1
|
Olivieri A, Nardi AN, D'Abramo M. Theoretical Insights into MutY Glycosylase DNA Repair Mechanism. Biochemistry 2024; 63:1991-1998. [PMID: 38990758 DOI: 10.1021/acs.biochem.4c00153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Maintaining the integrity of the genome is fundamental to living organisms. To this end, nature developed several mechanisms to find and promptly repair DNA lesions. Among them, base excision repair (BER) enzymes evolved to efficiently carry out this task. Notably, the mechanisms allowing these proteins to search for, detect, and fix DNA damage on a biologically relevant time scale still remain partially unclear. By taking MutY, a BER enzyme implied in the repair of the 8-oxoguanine-adenine mismatches, as a model system, we shed some light on the repair mechanism through a theoretical-computational approach. First, we estimated the effect of the oxidation state of the MutY iron-sulfur cluster on the protein-DNA binding. Then, the redox thermodynamics of both the protein cluster and DNA nucleobases are calculated. Finally, the charge migration kinetics along the double strand bound to the enzyme has been evaluated. The rationalization of our results indicates that the search for DNA lesions is essentially dictated by the redox chemistry of the species involved, i.e., the iron-sulfur redox cofactor and the DNA bound to the enzyme.
Collapse
Affiliation(s)
- Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
2
|
Alawneh A, Wettasinghe AP, McMullen R, Seifi MO, Breton I, Slinker JD, Kuchta RD. A Redox-Reversible Switch of DNA Hydrogen Bonding and Structure. ACS APPLIED BIO MATERIALS 2024. [PMID: 38978451 DOI: 10.1021/acsabm.4c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Modulating molecular structure and function at the nanoscale drives innovation across wide-ranging technologies. Electrical control of the bonding of individual DNA base pairs endows DNA with precise nanoscale structural reconfigurability, benefiting efforts in DNA origami and actuation. Here, alloxazine DNA base surrogates were synthesized and incorporated into DNA duplexes to function as a redox-active switch of hydrogen bonding. Circular dichroism (CD) revealed that 24-mer DNA duplexes containing one or two alloxazines exhibited CD spectra and melting transitions similar to DNA with only canonical bases, indicating that the constructs adopt a B-form conformation. However, duplexes were not formed when four or more alloxazines were incorporated into a 24-mer strand. Thiolated duplexes incorporating alloxazines were self-assembled onto multiplexed gold electrodes and probed electrochemically. Square-wave voltammetry (SWV) revealed a substantial reduction peak centered at -0.272 V vs Ag/AgCl reference. Alternating between alloxazine oxidizing and reducing conditions modulated the SWV peak in a manner consistent with the formation and loss of hydrogen bonding, which disrupts the base pair stacking and redox efficiency of the DNA construct. These alternating signals support the assertion that alloxazine can function as a redox-active switch of hydrogen bonding, useful in controlling DNA and bioinspired assemblies.
Collapse
Affiliation(s)
- Ayman Alawneh
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Ashan P Wettasinghe
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Reema McMullen
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Melodee O Seifi
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Ivan Breton
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| | - Jason D Slinker
- Department of Physics, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080, United States
- Department of Chemistry, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080 United States
- Department of Materials Science and Engineering, The University of Texas at Dallas, 800 West Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Robert D Kuchta
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, United States
| |
Collapse
|
3
|
Song Y, Gao Y, Fang H. Unexpected large charge transfer rate mediated by adenine in twisted DNA structure. Phys Rev E 2024; 109:064412. [PMID: 39020924 DOI: 10.1103/physreve.109.064412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/15/2024] [Indexed: 07/20/2024]
Abstract
DNA exhibits remarkable charge transfer ability, which is crucial for its biological functions and potential electronic applications. The charge transfer process in DNA is widely recognized as primarily mediated by guanine, while the contribution of other nucleobases is negligible. Using the tight-binding models in conjunction with first-principles calculations, we investigated the charge transfer behavior of homogeneous GC and AT pairs. We found that the charge transfer rate of adenine significantly changes. With overstretching, the charge transfer rate of adenine can even surpass that of guanine, by as much as five orders of magnitude at a twist angle of around 26°. Further analysis reveals that it is attributed to the turnover of the relative coupling strength between homogeneous GC and AT base pairs, which is caused by the symmetry exchange between the two highest occupied molecular orbitals of base pairs occurring at different twist angles. Given the high degree of flexibility of DNA in vivo and in vitro conditions, these findings prompt us to reconsider the mechanism of biological functions concerning the charge transfer in DNA molecules and further open the potential of DNA as a biomaterial for electronic applications.
Collapse
|
4
|
Demir B, Akin Gultakti C, Koker Z, Anantram MP, Oren EE. Electronic Properties of DNA Origami Nanostructures Revealed by In Silico Calculations. J Phys Chem B 2024; 128:4646-4654. [PMID: 38712954 PMCID: PMC11103695 DOI: 10.1021/acs.jpcb.4c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/29/2024] [Indexed: 05/08/2024]
Abstract
DNA origami is a pioneering approach for producing complex 2- or 3-D shapes for use in molecular electronics due to its inherent self-assembly and programmability properties. The electronic properties of DNA origami structures are not yet fully understood, limiting the potential applications. Here, we conduct a theoretical study with a combination of molecular dynamics, first-principles, and charge transmission calculations. We use four separate single strand DNAs, each having 8 bases (4 × G4C4 and 4 × A4T4), to form two different DNA nanostructures, each having two helices bundled together with one crossover. We also generated double-stranded DNAs to compare electronic properties to decipher the effects of crossovers and bundle formations. We demonstrate that density of states and band gap of DNA origami depend on its sequence and structure. The crossover regions could reduce the conductance due to a lack of available states near the HOMO level. Furthermore, we reveal that, despite having the same sequence, the two helices in the DNA origami structure could exhibit different electronic properties, and electrode position can affect the resulting conductance values. Our study provides better understanding of the electronic properties of DNA origamis and enables us to tune these properties for electronic applications such as nanowires, switches, and logic gates.
Collapse
Affiliation(s)
- Busra Demir
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Caglanaz Akin Gultakti
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - Zeynep Koker
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| | - M. P. Anantram
- Department
of Electrical and Computer Engineering, University of Washington, Seattle, Washington 98115, United States
| | - Ersin Emre Oren
- Department
of Materials Science & Nanotechnology Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
- Bionanodesign
Laboratory, Department of Biomedical Engineering, TOBB University of Economics and Technology, Ankara 06560, Türkiye
| |
Collapse
|
5
|
Lee H, Lee D. Assembling Molecular Clips To Build π-Stacks. Chemistry 2023; 29:e202302523. [PMID: 37658276 DOI: 10.1002/chem.202302523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/03/2023]
Abstract
Nature utilizes an intimate stacking of aromatic motifs to construct functional structures, as demonstrated in protein folding and polynucleotide assembly. However, organized π-stacks of artificial molecules are difficult to build, primarily due to the weak, non-directional, and context-sensitive nature of van der Waals forces. To overcome these challenges, chemists have invented ingenious architectural designs to construct π-stacked supramolecular assemblies using clip-like molecules. This Concept article focuses on molecular clips that enable precise spatial control over assembly patterns, beyond the scope of simple host-guest chemistry. Different design strategies are analyzed and compared that leverage non-covalent interactions to create multi-layer π-stacks. Particular emphasis is placed on the choice of spine units as they play a crucial role in controlling the (i) spacing, (ii) orientation, and (iii) conformational pre-organization of linked aromatics to achieve long-range spatial ordering.
Collapse
Affiliation(s)
- Hyun Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Dongwhan Lee
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| |
Collapse
|
6
|
Huang Z, Wang W, Wang Y, Wang H, Pang Y, Yuan Q, Tan J, Tan W. Electrochemical Detection of Viral Nucleic Acids by DNA Nanolock-Based Porous Electrode Device. Anal Chem 2023; 95:16668-16676. [PMID: 37910393 DOI: 10.1021/acs.analchem.3c03168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Developing rapid, sensitive, and facile nucleic acid detection technologies is of paramount importance for preventing and controlling infectious diseases. Benefiting from the advantages such as rapid response, low cost, and simple operation, electrochemical impedance spectroscopy holds great promise for point-of-care nucleic acid detection. However, the sensitivity of electrochemical impedance spectroscopy for low molecular weight nucleic acids testing is still limited. This work presents a DNA nanolock-based porous electrode to improve the sensitivity of electrochemical impedance spectroscopy. Once the target nucleic acids are recognized by the DNA probes, the pore-attached DNA nanolock caused remarkable impedance amplification by blocking the nanopores. Taking SARS-CoV-2 nucleic acid as a model analyte, the detection limit of the porous electrode was as low as 0.03 fM for both SARS-CoV-2 RNA and DNA. The integration of a porous electrode with a wireless communicating unit generates a portable detection device that could be applied to direct SARS-CoV-2 nucleic acid testing in saliva samples. The portable device could effectively distinguish the COVID-19 positive and negative samples, showing a sensitivity of 100% and a specificity of 93%. Owing to its rapid, ultrasensitive, specific, and portable features, the as-designed DNA nanolock and porous electrode-based portable device holds great promise as a point-of-care platform for real-time screening of COVID-19 and other epidemics.
Collapse
Affiliation(s)
- Zhongnan Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Wenjie Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yingfei Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Han Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yimin Pang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| |
Collapse
|
7
|
Wen T, Kermarrec M, Dumont E, Gillet N, Greenberg MM. DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles. J Am Chem Soc 2023; 145:23702-23714. [PMID: 37856159 PMCID: PMC10652223 DOI: 10.1021/jacs.3c08135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA-protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone N-terminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.
Collapse
Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Maxime Kermarrec
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice UMR 7272, Université Côte d'Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
| | - Natacha Gillet
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
8
|
Zhou P, Fu Y, Wang M, Qiu R, Wang Y, Stoddart JF, Wang Y, Chen H. Robust Single-Supermolecule Switches Operating in Response to Two Different Noncovalent Interactions. J Am Chem Soc 2023; 145:18800-18811. [PMID: 37590178 DOI: 10.1021/jacs.3c03282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Supramolecular electronics provide an opportunity to introduce molecular assemblies into electronic devices through a combination of noncovalent interactions such as [π···π] and hydrogen-bonding interactions. The fidelity and dynamics of noncovalent interactions hold considerable promise when it comes to building devices with controllable and reproducible switching functions. Here, we demonstrate a strategy for building electronically robust switches by harnessing two different noncovalent interactions between a couple of pyridine derivatives. The single-supermolecule switch is turned ON when compressing the junction enabling [π···π] interactions to dominate the transport, while the switch is turned OFF by stretching the junction to form hydrogen-bonded dimers, leading to a dramatic decrease in conductance. The robustness and reproducibility of these single-supermolecule switches were achieved by modulating the junction with Ångström precision at frequencies of up to 190 Hz while obtaining high ON/OFF ratios of ∼600. The research presented herein opens up an avenue for designing robust bistable mechanoresponsive devices which will find applications in the building of integrated circuits for microelectromechanical systems.
Collapse
Affiliation(s)
- Ping Zhou
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yanjun Fu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Maolin Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Renhui Qiu
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Yuwei Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - J Fraser Stoddart
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Yuping Wang
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| | - Hongliang Chen
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311215, China
| |
Collapse
|
9
|
Han X, Wang J, Zhang J, Han B, Mei N, Fan R, Zhao J, Yao H, Yu X, Cai W. Digested extracellular DNA shortens the anodic startup of microbial electrolysis cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162642. [PMID: 36894072 DOI: 10.1016/j.scitotenv.2023.162642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/21/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
While the multiple functions of extracellular DNA (exDNA) in biofilm formation and electron transfer have been extensively studied in pure culture, its role in mixed anodic biofilm was still unknown. In this study, we employed DNase I enzyme to digest exDNA, thereby investigating its role in anodic biofilm formation based on the performance of four microbial electrolysis cells (MECs) groups with different DNase I enzyme concentration (0, 0.05, 0.1, 0.5 mg/mL). The responding time to reach 60 % maximum current of treatment group with DNase I enzyme has been significantly reduced to 83 %-86 % of the blank group (t-test, p < 0.01), indicating the exDNA digestion could promote the biofilm formation at the early stage. The anodic coulombic efficiency was enhanced by 10.74- 54.42 % in treatment group (t-test, p < 0.05), which could be ascribed to the higher absolute abundance of exoelectrogens. The lower relative abundance of exoelectrogens indicated the DNase I enzyme addition was beneficial for the enrichment of extensive species rather than exoelectrogens. As the DNase I enzyme augments the fluorescence signal of exDNA distribution in the small molecular weight region, implying the short chain exDNA could contribute to the biomass enhancement via boosting the most species enrichment. Furthermore, the exDNA alteration improved the complexity of microbial network. Our findings provide a new insight into the role of exDNA in the extracellular matrix of anodic biofilms.
Collapse
Affiliation(s)
- Xiangyu Han
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Jiaman Wang
- School of Engineering, Brown University, Providence, Rohde Island 02912, United States of America
| | - Jingjing Zhang
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Baohong Han
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Ning Mei
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Runchuan Fan
- School of Environment, Beijing Jiaotong University, Beijing 100044, China
| | - Jing Zhao
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Hong Yao
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Xiaohua Yu
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China
| | - Weiwei Cai
- School of Environment, Beijing Jiaotong University, Beijing 100044, China; Intelligent Environment Research Center, Beijing Jiaotong University, No. 1 Guanzhuang, Chaoyang District, Beijing 100080, China.
| |
Collapse
|
10
|
Iyer V, Issadore DA, Aflatouni F. The next generation of hybrid microfluidic/integrated circuit chips: recent and upcoming advances in high-speed, high-throughput, and multifunctional lab-on-IC systems. LAB ON A CHIP 2023; 23:2553-2576. [PMID: 37114950 DOI: 10.1039/d2lc01163h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Since the field's inception, pioneers in microfluidics have made significant progress towards realizing complete lab-on-chip systems capable of sophisticated sample analysis and processing. One avenue towards this goal has been to join forces with the related field of microelectronics, using integrated circuits (ICs) to perform on-chip actuation and sensing. While early demonstrations focused on using microfluidic-IC hybrid chips to miniaturize benchtop instruments, steady advancements in the field have enabled a new generation of devices that expand past miniaturization into high-performance applications that would not be possible without IC hybrid integration. In this review, we identify recent examples of labs-on-chip that use high-resolution, high-speed, and multifunctional electronic and photonic chips to expand the capabilities of conventional sample analysis. We focus on three particularly active areas: a) high-throughput integrated flow cytometers; b) large-scale microelectrode arrays for stimulation and multimodal sensing of cells over a wide field of view; c) high-speed biosensors for studying molecules with high temporal resolution. We also discuss recent advancements in IC technology, including on-chip data processing techniques and lens-free optics based on integrated photonics, that are poised to further advance microfluidic-IC hybrid chips.
Collapse
Affiliation(s)
- Vasant Iyer
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - David A Issadore
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Firooz Aflatouni
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| |
Collapse
|
11
|
Jamal RB, Vitasovic T, Gosewinkel U, Ferapontova EE. Detection of E.coli 23S rRNA by electrocatalytic "off-on" DNA beacon assay with femtomolar sensitivity. Biosens Bioelectron 2023; 228:115214. [PMID: 36906990 DOI: 10.1016/j.bios.2023.115214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Prevention of food spoilage, environmental bio-contamination, and pathogenic infections requires rapid and sensitive bacterial detection systems. Among microbial communities, the bacterial strain of Escherichia coli is most widespread, with pathogenic and non-pathogenic strains being biomarkers of bacterial contamination. Here, we have developed a fM-sensitive, simple, and robust electrocatalytically-amplified assay facilitating specific detection of E.coli 23S ribosomal rRNA, in the total RNA sample, after its site-specific cleavage by RNase H enzyme. Gold screen-printed electrodes (SPE) were electrochemically pre-treated to be productively modified with a methylene-blue (MB) - labelled hairpin DNA probes, which hybridization with the E. coli-specific DNA placed MB in the top region of the DNA duplex. The formed duplex acted as an electrical wire, mediating electron transfer from the gold electrode to the DNA-intercalated MB, and further to ferricyanide in solution, enabling its electrocatalytic reduction otherwise impeded on the hairpin-modified SPEs. The assay facilitated 20 min 1 fM detection of both synthetic E. coli DNA and 23S rRNA isolated from E.coli (equivalent to 15 CFU mL-1), and can be extended to fM analysis of nucleic acids isolated from any other bacteria.
Collapse
Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Toni Vitasovic
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
| |
Collapse
|
12
|
Gao D, Tang Z, Chen X, Wu R, Tian Y, Min Q, Zhang JR, Chen Z, Zhu JJ. Reversible Regulation of Long-Distance Charge Transport in DNA Nanowires by Dynamically Controlling Steric Conformation. NANO LETTERS 2023; 23:4201-4208. [PMID: 37188354 DOI: 10.1021/acs.nanolett.3c00102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.
Collapse
Affiliation(s)
- Di Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zhuodong Tang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Rong Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Ye Tian
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
- Shenzhen Research Institute of Nanjing University, Shenzhen 518000, People's Republic of China
| |
Collapse
|
13
|
Dal Co A, Ackermann M, van Vliet S. Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Syst 2023; 14:98-108. [PMID: 36796335 DOI: 10.1016/j.cels.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.
Collapse
Affiliation(s)
- Alma Dal Co
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Duebendorf, Switzerland.
| | | |
Collapse
|
14
|
Chen X, Yan B, Yao G. Towards atom manufacturing with framework nucleic acids. NANOTECHNOLOGY 2023; 34:172002. [PMID: 36669170 DOI: 10.1088/1361-6528/acb4f2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
Atom manufacturing has become a blooming frontier direction in the field of material and chemical science in recent years, focusing on the fabrication of functional materials and devices with individual atoms or with atomic precision. Framework nucleic acids (FNAs) refer to nanoscale nucleic acid framework structures with novel properties distinct from those of conventional nucleic acids. Due to their ability to be precisely positioned and assembled at the nanometer or even atomic scale, FNAs are ideal materials for atom manufacturing. They hold great promise for the bottom-up construction of electronic devices by precisely arranging and integrating building blocks with atomic or near-atomic precision. In this review, we summarize the progress of atom manufacturing based on FNAs. We begin by introducing the atomic-precision construction of FNAs and the intrinsic electrical properties of DNA molecules. Then, we describe various approaches for the fabrication of FNAs templated materials and devices, which are classified as conducting, insulating, or semiconducting based on their electrical properties. We highlight the role of FNAs in the fabrication of functional electronic devices with atomic precision, as well as the challenges and opportunities for atom manufacturing with FNAs.
Collapse
Affiliation(s)
- Xiaoliang Chen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Bingjie Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Guangbao Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| |
Collapse
|
15
|
Petronek MS, Allen BG. Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex. Front Genet 2023; 14:1152398. [PMID: 36968611 PMCID: PMC10031043 DOI: 10.3389/fgene.2023.1152398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023] Open
Abstract
Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.
Collapse
|
16
|
Funk RHW, Scholkmann F. The significance of bioelectricity on all levels of organization of an organism. Part 1: From the subcellular level to cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:185-201. [PMID: 36481271 DOI: 10.1016/j.pbiomolbio.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/24/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Bioelectricity plays an essential role in the structural and functional organization of biological organisms. In this first article of our three-part series, we summarize the importance of bioelectricity for the basic structural level of biological organization, i.e. from the subcellular level (charges, ion channels, molecules and cell organelles) to cells.
Collapse
Affiliation(s)
- Richard H W Funk
- Institute of Anatomy, Center for Theoretical Medicine, TU-Dresden, 01307, Dresden, Germany; Dresden International University, 01067, Dresden, Germany.
| | - Felix Scholkmann
- Biomedical Optics Research Laboratory, Department of Neonatology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland.
| |
Collapse
|
17
|
Molecular Tetris by sequence-specific stacking of hydrogen bonding molecular clips. Commun Chem 2022; 5:180. [PMID: 36697760 PMCID: PMC9814962 DOI: 10.1038/s42004-022-00802-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
A face-to-face stacking of aromatic rings is an effective non-covalent strategy to build functional architectures, as elegantly exemplified with protein folding and polynucleotide assembly. However, weak, non-directional, and context-sensitive van der Waals forces pose a significant challenge if one wishes to construct well-organized π-stacks outside the confines of the biological matrix. To meet this design challenge, we have devised a rigid polycyclic template to create a non-collapsible void between two parallel oriented π-faces. In solution, these shape-persistent aromatic clips self-dimerize to form quadruple π-stacks, the thermodynamic stability of which is enhanced by self-complementary N-H···N hydrogen bonds, and finely regulated by the regioisomerism of the π-canopy unit. With assistance from sufficient electrostatic polarization of the π-surface and bifurcated hydrogen bonds, a small polyheterocyclic guest can effectively compete against the self-dimerization of the host to afford a triple π-stack inclusion complex. A combination of solution spectroscopic, X-ray crystallographic, and computational studies aided a detailed understanding of this cooperative vs competitive process to afford layered aromatics with extraordinary structural regularity and fidelity.
Collapse
|
18
|
Lai Liang F, Segal D. Long-range charge transport in homogeneous and alternating-rigidity chains. J Chem Phys 2022; 157:104106. [DOI: 10.1063/5.0101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the interplay of intrinsic-electronic and environmental factors in long-range charge transport across molecular chains with up to N ∼ 80 monomers. We describe the molecular electronic structure of the chain with a tight-binding Hamiltonian. Thermal effects in the form of electron decoherence and inelastic scattering are incorporated with the Landauer–Büttiker probe method. In short chains of up to ten units, we observe the crossover between coherent (tunneling, ballistic) motion and thermally-assisted conduction, with thermal effects enhancing the current beyond the quantum coherent limit. We further show that unconventional (nonmonotonic with size) transport behavior emerges when monomer-to-monomer electronic coupling is made large. In long chains, we identify a different behavior, with thermal effects suppressing the conductance below the coherent-ballistic limit. With the goal to identify a minimal model for molecular chains displaying unconventional and effective long-range transport, we simulate a modular polymer with alternating regions of high and low rigidity. Simulations show that, surprisingly, while charge correlations are significantly affected by structuring environmental conditions, reflecting charge delocalization, the electrical resistance displays an averaging effect, and it is not sensitive to this patterning. We conclude by arguing that efficient long-range charge transport requires engineering both internal electronic parameters and environmental conditions.
Collapse
Affiliation(s)
- Francisco Lai Liang
- Department of Chemistry and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
| | - Dvira Segal
- Department of Chemistry and Centre for Quantum Information and Quantum Control, University of Toronto, 80 Saint George St., Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| |
Collapse
|
19
|
Zhao C, Guo W, Umar A, Algadi H, Pei M, Ibrahim AA, Yang X, Ren Z, Mi X, Wang L. High-sensitive ferrocene labeled aptasensor for the detection of Mucin 1 by tuning the sequence constitution of complementary probe. Mikrochim Acta 2022; 189:332. [PMID: 35971003 DOI: 10.1007/s00604-022-05424-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
A strand displacement-based "signal-off" electrochemical aptasensor is reported for the detection of Mucin 1 (MUC 1) based on a high original signal. Different from the conventional "signal-off" electrochemical biosensors where electrochemical substances are dispersed in electrolyte solution, here the current signal was generated by the complementary probe (CP) associated with ferrocene (Fc) labeled aptamer (Apt.-Fc). Because Apt.-Fc and MUC 1 have a higher affinity, Apt.-Fc dissociates from CP in the presence of MUC 1, resulting in a reduction of detection current signal generated by oxidation of labeled Fc. In this system, high detection signal is necessary to improve the sensor's performance. For this aim, a strategy is proposed for changing the modalities of electron transport and the quantity of Apt.-Fc introduced by simply tuning the sequence constitution of CP. As expected, a high detection current signal was obtained after selecting CP(Apt.-Fc)-TTT as the optimal CP. The aptasensor was then employed to detect MUC 1, and satisfactory detection results with a low detection limit (LOD) of 0.087 pM (S/N = 3), good specificity, good stability, and feasibility of detection of MUC 1 in artificial serum (recovery of 92-101%, RSD of 1.36-5.23%) were obtained.
Collapse
Affiliation(s)
- Chengxian Zhao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Wenjuan Guo
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, 250022, China.
| | - Ahmad Umar
- Department of Chemistry, College of Science and Arts, Najran University, Najran, 11001, Kingdom of Saudi Arabia. .,Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001, Kingdom of Saudi Arabia. .,Department of Materials Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA.
| | - Hassan Algadi
- Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001, Kingdom of Saudi Arabia.,Department of Electrical Engineering, Faculty of Engineering, Najran University, Najran, 11001, Kingdom of Saudi Arabia
| | - Meishan Pei
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China.
| | - Ahmed A Ibrahim
- Department of Chemistry, College of Science and Arts, Najran University, Najran, 11001, Kingdom of Saudi Arabia.,Promising Centre for Sensors and Electronic Devices (PCSED), Najran University, Najran, 11001, Kingdom of Saudi Arabia
| | - Xueying Yang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Zhe Ren
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, 250022, China
| | - Xiangyun Mi
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| | - Luyan Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, China
| |
Collapse
|
20
|
Lima RPA, Malyshev AV. Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer. Phys Rev E 2022; 106:024414. [PMID: 36109995 DOI: 10.1103/physreve.106.024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
We address various regimes of charge transfer in DNA within the framework of the Peyrard-Bishop-Holstein model and analyze them from the standpoint of the characteristic size and timescales of the electronic and vibrational subsystems. It is demonstrated that a polaron is an unstable configuration within a broad range of temperatures and therefore polaronic contribution to the charge transport is irrelevant. We put forward an alternative fluctuation-governed charge transfer mechanism and show that the charge transfer can be quasiballistic at low temperatures, diffusive or mixed at intermediate temperatures, and subdiffusive close to the DNA denaturation transition point. Dynamic fluctuations in the vibrational subsystem is the key ingredient of our proposed mechanism which allows for explanation of all charge transfer regimes at finite temperatures. In particular, we demonstrate that in the most relevant regime of high temperatures (above the aqueous environment freezing point), the electron dynamics is completely governed by relatively slow fluctuations of the mechanical subsystem. We argue also that our proposed analysis methods and mechanisms can be relevant for the charge transfer in other organic systems, such as conjugated polymers, molecular aggregates, α-helices, etc.
Collapse
Affiliation(s)
- R P A Lima
- GISC and GFTC, Instituto de Física, Universidade Federal de Alagoas, Maceió AL 57072-970, Brazil
| | - A V Malyshev
- GISC, Departamento de Física de Materiales, Universidad Complutense, E-28040 Madrid, Spain
- Ioffe Physical-Technical Institute, St-Petersburg, Russia
| |
Collapse
|
21
|
Cryo-EM structure of an extracellular Geobacter OmcE cytochrome filament reveals tetrahaem packing. Nat Microbiol 2022; 7:1291-1300. [PMID: 35798889 PMCID: PMC9357133 DOI: 10.1038/s41564-022-01159-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/23/2022] [Indexed: 12/11/2022]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens were first observed two decades ago, with genetic and biochemical data suggesting that conductive fibres were type IV pili. Recently, an extracellular conductive filament of G. sulfurreducens was found to contain polymerized c-type cytochrome OmcS subunits, not pilin subunits. Here we report that G. sulfurreducens also produces a second, thinner appendage comprised of cytochrome OmcE subunits and solve its structure using cryo-electron microscopy at ~4.3 Å resolution. Although OmcE and OmcS subunits have no overall sequence or structural similarities, upon polymerization both form filaments that share a conserved haem packing arrangement in which haems are coordinated by histidines in adjacent subunits. Unlike OmcS filaments, OmcE filaments are highly glycosylated. In extracellular fractions from G. sulfurreducens, we detected type IV pili comprising PilA-N and -C chains, along with abundant B-DNA. OmcE is the second cytochrome filament to be characterized using structural and biophysical methods. We propose that there is a broad class of conductive bacterial appendages with conserved haem packing (rather than sequence homology) that enable long-distance electron transport to chemicals or other microbial cells.
Collapse
|
22
|
Howe A, Liseev T, Gil-Sepulcre M, Gimbert-Suriñach C, Benet-Buchholz J, Llobet A, Ott S. Electrocatalytic water oxidation from a mixed linker MOF based on NU-1000 with an integrated ruthenium-based metallo-linker. MATERIALS ADVANCES 2022; 3:4227-4234. [PMID: 35693428 PMCID: PMC9125567 DOI: 10.1039/d2ma00128d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 04/04/2022] [Indexed: 05/28/2023]
Abstract
A novel tetratopic metallo-linker, [Ru(tda)(py(PhCOOH)2)2], 1, (tda = 2,2':6',2''-terpyridine-6,6''-dicarboxylate; py(PhCOOH)2 = (4,4'-(pyridine-3,5-diyl)dibenzoic acid), that is structurally based on one of the most active molecular water oxidation catalysts has been prepared and fully characterized, including single crystal X-ray diffraction. 1 bears geometric similarities to H4TBAPy (H4TBAPy = 4,4',4'',4'''-(pyrene-1,3,6,8-tetrayl)tetrabenzoic acid), i.e. the native linker in NU-1000, which offers the possibility to synthesize NU-1000-Ru mixed linker MOFs solvothermally. Mixed linker MOF formation was demonstrated by powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM), and Ru linker incorporation confirmed by FT-IR, energy-dispersive X-ray (EDX) spectroscopy and inductively coupled plasma optical emission spectroscopy (ICP-OES). It was found that the Ru contents in the final mixed linker MOFs correlate with the amount of Ru linker present during solvothermal synthesis, albeit not in a linear fashion. The cyclic voltammograms (CV) of the mixed linker MOFs are largely dominated by TBAPy-based oxidations with features attributed to 1. Interestingly, Ru linkers near the crystal surface are oxidized directly by interfacial hole transfer form the electrode, while those in the crystal interior can be oxidized indirectly from oxidized TBAPy linkers at more anodic potential. Upon repeated scanning, the CVs show the appearance of new waves that arise from irreversible TBAPy oxidation, as well as from the activation of the Ru-based water oxidation catalyst. Of the materials prepared, the one with the highest Ru content, NU-1000-Ruhigh, was shown to catalyze the electrochemical oxidation of water to dioxygen. The Faradaic efficiency (FE) of the construct is 37%, due to water oxidation being accompanied by oxidative transformations of the TBAPy linkers. Despite the low FE, NU-1000-Ruhigh is still among the best MOF-based water oxidation catalysts, operating by a unique co-linker mediated hole-transport mechanism to supply oxidizing equivalents also to catalysts in the crystal interior.
Collapse
Affiliation(s)
- Andrew Howe
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523 75120 Uppsala Sweden
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans 16 43007, Tarragona Spain
| | - Timofey Liseev
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523 75120 Uppsala Sweden
| | - Marcos Gil-Sepulcre
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans 16 43007, Tarragona Spain
| | - Carolina Gimbert-Suriñach
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans 16 43007, Tarragona Spain
| | - Jordi Benet-Buchholz
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans 16 43007, Tarragona Spain
| | - Antoni Llobet
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST) Av. Països Catalans 16 43007, Tarragona Spain
| | - Sascha Ott
- Department of Chemistry - Ångström Laboratory, Uppsala University, Box 523 75120 Uppsala Sweden
| |
Collapse
|
23
|
Jensen PWK, Kristensen LB, Lavigne C, Aspuru-Guzik A. Toward Quantum Computing with Molecular Electronics. J Chem Theory Comput 2022; 18:3318-3326. [PMID: 35535588 DOI: 10.1021/acs.jctc.2c00162] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this study, we explore the use of molecules and molecular electronics for quantum computing. We construct one-qubit gates using one-electron scattering in molecules and two-qubit controlled-phase gates using electron-electron scattering along metallic leads. Furthermore, we propose a class of circuit implementations, and show initial applications of the framework by illustrating one-qubit gates using the molecular electronic structure of molecular hydrogen as a baseline model.
Collapse
Affiliation(s)
- Phillip W K Jensen
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5G 1Z8, Canada
| | - Lasse Bjørn Kristensen
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5G 1Z8, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1Z8, Canada
| | - Cyrille Lavigne
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5G 1Z8, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1Z8, Canada
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5G 1Z8, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5G 1Z8, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario M5S 1M1, Canada.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
| |
Collapse
|
24
|
Qiu X, Chiechi RC. Printable logic circuits comprising self-assembled protein complexes. Nat Commun 2022; 13:2312. [PMID: 35484124 PMCID: PMC9050843 DOI: 10.1038/s41467-022-30038-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
This paper describes the fabrication of digital logic circuits comprising resistors and diodes made from protein complexes and wired together using printed liquid metal electrodes. These resistors and diodes exhibit temperature-independent charge-transport over a distance of approximately 10 nm and require no encapsulation or special handling. The function of the protein complexes is determined entirely by self-assembly. When induced to self-assembly into anisotropic monolayers, the collective action of the aligned dipole moments increases the electrical conductivity of the ensemble in one direction and decreases it in the other. When induced to self-assemble into isotropic monolayers, the dipole moments are randomized and the electrical conductivity is approximately equal in both directions. We demonstrate the robustness and utility of these all-protein logic circuits by constructing pulse modulators based on AND and OR logic gates that function nearly identically to simulated circuits. These results show that digital circuits with useful functionality can be derived from readily obtainable biomolecules using simple, straightforward fabrication techniques that exploit molecular self-assembly, realizing one of the primary goals of molecular electronics. Proteins are promising molecular materials for next-generation electronic devices. Here, the authors fabricated printable digital logic circuits comprising resistors and diodes from self-assembled photosystem I complexes that enable pulse modulation.
Collapse
Affiliation(s)
- Xinkai Qiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. .,Optoelectronics Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
| | - Ryan C Chiechi
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. .,Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, United States.
| |
Collapse
|
25
|
Zhang M, Li Z, Jia Y, Wang F, Tian J, Zhang C, Han T, Xing R, Ye W, Wang C. Observing Mesoscopic Nucleic Acid Capacitance Effect and Mismatch Impact via Graphene Transistors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105890. [PMID: 35072345 DOI: 10.1002/smll.202105890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/05/2021] [Indexed: 06/14/2023]
Abstract
This work reports a molecular-scale capacitance effect of the double helical nucleic acid duplex structure for the first time. By quantitatively conducting large sample measurements of the electrostatic field effect using a type of high-accuracy graphene transistor biosensor, an unusual charge-transport behavior is observed in which the end-immobilized nucleic acid duplexes can store a part of ionization electrons like molecular capacitors, other than electric conductors. To elucidate this discovery, a cascaded capacitive network model is proposed as a novel equivalent circuit of nucleic acid duplexes, expanding the point-charge approximation model, by which the partial charge-transport observation is reasonably attributed to an electron-redistribution behavior within the capacitive network. Furthermore, it is experimentally confirmed that base-pair mismatches hinder the charge transport in double helical duplexes, and lead to directly identifiable alterations in electrostatic field effects. The bioelectronic principle of mismatch impact is also self-consistently explained by the newly proposed capacitive network model. The mesoscopic nucleic acid capacitance effect may enable a new kind of label-free nucleic acid analysis tool based on electronic transistor devices. The in situ and real-time nucleic acid detections for virus biomarkers, somatic mutations, and genome editing off-target may thus be predictable.
Collapse
Affiliation(s)
- Mingfeng Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Zhibo Li
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Yuan Jia
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Fuquan Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Jinpeng Tian
- Industrialization Center of Micro & Nano ICs and Devices Sino-German College of Intelligent Manufacturing, Shenzhen Technology University, Shenzhen, 518118, China
| | - Cuiping Zhang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
| | - Tingting Han
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Ruiqing Xing
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| | - Weixiang Ye
- Department of Physics, School of Science, Hainan University, Haikou, 570228, China
- Key Laboratory of Engineering Modeling and Statistical Computation of Hainan Province, School of Science, Hainan University, Haikou, 570228, China
| | - Cheng Wang
- Tianjin Key Laboratory of Wireless Mobile Communications and Power Transmission, College of Electronic and Communication Engineering, Tianjin Normal University, Tianjin, 300387, China
- Department of Intelligence Science and Technology, College of Artificial Intelligence, Tianjin Normal University, Tianjin, 300387, China
| |
Collapse
|
26
|
Xu L, Zhou B, Song Y, Cai X, Lu W. Electron-Transfer Study and Single Nucleotide Discrimination of a DNA Sequence on a Polymer Gold Electrode (PGE) by Differential Pulse Voltammetry (DPV). ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2035390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Long Xu
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, China
| | - Binyu Zhou
- Department of Interventional Oncology, the People's Hospital of China Medical University, Shenyang, China
| | - Yaling Song
- Zhejiang GeneX Precision Medicine Co., Ltd, Hangzhou, P.R. China
| | - Xu Cai
- Department of Songbei Respiratory Medicine, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Lu
- Zhejiang GeneX Precision Medicine Co., Ltd, Hangzhou, P.R. China
| |
Collapse
|
27
|
Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity. Proc Natl Acad Sci U S A 2022; 119:2112812119. [PMID: 35074874 PMCID: PMC8812571 DOI: 10.1073/pnas.2112812119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Detection of molecular interactions is the foundation for many important biotechnology applications in society and industry, such as drug discovery, diagnostics, and DNA sequencing. This report describes a broadly applicable platform for detecting molecular interactions at the single-molecule scale, in real-time, label-free, and potentially highly multiplexable fashion, using single-molecule sensors on a highly scalable semiconductor sensor array chip. Such chips are both practically manufacturable in the near term, and have a durable long-term scaling roadmap, thus providing an ideal way to bring the power of modern chip technology to the broad area of biosensing. This work also realizes a 50-year-old scientific vision of integrating single molecules into electronic chips to achieve the ultimate miniaturization of electronics. For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.
Collapse
|
28
|
Billon J, Shkirskiy V, Dabos-Seignon S, Breton T, Gautier C. No more compromise: A facile route towards functionalized surfaces with stable monolayers. Phys Chem Chem Phys 2022; 24:14294-14298. [DOI: 10.1039/d2cp02129c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The results reported in this study clearly show that it is possible to easily control the formation of a functional monolayer by spontaneous reduction of an aryldiazonium salt on gold...
Collapse
|
29
|
Kogikoski S, Dutta A, Bald I. Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire. ACS NANO 2021; 15:20562-20573. [PMID: 34875168 PMCID: PMC8717627 DOI: 10.1021/acsnano.1c09176] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.
Collapse
Affiliation(s)
- Sergio Kogikoski
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
- Department
of Analytical Chemistry, Institute of Chemistry, State University of Campinas (UNICAMP), P.O. Box 6154, 13083-970, Campinas São Paulo, Brazil
| | - Anushree Dutta
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Ilko Bald
- Institute
of Chemistry, Physical Chemistry, University
of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| |
Collapse
|
30
|
Gupta N, Wilkinson EA, Karuppannan SK, Bailey L, Vilan A, Zhang Z, Qi DC, Tadich A, Tuite EM, Pike AR, Tucker JHR, Nijhuis CA. Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions. J Am Chem Soc 2021; 143:20309-20319. [PMID: 34826219 PMCID: PMC8662729 DOI: 10.1021/jacs.1c09549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Indexed: 11/29/2022]
Abstract
Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.
Collapse
Affiliation(s)
- Nipun
Kumar Gupta
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
| | - Edward A. Wilkinson
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Senthil Kumar Karuppannan
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Lily Bailey
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 76100, Israel
| | - Ziyu Zhang
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Dong-Chen Qi
- Centre
for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Anton Tadich
- Australian
Synchrotron Clayton, 800 Blackburn Rd, Clayton, Victoria 3168, Australia
| | - Eimer M. Tuite
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Andrew R. Pike
- Chemistry-School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, United Kingdom
| | - Christian A. Nijhuis
- Department
of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- Centre
for Advanced 2D Materials, National University
of Singapore, 6 Science Drive 2, Singapore 117546, Singapore
- Department
of Molecules & Materials, MESA+ Institute for Nanotechnology,
Faculty of Science and Technology, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| |
Collapse
|
31
|
Su J, Ke Y, Maboyi N, Zhi X, Yan S, Li F, Zhao B, Jia X, Song S, Ding X. CRISPR/Cas12a Powered DNA Framework-Supported Electrochemical Biosensing Platform for Ultrasensitive Nucleic Acid Analysis. SMALL METHODS 2021; 5:e2100935. [PMID: 34928030 DOI: 10.1002/smtd.202100935] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 06/14/2023]
Abstract
Nucleic acid analysis using ultrasensitive and simple methods is critically important for the early-stage diagnosis and treatment of diseases. The CRISPR/Cas proteins, guided by a single-stranded RNA have shown incredible capability for sequence-specific targeting and detection. Herein, in order to improve and expand the application of CRISPR/Cas technology to the electrochemical interface-based nucleic acids analysis, the authors develop a CRISPR/Cas12a powered DNA framework-supported electrochemical biosensing platform via the cis and trans cleavage of Cas12a on the heterogeneous carbon interface (the existing publications which commonly adopted trans-cleavage). Their solid-liquid interface is first immobilized by 3D tetrahedral framework nucleic acids (FNAs) with specific DNA recognition probe. Based on the recognition of the complementary target through protospacer adjacent motif (PAM) confirmation and CRISPR-derived RNA (crRNA) matching, the easily formed Cas12a/crRNA duplex can get access to the interface, and the cis and trans cleavage of Cas12a can be easily activated. In combination with the enzyme catalyzed reaction, they achieved an ultralow limit of detection (LOD) of 100 fm in HPV-16 detection without pre-amplification. Furthermore, the platform is compatible with a spike-in human serum sample and has superior stability. Thus, their reported platform offers a practical, versatile, and amplification-free toolbox for ultrasensitive nucleic acid analysis.
Collapse
Affiliation(s)
- Jing Su
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yuqing Ke
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Nokuzola Maboyi
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiao Zhi
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Sijia Yan
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Fuwu Li
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Bo Zhao
- Stony Brook University, Stony Brook, NY, 11794, USA
| | - Xiaolong Jia
- Department of Urology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, 17 Ningbo, Zhejiang Province, China
| | - Shiping Song
- Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China
| |
Collapse
|
32
|
Wagenknecht HA. Remote Photodamaging of DNA by Photoinduced Energy Transport. Chembiochem 2021; 23:e202100265. [PMID: 34569126 PMCID: PMC9292490 DOI: 10.1002/cbic.202100265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 09/14/2021] [Indexed: 12/11/2022]
Abstract
Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.
Collapse
Affiliation(s)
- Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| |
Collapse
|
33
|
Valdiviezo J, Zhang P, Beratan DN. Electron ratcheting in self-assembled soft matter. J Chem Phys 2021; 155:055102. [PMID: 34364335 DOI: 10.1063/5.0044420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 109 V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source-drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.
Collapse
Affiliation(s)
- Jesús Valdiviezo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| |
Collapse
|
34
|
Wettasinghe AP, Singh N, Starcher CL, DiTusa CC, Ishak-Boushaki Z, Kahanda D, McMullen R, Motea EA, Slinker JD. Detecting Attomolar DNA-Damaging Anticancer Drug Activity in Cell Lysates with Electrochemical DNA Devices. ACS Sens 2021; 6:2622-2629. [PMID: 34156840 DOI: 10.1021/acssensors.1c00365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we utilize electrochemical DNA devices to quantify and understand the cancer-specific DNA-damaging activity of an emerging drug in cellular lysates at femtomolar and attomolar concentrations. Isobutyl-deoxynyboquinone (IB-DNQ), a potent and tumor-selective NAD(P)H quinone oxidoreductase 1 (NQO1) bioactivatable drug, was prepared and biochemically verified in cancer cells highly expressing NQO1 (NQO1+) and knockdowns with low NQO1 expression (NQO1-) by Western blot, NQO1 activity analysis, survival assays, oxygen consumption rate, extracellular acidification rate, and peroxide production. Lysates from these cells and the IB-DNQ drug were then introduced to a chip system bearing an array of DNA-modified electrodes, and their DNA-damaging activity was quantified by changes in DNA-mediated electrochemistry arising from base-excision repair. Device-level controls of NQO1 activity and kinetic analysis were used to verify and further understand the IB-DNQ activity. A 380 aM IB-DNQ limit of detection and a 1.3 fM midpoint of damage were observed in NQO1+ lysates, both metrics 2 orders of magnitude lower than NQO1- lysates, indicating the high IB-DNQ potency and selectivity for NQO1+ cancers. The device-level damage midpoint concentration in NQO1+ lysates was over 8 orders of magnitude lower than cell survival benchmarks, likely due to poor IB-DNQ cellular uptake, demonstrating that these devices can identify promising drugs requiring improved cell permeability. Ultimately, these results indicate the noteworthy potency and selectivity of IB-DNQ and the high sensitivity and precision of electrochemical DNA devices to analyze agents/drugs involved in DNA-damaging chemotherapies.
Collapse
Affiliation(s)
- Ashan P. Wettasinghe
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Naveen Singh
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Colton L. Starcher
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Chloe C. DiTusa
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Zakari Ishak-Boushaki
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Dimithree Kahanda
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
- Department of Physics, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Reema McMullen
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| | - Edward A. Motea
- Department of Biochemistry and Molecular Biology, Simon Comprehensive Cancer Center, Indiana University School of Medicine, 980 W. Walnut Street, Walther Hall R3 C551, Indianapolis, Indiana 46202, United States
| | - Jason D. Slinker
- Department of Physics, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
- Department of Materials Science and Engineering, The University of Texas at Dallas, 800 W. Campbell Road, SCI 10, Richardson, Texas 75080, United States
| |
Collapse
|
35
|
Hybridization chain reaction and its applications in biosensing. Talanta 2021; 234:122637. [PMID: 34364446 DOI: 10.1016/j.talanta.2021.122637] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022]
Abstract
To pursue the sensitive and efficient detection of informative biomolecules for bioanalysis and disease diagnosis, a series of signal amplification techniques have been put forward. Among them, hybridization chain reaction (HCR) is an isothermal and enzyme-free process where the cascade reaction of hybridization events is initiated by a target analyte, yielding a long nicked dsDNA molecule analogous to alternating copolymers. Compared with conventional polymerase chain reaction (PCR) that can proceed only with the aid of polymerases and complicated thermal cycling, HCR has attracted increasing attention because it can occur under mild conditions without using enzymes. As a powerful signal amplification tool, HCR has been employed to construct various simple, sensitive and economic biosensors for detecting nucleic acids, small molecules, cells, and proteins. Moreover, HCR has also been applied to assemble complex nanostructures, some of which even act as the carriers to execute the targeted delivery of anticancer drugs. Recently, HCR has engendered tremendous progress in RNA imaging applications, which can not only achieve endogenous RNA imaging in living cells or even living animals but also implement imaging-guided photodynamic therapy, paving a promising path to promote the development of theranostics. In this review, we begin with the fundamentals of HCR and then focus on summarizing the recent advances in HCR-based biosensors for biosensing and RNA imaging strategies. Further, the challenges and future perspective of HCR-based signal amplification in biosensing and theranostic application are discussed.
Collapse
|
36
|
Magriñá I, Ortiz M, Simonova A, Hocek M, O’ Sullivan CK, Forster RJ. Ferrocene-Containing DNA Monolayers: Influence of Electrostatics on the Electron Transfer Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3359-3369. [PMID: 33705153 PMCID: PMC8819689 DOI: 10.1021/acs.langmuir.0c03485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/01/2021] [Indexed: 06/12/2023]
Abstract
A 153-mer target DNA was amplified using ethynyl ferrocene dATP and a tailed forward primer resulting in a duplex with a single-stranded DNA tail for hybridization to a surface-tethered probe. A thiolated probe containing the sequence complementary to the tail as well as a 15 polythimine vertical spacer with a (CH2)6 spacer was immobilized on the surface of a gold electrode and hybridized to the ferrocene-modified complementary strand. Potential step chronoamperometry and cyclic voltammetry were used to probe the potential of zero charge, PZC, and the rate of heterogeneous electron transfer between the electrode and the immobilized ferrocene moieties. Chronoamperometry gives three, well-resolved exponential current-time decays corresponding to ferrocene centers located within 13 Å (4 bases) along the duplex. Significantly, the apparent standard heterogeneous electron transfer rate constant, kappo, observed depends on the initial potential, i.e., the rate of electron transfer at zero driving force is not the same for oxidation and reduction of the ferrocene labels. Moreover, the presence of ions, such as Sr2+, that strongly ion pair with the negatively charged DNA backbone modulates the electron transfer rate significantly. Specifically, kappo = 246 ± 23.5 and 14 ± 1.2 s-1 for reduction and oxidation, respectively, where the Sr2+ concentration is 10 mM, but the corresponding values in 1 M Sr2+ are 8 ± 0.8 and 150 ± 12 s-1. While other factors may be involved, these results are consistent with a model in which a low Sr2+ concentration and an initial potential that is negative of the PZC lead to electrostatic repulsion of the negatively charged DNA backbone and the negatively charged electrode. This leads to the DNA adopting an extended configuration (concertina open), resulting in a slow rate of heterogeneous electron transfer. In contrast, for ferrocene reduction, the initial potential is positive of PZC and the negatively charged DNA is electrostatically attracted to the electrode (concertina closed), giving a shorter electron transfer distance and a higher rate of heterogeneous electron transfer. When the Sr2+ concentration is high, the charge on the DNA backbone is compensated by the electrolyte and the charge on the electrode dominates the electron transfer dynamics and the opposite potential dependence is observed. These results open up the possibility of electromechanical switching using DNA superstructures.
Collapse
Affiliation(s)
- Ivan Magriñá
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
| | - Mayreli Ortiz
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
| | - Anna Simonova
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Ciara K. O’ Sullivan
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Robert J. Forster
- School
of Chemical Sciences, FutureNeuro SFI Research Centre, National Centre
for Sensor Research, Dublin City University, Dublin D09 V209, Ireland
| |
Collapse
|
37
|
Teo RD, Du X, Vera HLT, Migliore A, Beratan DN. Correlation between Charge Transport and Base Excision Repair in the MutY-DNA Glycosylase. J Phys Chem B 2021; 125:17-23. [PMID: 33371674 DOI: 10.1021/acs.jpcb.0c08598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Experimental evidence suggests that DNA-mediated redox signaling between high-potential [Fe4S4] proteins is relevant to DNA replication and repair processes, and protein-mediated charge transfer (CT) between [Fe4S4] clusters and nucleic acids is a fundamental process of the signaling and repair mechanisms. We analyzed the dominant CT pathways in the base excision repair glycosylase MutY using molecular dynamics simulations and hole hopping pathway analysis. We find that the adenine nucleobase of the mismatched A·oxoG DNA base pair facilitates [Fe4S4]-DNA CT prior to adenine excision by MutY. We also find that the R153L mutation in MutY (linked to colorectal adenomatous polyposis) influences the dominant [Fe4S4]-DNA CT pathways and appreciably decreases their effective CT rates.
Collapse
Affiliation(s)
- Ruijie D Teo
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xiaochen Du
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Computer Science, Duke University, Durham, North Carolina 27708, United States
| | - Héctor Luis Torres Vera
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Agostino Migliore
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States
| |
Collapse
|
38
|
Affiliation(s)
- Jennifer Frommer
- Institute for Biochemistry University Greifswald Felix Hausdorff Str. 4 17487 Greifswald Germany
- present address: School of Chemistry University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Sabine Müller
- Institute for Biochemistry University Greifswald Felix Hausdorff Str. 4 17487 Greifswald Germany
| |
Collapse
|
39
|
Englert K, Hendi R, Robbs PH, Rees NV, Robinson APG, Tucker JHR. Cisplatin adducts of DNA as precursors for nanostructured catalyst materials. NANOSCALE ADVANCES 2020; 2:4491-4497. [PMID: 36132916 PMCID: PMC9417135 DOI: 10.1039/d0na00528b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/17/2020] [Indexed: 06/16/2023]
Abstract
The synthesis and characterisation of novel metal-modified DNA precursors for fuel cell catalyst development are described. Material precursors in the form of metal-DNA complexes were prepared through the reaction of DNA with cisplatin at various loadings and spectroscopically tested to confirm the platinum binding mode and the degree of complexation. The surface morphology of the DNA-metal material was analysed by Scanning Transmission Electron Microscopy (STEM), which revealed the extent of platinum nanocluster formation, with low metal loadings leading to observation of individual platinum atoms. Electrochemical measurements showed a greater electrocatalytic activity for the hydrogen evolution reaction (HER) with increased platinum loadings, shifting the half wave potential, E 1/2, away from the glassy carbon limit towards that of a bulk Pt electrode. This is explained further by Tafel plots, from which a change in the mechanism of the apparent rate limiting step for proton reduction from a Volmer to a Heyrovsky mechanism is postulated as the platinum loading increases.
Collapse
Affiliation(s)
- Klaudia Englert
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Ruba Hendi
- School of Chemical Engineering, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Peter H Robbs
- School of Chemical Engineering, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Neil V Rees
- School of Chemical Engineering, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - Alex P G Robinson
- School of Chemical Engineering, University of Birmingham Edgbaston Birmingham B15 2TT UK
| | - James H R Tucker
- School of Chemistry, University of Birmingham Edgbaston Birmingham B15 2TT UK
| |
Collapse
|
40
|
Frommer J, Müller S. Reductive Charge Transfer through an RNA Aptamer. Angew Chem Int Ed Engl 2020; 59:22999-23004. [PMID: 32852119 PMCID: PMC7756803 DOI: 10.1002/anie.202009430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/20/2020] [Indexed: 12/27/2022]
Abstract
The transfer of charges through double helical DNA is a very well investigated bioelectric phenomenon. RNA, on the contrary, has been less studied in this regard. The few available data report on charge transfer through RNA duplex structures mainly composed of homonucleotide sequences. In the light of the RNA world scenarios, it is an interesting question, if charge transfer can be coupled with RNA function. Functional RNAs however, contain versatile structural motifs. Therefore, electron transport also through non‐Watson–Crick base‐paired regions might be required. We here demonstrate distance‐dependent reductive charge transfer through RNA duplexes and through the non‐Watson–Crick base‐paired region of an RNA aptamer.
Collapse
Affiliation(s)
- Jennifer Frommer
- Institute for Biochemistry, University Greifswald, Felix Hausdorff Str. 4, 17487, Greifswald, Germany.,present address: School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Felix Hausdorff Str. 4, 17487, Greifswald, Germany
| |
Collapse
|
41
|
Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair. DNA Repair (Amst) 2020; 96:102972. [PMID: 33007515 DOI: 10.1016/j.dnarep.2020.102972] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/02/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022]
Abstract
Critical for transcription initiation and bulky lesion DNA repair, TFIIH provides an exemplary system to connect molecular mechanisms to biological outcomes due to its strong genetic links to different specific human diseases. Recent advances in structural and computational biology provide a unique opportunity to re-examine biologically relevant molecular structures and develop possible mechanistic insights for the large dynamic TFIIH complex. TFIIH presents many puzzles involving how its two SF2 helicase family enzymes, XPB and XPD, function in transcription initiation and repair: how do they initiate transcription, detect and verify DNA damage, select the damaged strand for incision, coordinate repair with transcription and cell cycle through Cdk-activating-kinase (CAK) signaling, and result in very different specific human diseases associated with cancer, aging, and development from single missense mutations? By joining analyses of breakthrough cryo-electron microscopy (cryo-EM) structures and advanced computation with data from biochemistry and human genetics, we develop unified concepts and molecular level understanding for TFIIH functions with a focus on structural mechanisms. We provocatively consider that TFIIH may have first evolved from evolutionary pressure for TCR to resolve arrested transcription blocks to DNA replication and later added its key roles in transcription initiation and global DNA repair. We anticipate that this level of mechanistic information will have significant impact on thinking about TFIIH, laying a robust foundation suitable to develop new paradigms for DNA transcription initiation and repair along with insights into disease prevention, susceptibility, diagnosis and interventions.
Collapse
|
42
|
Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Reprint of "Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces". J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
43
|
Saunders SH, Tse ECM, Yates MD, Otero FJ, Trammell SA, Stemp EDA, Barton JK, Tender LM, Newman DK. Extracellular DNA Promotes Efficient Extracellular Electron Transfer by Pyocyanin in Pseudomonas aeruginosa Biofilms. Cell 2020; 182:919-932.e19. [PMID: 32763156 DOI: 10.1016/j.cell.2020.07.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/19/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022]
Abstract
Redox cycling of extracellular electron shuttles can enable the metabolic activity of subpopulations within multicellular bacterial biofilms that lack direct access to electron acceptors or donors. How these shuttles catalyze extracellular electron transfer (EET) within biofilms without being lost to the environment has been a long-standing question. Here, we show that phenazines mediate efficient EET through interactions with extracellular DNA (eDNA) in Pseudomonas aeruginosa biofilms. Retention of pyocyanin (PYO) and phenazine carboxamide in the biofilm matrix is facilitated by eDNA binding. In vitro, different phenazines can exchange electrons in the presence or absence of DNA and can participate directly in redox reactions through DNA. In vivo, biofilm eDNA can also support rapid electron transfer between redox active intercalators. Together, these results establish that PYO:eDNA interactions support an efficient redox cycle with rapid EET that is faster than the rate of PYO loss from the biofilm.
Collapse
Affiliation(s)
- Scott H Saunders
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA
| | - Edmund C M Tse
- Division of Chemistry and Chemical Engineering, Caltech, Pasadena, CA, USA; Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Matthew D Yates
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | | | - Scott A Trammell
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA
| | - Eric D A Stemp
- Department of Physical Sciences, Mt. Saint Mary's University, Los Angeles, CA, USA
| | | | - Leonard M Tender
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA.
| | - Dianne K Newman
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA; Division of Geological and Planetary Sciences, Caltech, Pasadena, CA, USA.
| |
Collapse
|
44
|
Zeng D, Salvatore P, Karlsen KK, Zhang J, Wengel J, Ulstrup J. Electrochemical intercalator binding to single- and double-strand DNA- and LNA-based molecules on Au(111)-electrode surfaces. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
45
|
Xu W, Jin T, Dai Y, Liu CC. Surpassing the detection limit and accuracy of the electrochemical DNA sensor through the application of CRISPR Cas systems. Biosens Bioelectron 2020; 155:112100. [PMID: 32090878 DOI: 10.1016/j.bios.2020.112100] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 12/26/2022]
Abstract
Robust developments of personalized medicine for next-generation healthcare highlight the need for sensitive and accurate point-of-care platforms for quantification of disease biomarkers. Broad presentations of clustered regularly interspaced short palindromic repeats (CRISPR) as an accurate gene editing tool also indicate that the high-specificity and programmability of CRISPR system can be utilized for the development of biosensing systems. Herein, we present a CRISPR Cas system enhanced electrochemical DNA (E-DNA) sensor with unprecedented sensitivity and accuracy. The principle of the E-DNA sensor is the target induced conformational change of the surface signaling probe (containing an electrochemical tag), leading to the variation of the electron transfer rate of the electrochemical tag. With the introduction of CRISPR cleavage activity into the E-DNA sensor, a more apparent signal change between with and without the presence of the target can be achieved. We compared the performance of Cas9 and Cas12a enhanced E-DNA sensor and optimized the chemical environment of CRISPR, achieving a femto-molar detection limit without enzymatic amplification. Moreover, we correlated the CRISPR cleavage signal with the original E-DNA signal as a strategy to indicate potential mismatches in the target sequence. Comparing with classic DNA electrochemistry based mutation detection strategy, CRISPR enhanced E-DNA sensor can determine the presence of a single mutation at an unknown concentration condition. Overall, we believe that the CRISPR enhanced E-DNA sensing strategy will be of especially high utility for point-of-care systems owing to the programmability, modularity, high-sensitivity and high-accuracy.
Collapse
Affiliation(s)
- Wei Xu
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Tian Jin
- College of Biological Sciences, University of California, Davis, CA, 95616, USA
| | - Yifan Dai
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA; Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Chung Chiun Liu
- Department of Chemical and Biomolecular Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA; Electronics Design Center, Case Western Reserve University, Cleveland, OH, 44106, USA
| |
Collapse
|
46
|
Gee A, Jaafar AH, Kemp NT. Nanoscale junctions for single molecule electronics fabricated using bilayer nanoimprint lithography combined with feedback controlled electromigration. NANOTECHNOLOGY 2020; 31:155203. [PMID: 31860883 DOI: 10.1088/1361-6528/ab6473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanoimprint lithography (NIL) is a fast, simple and high throughput technique that allows fabrication of structures with nanometre precision features at low cost. We present an advanced bilayer nanoimprint lithography approach to fabricate four terminal nanojunction devices for use in single molecule electronic studies. In the first part of this work, we demonstrate a NIL lift-off process using a bilayer resist technique that negates problems associated with metal side-wall tearing during lift-off. In addition to precise nanoscale feature replication, we show that it is possible to imprint micron-sized features while still maintaining a bilayer structure enabling an undercut resist structure to be formed. This is accomplished by choosing suitable imprint parameters as well as residual layer etching depth and development time. We then use a feedback controlled electromigration procedure, to produce room-temperature stable nanogap electrodes with sizes below 2 nm. This approach facilitates the integration of molecules in stable, solid-state molecular electronic devices as demonstrated by incorporating benzenethiol as molecular bridges between the electrodes and characterizing its electronics properties through current-voltage measurements. The observation of molecular transport signatures, showing current suppression in the I-V behaviour at low voltage, which is then lifted at high voltage, signifying on- and off-resonant transport through molecular levels as a function of voltage, is confirmed in repeated I-V sweeps. The large conductance, symmetry of the I-V sweep and small value of the voltage minimum in transition voltage spectroscopy indicates the bridging of the two benzenethiol molecules is by π-stacking.
Collapse
Affiliation(s)
- Alex Gee
- Department of Physics and Mathematics, University of Hull, Hull, HU6 7RX, United Kingdom
| | | | | |
Collapse
|
47
|
Likhachev VN, Vinogradov GA. Polaron on a Lattice with a Trap in the Su–Schrieffer–Heeger Approximation. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2020. [DOI: 10.1134/s1990793120020098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
48
|
Murgunde BK, Rabinal MK. Tuning DNA electrical conductivity by silver photo-doping. Biomed Phys Eng Express 2020; 6:015017. [DOI: 10.1088/2057-1976/ab5c04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
49
|
Wang C, Wu J, He Y, Song Z, Shi S, Zhu Y, Jia Y, Ye W. Fully Solid-State Graphene Transistors with Striking Homogeneity and Sensitivity for the Practicalization of Single-Device Electronic Bioassays. NANO LETTERS 2020; 20:166-175. [PMID: 31815482 DOI: 10.1021/acs.nanolett.9b03528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
To break through a critical barrier in the practical application of graphene biosensors, namely, device-to-device performance inhomogeneity, this work presents a novel scenario employing a fully solid-state (FSS) transistor configuration. Herein, the graphene sensing unit is completely encapsulated by a high-κ solid dielectric material, which isolates the sensing unit from solution contaminants and thus homogeneously maintains the extraordinary carrier mobility of pristine graphene in batch-made devices. To create an interface sensitive to biomolecular interactions based on the FSS configuration, a metallic floating gate functionalized by conductive mercapto-phenyl molecular linkers is defined on the top-layer solid dielectric. As the solid dielectric layer beneath the metal floating gate enables a higher capacitive gating efficiency than the regular graphene-solution electrical double layer (EDL) interface, the overall transistor amplification gain is further enhanced. As a proof of principle, a label-free DNAzymatic bioassay of Pb2+ is conducted. Without the traditional one-by-one device normalization, an excellent concentration detection limit of 929.8 fM is achieved, which is almost 2 orders of magnitude lower than that in existing works. The FSS configuration allows enhanced sensitivity and homogeneity, thereby providing new developmental guidelines for graphene biosensors beyond the laboratory investigation stage. Additionally, it has the potential to be universally applicable for cost-efficient single-device bioassays.
Collapse
Affiliation(s)
| | | | | | | | | | - Yibo Zhu
- Department of Mechanical Engineering , Columbia University , New York 10027 , United States
| | - Yuan Jia
- Jiangsu Key Laboratory of Micro-Nano Biomedical Instrument Design and Manufacture, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Weixiang Ye
- Jiangsu Key Laboratory of Thin Films, School of Physical Science and Technology , Soochow University , Suzhou 215006 , China
| |
Collapse
|
50
|
Cheng R, Loire E, Martens J, Fridgen TD. An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase. Phys Chem Chem Phys 2020; 22:2999-3007. [DOI: 10.1039/c9cp06393e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.
Collapse
Affiliation(s)
- Ruodi Cheng
- Department of Chemistry
- Memorial University
- St. John's
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO
- Campus Universite d’Orsay
- France
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- Nijmegen
- The Netherlands
| | | |
Collapse
|