Article
Chemistry, Physical
Aderik Voorspoels, Jocelyne Vreede, Enrico Carlon
Summary: All-atom simulations are accurate but computationally expensive for studying nucleic acids. The RBB-NA algorithm controls rigid base parameters and allows for exploration of the high deformation regime, providing insights into the structure and dynamics of locally strongly deformed nucleic acids.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Chemistry, Multidisciplinary
Fei Ding, Shuangye Zhang, Qian Chen, Hao Feng, Zhilei Ge, Xiaolei Zuo, Chunhai Fan, Qian Li, Qiang Xia
Summary: Programmable nucleic acid nanotechnology allows the customization of synthetic nucleic acid nanodevices with unprecedented precision, showing potential for precise immunoengineering.
Article
Chemistry, Multidisciplinary
Obianuju A. Nwokolo, Brant Kidd, Te'Kara Allen, Alexander S. Minasyan, Suchitra Vardelly, Kristopher D. Johnson, Irina V. Nesterova
Summary: In this study, a memory-based sensor was designed based on the unique kinetic properties of nucleic acid quadruplexes to measure heat changes in small open systems. The sensors are biocompatible, operate homogeneously, and measure small heats released over long time periods, and have been successfully applied to water/propanol mixing and ligand/protein binding.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Analytical
Siyu Chen, Bo Gong, Cong Zhu, Chunyang Lei, Zhou Nie
Summary: Nucleic acid molecules possess attractive properties for biosensing and bioimaging due to their high designability and structural predictability. CRISPR-Cas systems, with high programmability and flexibility, recognize and cleave nucleic acid targets and have been engineered as multifunctional tools. Integration of nucleic acids with CRISPR-Cas systems has advanced biosensing and bioimaging methodologies, holding great promise in biochemical research and clinical diagnosis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Julia Dietzsch, David Bialas, Johannes Bandorf, Frank Wuerthner, Claudia Hoebartner
Summary: This study reports the tuning of exciton coupling by changing the double helix conformation. Different arrangements of dyes were achieved by changing the backbone constitution and geometry of nucleic acids, resulting in distinct optical characteristics.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Rachelle Turiello, Leah M. Dignan, Brayton Thompson, Melinda Poulter, Jeff Hickey, Jeff Chapman, James P. Landers
Summary: This article describes an automatable rotationally driven microfluidic platform for efficient extraction of SARS-CoV-2 RNA from multiple sample types. The method enables rapid enrichment and extraction of RNA, allowing reliable detection of SARS-CoV-2 using real-time RT-PCR.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Tina Y. Liu, Gavin J. Knott, Dylan C. J. Smock, John J. Desmarais, Sungmin Son, Abdul Bhuiya, Shrutee Jakhanwal, Noam Prywes, Shreeya Agrawal, Maria Diaz de Leon Derby, Neil A. Switz, Maxim Armstrong, Andrew R. Harris, Emeric J. Charles, Brittney W. Thornton, Parinaz Fozouni, Jeffrey Shu, Stephanie Stephens, G. Renuka Kumar, Chunyu Zhao, Amanda Mok, Anthony T. Iavarone, Arturo M. Escajeda, Roger McIntosh, Shin E. Kim, Eli J. Dugan, Katherine S. Pollard, Ming X. Tan, Melanie Ott, Daniel A. Fletcher, Liana F. Lareau, Patrick D. Hsu, David F. Savage, Jennifer A. Doudna
Summary: The direct, amplification-free detection of RNA through CRISPR nucleases enables rapid and sensitive RNA detection, particularly suitable for point-of-care infection diagnosis.
NATURE CHEMICAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Siqi Gao, Ranfeng Wu, Qiang Zhang
Summary: This article introduces a controllable DNA cross circuit based on a new control method and realizes a programmable DNA tile self-assembly strategy by integrating a DNA cross circuit and DNA tile self-assembly. The design of this system provides a new idea for generating dynamic and controllable trigger elements and broadens the programmable range of stimuli-responsive self-assembly.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Biology
Hajime Shinoda, Tatsuya Iida, Asami Makino, Mami Yoshimura, Junichiro Ishikawa, Jun Ando, Kazue Murai, Katsumi Sugiyama, Yukiko Muramoto, Masahiro Nakano, Kotaro Kiga, Longzhu Cui, Osamu Nureki, Hiroaki Takeuchi, Takeshi Noda, Hiroshi Nishimasu, Rikiya Watanabe
Summary: opn-SATORI is an automated amplification-free digital RNA detection platform that utilizes CRISPR-Cas13a and microchamber device to complete the detection process from sample mixing to RNA quantification in a short period of time. It is capable of detecting SARS-CoV-2 genomic RNA with a low limit of detection and discriminating between variants with high accuracy.
COMMUNICATIONS BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Huating Kong, Bo Sun, Feng Yu, Qisheng Wang, Kai Xia, Dawei Jiang
Summary: DNA is a robust material with unique properties, making it suitable for building various nanoscale structures and devices. Structural DNA nanotechnology has found applications in computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery. The goal of structural DNA nanotechnology is to use DNA molecules to construct three-dimensional crystals as molecular scaffolds for precise alignment and collection of desired molecules. This review showcases different 3D DNA crystals, discussing their design, optimization, applications, and crystallization conditions, as well as the history of nucleic acid crystallography and potential future directions in the era of nanotechnology.
Article
Nanoscience & Nanotechnology
Marta Broto, Michael M. Kaminski, Christopher Adrianus, Nayoung Kim, Robert Greensmith, Schan Dissanayake-Perera, Alexander J. Schubert, Xiao Tan, Hyemin Kim, Anand S. Dighe, James J. Collins, Molly M. Stevens
Summary: This study combines CRISPR-Cas reaction with nanozyme-linked ELISA to achieve quantitative detection of Cas13-mediated RNA detection through catalytic metallic nanoparticles at room temperature (CrisprZyme). The study shows that CrisprZyme is adaptable to lateral flow reading and different Cas enzymes, and can detect various non-coding RNAs. The platform can be used to identify disease patients and monitor cellular differentiation. CrisprZyme can serve as a universally applicable signal catalyst for CRISPR-based diagnostics, expanding the target range of preamplification-free, quantitative detection.
NATURE NANOTECHNOLOGY
(2022)
Review
Chemistry, Analytical
Yuxin Zhang, Yunping Wu, Yanfang Wu, Yangyang Chang, Meng Liu
Summary: The increasing demand for developing biosensors in various fields poses challenges on sensor performance requirements such as sensitivity, selectivity, and operating costs. CRISPR-Cas systems, known as molecular scissors, are highly accurate in cleaving specific DNA and RNA sequences, and recent studies have shown the establishment of versatile biosensing platforms based on CRISPR-Cas. The review introduces the general characteristics and mechanisms of class II CRISPR-Cas systems, highlighting their biosensing strategies for detecting a wide range of nucleic acid and non-nucleic acid analytes.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Nicole L. Welch, Meilin Zhu, Catherine Hua, Juliane Weller, Marzieh Ezzaty Mirhashemi, Tien G. Nguyen, Sreekar Mantena, Matthew R. Bauer, Bennett M. Shaw, Cheri M. Ackerman, Sri Gowtham Thakku, Megan W. Tse, Jared Kehe, Marie-Martine Uwera, Jacqueline S. Eversley, Derek A. Bielwaski, Graham McGrath, Joseph Braidt, Jeremy Johnson, Felecia Cerrato, Gage K. Moreno, Lydia A. Krasilnikova, Brittany A. Petros, Gabrielle L. Gionet, Ewa King, Richard C. Huard, Samantha K. Jalbert, Michael L. Cleary, Nicholas A. Fitzgerald, Stacey B. Gabriel, Glen R. Gallagher, Sandra C. Smole, Lawrence C. Madoff, Catherine M. Brown, Matthew W. Keller, Malania M. Wilson, Marie K. Kirby, John R. Barnes, Daniel J. Park, Katherine J. Siddle, Christian T. Happi, Deborah T. Hung, Michael Springer, Bronwyn L. MacInnis, Jacob E. Lemieux, Eric Rosenberg, John A. Branda, Paul C. Blainey, Pardis C. Sabeti, Cameron Myhrvold
Summary: A microfluidic CRISPR-based platform called mCARMEN enables multiplexed and high-throughput identification of a wide range of respiratory viruses, including specific SARS-CoV-2 variants. The platform combines cost-effectiveness, diagnostic-grade performance, and a streamlined workflow for clinical use.
Article
Chemistry, Multidisciplinary
Mengting Xu, Yuedong Zhu, Yan Zhang, Bin Gong, Yuliang Kang, Gaoxing Su, Yanyan Yu
Summary: A Cas12a platform programmed by split G-quadruplex (G4) was established, validated, and optimized, which utilized split G4 motif as a substrate and demonstrated a concentration-dependent response to the input target in a label-free sensing platform. Moreover, the platform successfully detected and profiled exosomal surface proteins from cultured cancer cells and clinical samples.
CHEMICAL COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Pooja Bhardwaj, Rajni Kant, Sthita Pragnya Behera, Gaurav Raj Dwivedi, Rajeev Singh
Summary: This article emphasizes the importance of CRISPR/Cas technology as a diagnostic tool for early management, diagnosis, and treatment of infections and diseases, and explores its detection capabilities for non-nucleic acid targets as well as the technical challenges and improvements in clinical assessment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Tatsiana Charnavets, Jaroslav Nunvar, Iva Necasova, Jens Voelker, Kenneth J. Breslauer, Bohdan Schneider
Editorial Material
Biochemistry & Molecular Biology
Jens Voelker, Roland Winter
BIOPHYSICAL CHEMISTRY
(2011)
Meeting Abstract
Biophysics
William Braunlin, Jens Voelker, Eric Plum, Kenneth J. Breslauer
BIOPHYSICAL JOURNAL
(2013)
Article
Biochemistry & Molecular Biology
Jens Voelker, G. Eric Plum, Horst H. Klump, Kenneth J. Breslauer
Article
Biochemistry & Molecular Biology
Jens Voelker, G. Eric Plum, Vera Gindikin, Horst H. Klump, Kenneth J. Breslauer
Article
Biochemistry & Molecular Biology
William Braunlin, Jens Voelker, G. Eric Plum, Kenneth J. Breslauer
Article
Biochemistry & Molecular Biology
Mengxia Li, Jens Voelker, Kenneth J. Breslauer, David M. Wilson
JOURNAL OF MOLECULAR BIOLOGY
(2014)
Article
Chemistry, Multidisciplinary
Jens Voelker, G. Eric Plum, Horst H. Klump, Kenneth J. Breslauer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2009)
Article
Chemistry, Multidisciplinary
Jens Voelker, G. Eric Plum, Horst H. Klump, Kenneth J. Breslauer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2010)
Article
Chemistry, Multidisciplinary
Jens Voelker, Vera Gindikin, Horst H. Klump, G. Eric Plum, Kenneth J. Breslauer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2012)
Article
Multidisciplinary Sciences
Matthew D. Johnson, Jens Voelker, Holly V. Moeller, Edward Laws, Kenneth J. Breslauer, Paul G. Falkowski
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2009)
Article
Biochemistry & Molecular Biology
Jens Volker, G. Eric Plum, Vera Gindikin, Kenneth J. Breslauer
Article
Chemistry, Physical
Jens Volker, G. Eric Plum, Kenneth J. Breslauer
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Review
Biophysics
J. Volker, K. J. Breslauer
Summary: This study demonstrates that the presence of an abasic site in DNA triplet repeat ensembles reshapes the dynamic, bulged-loop energy landscape, altering repair outcomes by the APE1 enzyme. Despite the abasic site having the same neighboring sequences, repair outcomes are impacted by the structural context of the lesion. The redistribution of DNA states induced by the lesion affects APE1 repair outcomes and interconversions, with implications for DNA regulation.
QUARTERLY REVIEWS OF BIOPHYSICS
(2021)
Meeting Abstract
Biophysics
Jens Voelker, Vera Gindikin, Horst H. Klump, G. Eric Plum, Kenneth J. Breslauer
BIOPHYSICAL JOURNAL
(2013)