthur Rand, Walter Reisner, William B. Dunbar, Robert Sladek, Aniket Bhattacharya
Summary: This study reports the results of Brownian dynamics simulations aimed at identifying key parameters that control the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. The simulation scheme is validated by reproducing and explaining the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on the dsDNA. The effect of the electric field inside and beyond the pores is studied to discriminate protein tags based on their effective charges and masses. The simulation protocols and chosen parameters are justified by calculating the Peclet number, which agrees closely with the experiment. It is demonstrated that the carefully chosen simulation strategies can effectively discriminate different types of neutral and charged tags on a dsDNA construct and provide insights to improve the efficiency and accuracy of an experimental dual-nanopore setup.
SCIENTIFIC REPORTS
(2022)
Article
Chemistry, Multidisciplinary
Yudai Tabuchi, Jay Yang, Masumi Taki
Summary: This study created a DNA-aptamer-type covalent drug which can be deactivated and reactivated through a specific structure, providing a new approach to alleviate irreversible adverse drug effects.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Feng Yang, Ping Wen, Wenwen Jia, Gang Li, Chengfu Yang, Bao Li, Dongling Li, Li Chen
Summary: This research introduces a novel microlens SERS substrate @ Au film detection system, which achieves outstanding SERS performance through optical convergence and enhancement effects of the Au film, while also enhancing signal collection efficiency. The system demonstrates high time stability, low cost, and applicability in diverse practical fields.
Article
Biochemistry & Molecular Biology
Carolina Carrasco, Cesar L. Pastrana, Clara Aicart-Ramos, Sanford H. Leuba, Saleem A. Khan, Fernando Moreno-Herrero
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Alberto Marin-Gonzalez, Cesar L. Pastrana, Rebeca Bocanegra, Alejandro Martin-Gonzalez, J. G. Vilhena, Ruben Perez, Borja Ibarra, Clara Aicart-Ramos, Fernando Moreno-Herrero
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Raquel Arroyo, Mercedes Echaide, Fernando Moreno-Herrero, Jesus Perez-Gil, Paul S. Kingma
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2020)
Article
Biochemistry & Molecular Biology
Oliver J. Wilkinson, Carolina Carrasco, Clara Aicart-Ramos, Fernando Moreno-Herrero, Mark S. Dillingham
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Pilar Gutierrez-Escribano, Silvia Hormeno, Julene Madariaga-Marcos, Roger Sole-Soler, Francis J. O'Reilly, Kyle Morris, Clara Aicart-Ramos, Ricardo Aramayo, Alex Montoya, Holger Kramer, Juri Rappsilber, Jordi Torres-Rosell, Fernando Moreno-Herrero, Luis Aragon
Article
Biochemistry & Molecular Biology
Alberto Marin-Gonzalez, Clara Aicart-Ramos, Mikel Marin-Baquero, Alejandro Martin-Gonzalez, Maarit Suomalainen, Abhilash Korman, J. G. Vilhena, Urs F. Greber, Fernando Moreno-Herrero, Ruben Perez
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biology
Francisco de Asis Balaguer, Clara Aicart-Ramos, Gemma L. M. Fisher, Sara de Braganca, Eva M. Martin-Cuevas, Cesar L. Pastrana, Mark Simon Dillingham, Fernando Moreno-Herrero
Summary: This study investigated the role of CTP binding and hydrolysis in the critical interaction between ParB protein and parS DNA sequences using single-molecule techniques. The research found that the presence of CTP or CTPγS enhances the binding of ParB around parS, and ParB also binds to distal non-specific DNA with the presence of a parS loading site. The results suggest that ParB diffusion on non-specific DNA is consistent with one-dimensional diffusion by a sliding clamp.
Article
Oncology
Samuel D. Zwernik, Beau H. Adams, Daniel A. Raymond, Catherine M. Warner, Amin B. Kassam, Richard A. Rovin, Parvez Akhtar
Summary: Recent studies have shown that Zika virus can enter human glioblastoma cells through the AXL receptor, leading to productive infection, while inhibition of the AXL receptor can significantly weaken virus entry. Knocking out the AXL gene in GBM cells completely eliminates Zika virus infection, inhibits viral replication, and reduces apoptosis. Introducing the AXL receptor into non-expressing cell lines makes the cells susceptible to Zika virus infection.
MOLECULAR THERAPY-ONCOLYTICS
(2021)
Article
Multidisciplinary Sciences
Silvia Hormeno, Oliver J. Wilkinson, Clara Aicart-Ramos, Sahiti Kuppa, Edwin Antony, Mark S. Dillingham, Fernando Moreno-Herrero
Summary: Human DNA helicase B (HELB) plays important regulatory roles in DNA replication and recombination. It interacts with Replication Protein A (RPA) and RPA-single-stranded DNA (ssDNA) filaments to exhibit ATP hydrolysis translocation and helicase activities, and its ability to clear RPA from ssDNA allows other proteins to access these intermediates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Javier Coloma, Nayim Gonzalez-Rodriguez, Francisco A. Balaguer, Karolina Gmurczyk, Clara Aicart-Ramos, oscar M. Nuero, Juan Roman Luque-Ortega, Kimberly Calugaru, Neal F. Lue, Fernando Moreno-Herrero, Oscar Llorca
Summary: Cdc13 plays a crucial role in telomere replication and stability by forming dimers and higher-order complexes, which regulate binding and structure of DNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Sara De Braganc, Clara Aicart-Ramos, Raquel Arribas-Bosacoma, Angel Rivera-Calzada, Juan Pablo Unfried, Laura Prats-Mari, Mikel Marin-Baquero, Puri Fortes, Oscar Llorca, Fernando Moreno-Herrero
Summary: The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). In this study, the contributions of core NHEJ proteins and accessory factors APLF and lncRNA NIHCOLE to DNA synapsis were investigated using magnetic tweezers. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF, and this effect is enhanced by a small structured RNA domain within NIHCOLE. A model is proposed where Ku70-Ku80 can bind DNA, APLF, and structured RNAs simultaneously to promote stable DNA end joining.
Review
Genetics & Heredity
Sara De Braganca, Mark S. Dillingham, Fernando Moreno-Herrero
Summary: Genome integrity and maintenance are crucial for the survival of all organisms. Double-strand breaks (DSBs) are highly toxic DNA lesions, and two major pathways, homologous recombination (HR) and non-homologous end joining (NHEJ), are responsible for repairing DSBs. Single-molecule techniques provide insights into the mechanisms of HR and NHEJ repair.
TRENDS IN GENETICS
(2023)
Review
Biophysics
Alberto Marin-Gonzalez, J. G. Vilhena, Ruben Perez, Fernando Moreno-Herrero
Summary: Understanding the complex mechanical behavior of DNA at different scales requires taking a molecular perspective, which recent single-molecule experiments and molecular dynamics simulations have provided insights into. These studies have identified sequence-dependent properties, effects of cytosine methylation and DNA mismatches, as well as differences in mechanical properties between DNA and double-stranded RNA. Thorough examination of single-molecule literature has led to the establishment of general 'rules' explaining the mechanics of nucleic acids at the base pair level, which can be valuable for designing DNA and RNA nanostructures in the future.
QUARTERLY REVIEWS OF BIOPHYSICS
(2021)