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Lally P, Gómez-Romero L, Tierrafría VH, Aquino P, Rioualen C, Zhang X, Kim S, Baniulyte G, Plitnick J, Smith C, Babu M, Collado-Vides J, Wade JT, Galagan JE. Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.594371. [PMID: 38826350 PMCID: PMC11142182 DOI: 10.1101/2024.05.23.594371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We used these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We used BoltzNet to quantitatively design novel binding sites, which we validated with biophysical experiments on purified protein. We have generated models for 125 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.
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Affiliation(s)
- Patrick Lally
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, Periférico Sur 4809, Arenal Tepepan, Ciudad de México 14610, México
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, Ciudad de México, México
| | - Víctor H. Tierrafría
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
| | - Patricia Aquino
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Claire Rioualen
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
| | - Xiaoman Zhang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
| | - Sunyoung Kim
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, SK S4S 0A2, Canada
| | | | - Jonathan Plitnick
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, SK S4S 0A2, Canada
| | - Julio Collado-Vides
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad s/n, Cuernavaca 62210, Morelos, México
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
- Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY, USA
| | - James E. Galagan
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215
- Bioinformatics Program, Boston University, 24 Cummington Mall, Boston, MA 02215
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Sankar K, Kuzmanović U, Schaus SE, Galagan JE, Grinstaff MW. Strategy, Design, and Fabrication of Electrochemical Biosensors: A Tutorial. ACS Sens 2024; 9:2254-2274. [PMID: 38636962 DOI: 10.1021/acssensors.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Advanced healthcare requires novel technologies capable of real-time sensing to monitor acute and long-term health. The challenge relies on converting a real-time quantitative biological and chemical signal into a desired measurable output. Given the success in detecting glucose and the commercialization of glucometers, electrochemical biosensors continue to be a mainstay of academic and industrial research activities. Despite the wealth of literature on electrochemical biosensors, reports are often specific to a particular application (e.g., pathogens, cancer markers, glucose, etc.), and most fail to convey the underlying strategy and design, and if it is transferable to detection of a different analyte. Here we present a tutorial review for those entering this research area that summarizes the basic electrochemical techniques utilized as well as discusses the designs and optimization strategies employed to improve sensitivity and maximize signal output.
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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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Pang J, Peng S, Hou C, Zhao H, Fan Y, Ye C, Zhang N, Wang T, Cao Y, Zhou W, Sun D, Wang K, Rümmeli MH, Liu H, Cuniberti G. Applications of Graphene in Five Senses, Nervous System, and Artificial Muscles. ACS Sens 2023; 8:482-514. [PMID: 36656873 DOI: 10.1021/acssensors.2c02790] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Graphene remains of great interest in biomedical applications because of biocompatibility. Diseases relating to human senses interfere with life satisfaction and happiness. Therefore, the restoration by artificial organs or sensory devices may bring a bright future by the recovery of senses in patients. In this review, we update the most recent progress in graphene based sensors for mimicking human senses such as artificial retina for image sensors, artificial eardrums, gas sensors, chemical sensors, and tactile sensors. The brain-like processors are discussed based on conventional transistors as well as memristor related neuromorphic computing. The brain-machine interface is introduced for providing a single pathway. Besides, the artificial muscles based on graphene are summarized in the means of actuators in order to react to the physical world. Future opportunities remain for elevating the performances of human-like sensors and their clinical applications.
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Affiliation(s)
- Jinbo Pang
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, China
| | - Songang Peng
- High-Frequency High-Voltage Device and Integrated Circuits R&D Center and Key Laboratory of Microelectronic Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing, 100029, China
| | - Chongyang Hou
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, China
| | - Hongbin Zhao
- State Key Laboratory of Advanced Materials for Smart Sensing, GRINM Group Co. Ltd., Xinwai Street 2, Beijing 100088, People's Republic of China
| | - Yingju Fan
- School of Chemistry and Chemical Engineering, University of Jinan, Shandong, Jinan 250022, China
| | - Chen Ye
- School of Chemistry and Chemical Engineering, University of Jinan, Shandong, Jinan 250022, China
| | - Nuo Zhang
- School of Chemistry and Chemical Engineering, University of Jinan, Shandong, Jinan 250022, China
| | - Ting Wang
- State Key Laboratory of Biobased Material and Green Papermaking and People's Republic of China School of Bioengineering, Qilu University of Technology, Shandong Academy of Sciences, No. 3501 Daxue Road, Jinan 250353, People's Republic of China
| | - Yu Cao
- Key Laboratory of Modern Power System Simulation and Control & Renewable Energy Technology (Ministry of Education) and School of Electrical Engineering, Northeast Electric Power University, Jilin 132012, China
| | - Weijia Zhou
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, China
| | - Ding Sun
- School of Electrical and Computer Engineering, Jilin Jianzhu University, Changchun 130118, P. R. China
| | - Kai Wang
- School of Electrical Engineering, Weihai Innovation Research Institute, Qingdao University, Qingdao 266000, China
| | - Mark H Rümmeli
- Leibniz Institute for Solid State and Materials Research Dresden, Dresden, D-01171, Germany.,College of Energy, Soochow Institute for Energy and Materials Innovations, and Key Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu Province, Soochow University, Suzhou 215006, China.,Centre of Polymer and Carbon Materials, Polish Academy of Sciences, M. Curie Sklodowskiej 34, Zabrze 41-819, Poland.,Institute for Complex Materials, IFW Dresden, 20 Helmholtz Strasse, Dresden 01069, Germany.,Center for Energy and Environmental Technologies, VŠB-Technical University of Ostrava, 17. Listopadu 15, Ostrava 708 33, Czech Republic
| | - Hong Liu
- Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan 250022, China.,State Key Laboratory of Crystal Materials, Center of Bio & Micro/Nano Functional Materials, Shandong University, 27 Shandanan Road, Jinan 250100, China
| | - Gianaurelio Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials and Center for Advancing Electronics Dresden, Technische Universität Dresden, Dresden 01069, Germany
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Bi H, Zhao C, Zhang Y, Zhang X, Xue B, Li C, Wang S, Yang X, Li C, Qiu Z, Wang J, Shen Z. IVT cell-free biosensors for tetracycline and macrolide detection based on allosteric transcription factors (aTFs). ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4545-4554. [PMID: 36314439 DOI: 10.1039/d2ay01316a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In recent years, the issue of food safety has received a lot of attention. The Food and Drug Administration (FDA) prescribes the antibiotic's maximum residue limit (MRL) in food production. The standard detection methods of antibiotics are liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) and high-performance liquid chromatography (HPLC), with complex operations and precision instruments. In this study, allosteric transcription factor (aTF)-based in vitro transcription (IVT) cell-free biosensors were developed for tetracyclines and macrolides with nucleic acid sequence-based amplification (NASBA). Characterization of binding and dissociation processes between aTF and DNA was carried out by BIAcore assay and electrophoretic mobility shift assay (EMSA). BIAcore was innovatively used to directly observe the real-time process of binding and dissociation of aTF with DNA. The biosensors produce more fluorescence RNA when target antibiotics are added to the three-way junction dimeric Broccoli (3WJdB). Four tetracyclines and two macrolides were quantified in the 0.5-15 μM range, while erythromycin and clarithromycin were detected over a range of 0.1-15 μM. NASBA, commonly used for viral detection, was used to amplify 3WJdB RNA generated by IVT, which greatly increased the LOD for tetracyclines and macrolides to 0.01 μM. The use of biosensors in milk samples demonstrated their on-site detection performance. Overall, our proposed biosensors are simple, rapid, selective, and sensitive, with the potential for field application.
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Affiliation(s)
- Huaixiu Bi
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chen Zhao
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Yongkang Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Xi Zhang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Bin Xue
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chenyu Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Shang Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Xiaobo Yang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Chao Li
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Zhigang Qiu
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Jingfeng Wang
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
| | - Zhiqiang Shen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
- Department of Hygienic Toxicology and Environmental Hygiene, Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China.
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