Article
Chemistry, Multidisciplinary
Yoshiya Kikukawa, Ryoji Kawazoe, Ryo Miyahara, Takato Sakurada, Yusuke Nagata, Shigeki Sasaki, Yosuke Taniguchi
Summary: In this study, a method for detecting the presence of 8-oxo-2'-deoxyguanosine in DNA was developed, and the signal was successfully amplified. This has important implications for elucidating the pathogenesis of various diseases.
CHEMICAL COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Makusu Tsutsui, Akihide Arima, Kazumichi Yokota, Yoshinobu Baba, Tomoji Kawai
Summary: This study evaluates the heating phenomenon caused by diffusive ion transport in nanoscale conduits using thermocouple-embedded SiNx pores. The research found steady-state ionic heat dissipation in confined nanospace. Additionally, smaller pores exhibited higher heating efficiency due to a decrease in through-water thermal conduction.
Article
Chemistry, Multidisciplinary
Victoria E. Paluzzi, Cuizheng Zhang, Chengde Mao
Summary: Small ssDNA circles are difficult to prepare, as they often form concatemers instead of monomeric circles. This study presents a simple method to overcome this problem by designing complementary linker molecules. The method allows for the enzymatic ligation of ssDNA as short as 16 nts into monomeric circles at high concentration and high yield.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Physical
Nicholas M. Gravina, James C. Gumbart, Harold D. Kim
Summary: This study investigates the interactions between DNA sticky ends using the coarse-grained oxDNA model, finding that the orientation of double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind. Specifically, the binding time is fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Fatih N. Gur, Susanne Kempter, Florian Schueder, Christoph Sikeler, Maximilian J. Urban, Ralf Jungmann, Philipp C. Nickels, Tim Liedl
Summary: The study demonstrates a DNA origami switch that utilizes the transition from double-stranded DNA to single-stranded DNA to drive a reversible conformational change. By using the unique properties of DNA, the switch exerts a contractive force produced by the extended single-stranded DNA to achieve large-scale motion. The operation of this switch is shown through various microscopy techniques, illustrating the intricate forces at play in nanoscale physical systems operating in fluids.
ADVANCED MATERIALS
(2021)
Review
Biochemistry & Molecular Biology
Jun-Tao Guo, Fareeha Malik
Summary: Single-stranded DNA binding proteins (SSBs) play critical roles in maintaining genome stability and transcriptional regulation, and machine learning-based approaches have been developed for predicting SSBs from double-stranded DNA binding proteins (DSBs).
Article
Multidisciplinary Sciences
Felipe Rivas, Paul L. DeAngelis, Elaheh Rahbar, Adam R. Hall
Summary: In this study, we used model quasi-monodisperse HA polymers to investigate the dependence of HA signal characteristics on various SS-nanopore measurement conditions. Our findings provide important insights for improving the signal-to-noise ratio, resolution, and sensitivity of HA analysis with SS-nanopores.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Amedeo Capobianco, Alessandro Landi, Andrea Peluso
Summary: Molecular dynamics simulations and quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations similar to crystallographic B-DNA in solution. Single strands rich in adjacent purine nucleobases have more regular arrangements, and poly-thymine single strands also retain helical structure in solution.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Ryan J. Sapia, Colin Campbell, Adam J. Reed, Vladimir B. Tsvetkov, Yulia Gerasimova
Summary: GelRed is a widely used nucleic acid-binding dye that preferentially binds to thymine-rich sequences in DNA. The interactions between GelRed and oligothymidylate are likely stabilized by electrostatic interactions and hydrogen bonding. The molecular dynamic simulations propose a possible structure of the GelRed-oligothymidilate complex.
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
Jae Young Lee, Myoungseok Kim, Chanseok Lee, Do-Nyun Kim
Summary: Precise engineering of DNA structures is increasingly important in biomolecular applications, with single-stranded DNA playing a key role in providing high controllability of critical structural features. The computational model of single-stranded DNA presented in this study allows for harnessing its characteristics for structural applications, enabling the construction of structural models across length scales. The programmability of structural bending, twisting, and persistence length by implementing single-stranded DNA in various DNA structures has significant implications for expanding the design and analysis boundaries of DNA nanotechnology.
Article
Physics, Fluids & Plasmas
Alessandro Fiasconaro, Fernando Falo
Summary: In this study, the relationship between the end-to-end distance and the applied force of an extensible discrete wormlike chain polymer was calculated using both numerical and analytical methods. The numerical approach used the transfer matrix formalism to obtain an exact calculation of the partition function, while the analytical derivations generalized the simple phenomenological formulas commonly used. The obtained formulas are simple enough to be applied in fitting experimental data, and the results showed that the elastic parameters obtained are consistent with previous measurements and have significantly improved accuracy in a wide range of chain extensibility.
Article
Biochemistry & Molecular Biology
Fadia Ibrahim, Jan Oppelt, Manolis Maragkakis, Zissimos Mourelatos
Summary: Direct sequencing of single, native RNA molecules through nanopores has the potential to revolutionize research in RNA biology and clinical diagnostics. TERA-Seq is a new platform that overcomes limitations of existing methods, allowing for comprehensive characterization of both poly- and non-polyadenylated RNA molecules and accurate identification of their native 5' and 3' ends. By ligating unique adapters to transcripts, TERA-Seq reveals insights into RNA processing, decay, and mRNA variation at the single molecule level.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Physical
Xun Gong, Nicholas Renegar, Retsef Levi, Michael S. Strano
Summary: Nanoparticle corona phase design allows for molecular recognition for sensing applications. In this study, the largest DNA-SWCNT PL response library was generated and machine learning techniques were utilized to understand the dependence of molecular recognition and DNA sequence.
NPJ COMPUTATIONAL MATERIALS
(2022)
Article
Virology
Elizabeth T. Ogunbunmi, Aaron P. Roznowski, Bentley A. Fane
Summary: Most icosahedral viruses condense their genomes into volume-constrained capsids, but ssDNA viruses have specific genome biosynthesis and packaging mechanisms. The packaging of ssDNA genomes combines elements from both dsDNA and ssRNA systems, potentially affecting both packaging and postpackaging phenomena.
JOURNAL OF VIROLOGY
(2021)
Article
Chemistry, Multidisciplinary
Simona Ranallo, Daniela Sorrentino, Elisabetta Delibato, Gianfranco Ercolani, Kevin W. Plaxco, Francesco Ricci
Summary: Here we report the design and optimization of an antibody-responsive, DNA-based device that enables communication between non-interacting proteins. The device recognizes and binds a specific antibody, causing a conformational change that releases a DNA strand regulating the activity of a target protein. We demonstrate the antibody-induced control of thrombin and Taq DNA polymerase, showcasing the versatility of this strategy in regulating protein-protein communication in artificial networks.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Multidisciplinary Sciences
Alex M. Downs, Julian Gerson, Kaylyn K. Leung, Kevin M. Honeywell, Tod Kippin, Kevin W. Plaxco
Summary: Electrochemical aptamer-based (EAB) sensors show great potential for real-time and high frequency measurement of pharmaceuticals and metabolites in the living body. This study investigates the quantification using EAB sensors and examines the impact of media selection and temperature on measurement performance. The results demonstrate the accuracy of better than +/- 10% for the measurement of vancomycin using freshly-collected, undiluted whole blood at body temperature. Matching the temperature of calibration curve collection to the measurement temperature improves quantification and calibrating in freshly collected blood can also enhance the accuracy. The use of non-blood proxy media for calibration is also explored.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Vinicius G. Contessoto, Ryan R. Cheng, Jose N. Onuchic
Summary: Recent efforts have focused on understanding the 3D organization of the genome and how this structure impacts nuclear function. Experimental techniques combining DNA proximity ligation with high-throughput sequencing, such as Hi-C, have improved knowledge about chromatin organization. Theoretical modeling is necessary to determine structural ensembles consistent with experimental data, providing insight into the physical mechanisms governing genome architecture.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Yuyang Wu, Simona Ranallo, Erica Del Grosso, Alejandro Chamoro-Garcia, Herbert L. Ennis, Nenad Milosavic, Kyungae Yang, Tod Kippin, Francesco Ricci, Milan Stojanovic, Kevin W. Plaxco
Summary: Electrochemical aptamer-based (EAB) sensors utilize conformational changes to transduce target recognition into electrochemical output, supporting high-frequency molecular measurements and working in complex environments. However, modification of the aptamer is required to achieve the necessary conformational change and balance affinity and signal gain.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Microbiology
Avi Flamholz, Samuel Saccomano, Kevin Cash, Dianne K. Newman
Summary: From a metabolic perspective, molecular oxygen (O-2) is vital in microbial physiology, but its measurement can be complicated by interactions with bacterial secretions. This study found that certain bacterial metabolites, such as phenazines and flavins, quench phosphorescent O-2 probes, leading to inaccurate measurements. Careful control and custom probe design are necessary for accurate O-2 measurements in the presence of bacteria.
Review
Chemistry, Multidisciplinary
Alex M. Downs, Kevin W. Plaxco
Summary: Electrochemical aptamer-based sensors provide a promising approach for real-time molecular monitoring, offering the ability to measure independently of chemical reactivity and supporting in vivo measurements. Despite significant progress, there are still limitations such as short measurement duration and challenges in obtaining high-performance aptamers for new targets.
Article
Chemistry, Multidisciplinary
Tony Tien, Samuel C. Saccomano, Pilar A. Martin, Madeleine S. Armstrong, Robert K. Prud'homme, Kevin J. Cash
Summary: Flash nanoprecipitation (FNP) is an efficient and scalable method for nanoparticle synthesis that has been successfully applied to fabricate nanosensors for measuring oxygen concentration in microbial metabolism. FNP improves replicability and consistency, enabling the production of sensors that respond to oxygen concentration in gas-bubbled solutions and microbial environments.
Article
Biochemical Research Methods
Claudio Parolo, Andrea Idili, Jason Heikenfeld, Kevin W. Plaxco
Summary: The functionality of lab on a chip (LOC) devices has expanded in recent years, providing scientists and developers with versatile platforms for various chemical and biological applications. However, real-time molecular measurements, which are crucial for guiding chemical responses, are still lacking in this field. Among the general sensing strategies, those relying on binding-induced conformational change of bioreceptors are expected to be the most successful in providing LOCs with real-time molecular monitoring capabilities.
Article
Chemistry, Multidisciplinary
Alejandro Chamorro-Garcia, Julian Gerson, Charlotte Flatebo, Lisa Fetter, Alex M. Downs, Nicole Emmons, Herbert L. Ennis, Nenad Milosavic, Kyungae Yang, Milan Stojanovic, Francesco Ricci, Tod E. Kippin, Kevin W. Plaxco
Summary: This study develops an electrochemical aptamer-based (EAB) sensor for real-time monitoring of drug levels in the living body. The sensor has wide applicability and high precision with seconds-resolved measurements.
Article
Multidisciplinary Sciences
Sophia L. Bidinger, Scott T. Keene, Sanggil Han, Kevin W. Plaxco, George G. Malliaras, Tawfique Hasan
Summary: This study demonstrates the translation of the AC pulsed potential approach to an organic electrochemical transistor (OECT) and shows the current modulation effect achieved through aptamer functionalization. Unlike traditional EAB sensors, this aptamer-based OECT sensor maintains stable output current even with miniaturization.
Review
Infectious Diseases
Ruvimbo Dephine Mishi, Michael Andrew Stokes, Craig Anthony Campbell, Kevin William Plaxco, Sophie Lena Stocker
Summary: Therapeutic drug monitoring (TDM) is important for optimizing drug exposure in critically ill patients. This paper explores the potential of biosensors as a solution to current challenges in measuring plasma drug concentrations and discusses their application in TDM of antibiotics. The authors argue that biosensors hold great promise for enhancing drug exposure optimization in critically ill patients.
Article
Biochemical Research Methods
Mark Friedel, Benjamin Werbovetz, Amy Drexelius, Zach Watkins, Ahilya Bali, Kevin W. Plaxco, Jason Heikenfeld
Summary: The ability to continuously collect diagnostic information from the body during daily activity has revolutionized health and disease monitoring. This study presents the first report of real-time human molecular data collected using electrochemical aptamer sensors, demonstrating their ability to measure the concentration of phenylalanine in dermal interstitial fluid after an oral bolus. The study also achieves an important milestone in moving such sensors to the clinic by demonstrating 90 days dry room-temperature shelf storage.
Article
Chemistry, Analytical
Kaylyn K. Leung, Julian Gerson, Nicole Emmons, Brian Roehrich, Elsi Verrinder, Lisa C. Fetter, Tod E. Kippin, Kevin W. Plaxco
Summary: Electrochemical, aptamer-based (EAB) sensors are a versatile molecular monitoring technology that can achieve high-frequency, real-time measurements within the living body. The positioning of the electrodes within or outside the catheter significantly affects the performance of the sensor, with external placement improving signal-to-noise ratio. The size of the counter electrode does not need to be larger than the working electrode. These findings have implications for the design of various electrochemical biosensors.
Article
Chemistry, Multidisciplinary
Alejandro Chamorro-Garcia, Claudio Parolo, Gabriel Ortega, Andrea Idili, Joshua Green, Francesco Ricci, Kevin W. Plaxco
Summary: Biosensors and bioassays that use proteins and nucleic acids to detect specific molecular targets have limitations in sensitivity to small variations in target concentration. This study introduces the sequestration mechanism to improve the responsiveness of these technologies, narrowing the dynamic range and enhancing the ability to measure small changes in target concentration.
Article
Chemistry, Multidisciplinary
Shaoguang Li, Lancy Lin, Xueman Chang, Zhixiao Si, Kevin W. Plaxco, Michelle Khine, Hui Li, Fan Xia
Summary: Using a wrinkled gold film to immobilize more DNA probes, the proposed E-AB sensors show increased sensitivity and accuracy, with a 5.5-fold increase in surface area and up to a 10-fold increase in current.