1
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Bardales AC, Mills JR, Kolpashchikov DM. DNA Nanostructures as Catalysts: Double Crossover Tile-Assisted 5' to 5' and 3' to 3' Chemical Ligation of Oligonucleotides. Bioconjug Chem 2024; 35:28-33. [PMID: 38135674 DOI: 10.1021/acs.bioconjchem.3c00502] [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: 12/24/2023]
Abstract
Accessibility of synthetic oligonucleotides and the success of DNA nanotechnology open a possibility to use DNA nanostructures for building sophisticated enzyme-like catalytic centers. Here we used a double DNA crossover (DX) tile nanostructure to enhance the rate, the yield, and the specificity of 5'-5' ligation of two oligonucleotides with arbitrary sequences. The ligation product was isolated via a simple procedure. The same strategy was applied for the synthesis of 3'-3' linked oligonucleotides, thus introducing a synthetic route to DNA and RNA with a switched orientation that is affordable by a low-resource laboratory. To emphasize the utility of the ligation products, we synthesized a circular structure formed from intramolecular complementarity that we named "an impossible DNA wheel" since it cannot be built from regular DNA strands by enzymatic reactions. Therefore, DX-tile nanostructures can open a route to producing useful chemical products that are unattainable via enzymatic synthesis. This is the first example of the use of DNA nanostructures as a catalyst. This study advocates for further exploration of DNA nanotechnology for building enzyme-like reactive systems.
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Affiliation(s)
- Andrea C Bardales
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Joseph R Mills
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, Florida 32816, United States
- National Center for Forensic Science, University of Central Florida, Orlando, Florida 32816, United States
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32816, United States
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2
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Zhang C, Zheng T, Ma Q, Yang L, Zhang M, Wang J, Teng X, Miao Y, Lin HC, Yang Y, Han D. Logical Analysis of Multiple Single-Nucleotide-Polymorphisms with Programmable DNA Molecular Computation for Clinical Diagnostics. Angew Chem Int Ed Engl 2022; 61:e202117658. [PMID: 35137499 DOI: 10.1002/anie.202117658] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Indexed: 11/07/2022]
Abstract
Analyzing complex single-nucleotide-polymorphism (SNP) combinations in the genome is important for research and clinical applications, given that different SNP combinations can generate different phenotypic consequences. Recent works have shown that DNA-based molecular computing is powerful for simultaneously sensing and analyzing complex molecular information. Here, we designed a switching circuit-based DNA computational scheme that can integrate the sensing of multiple SNPs and simultaneously perform logical analysis of the detected SNP information to directly report clinical outcomes. As a demonstration, we successfully achieved automatic and accurate identification of 21 different blood group genotypes from 83 clinical blood samples with 100 % accuracy compared to sequencing data in a more rapid manner (3 hours). Our method enables a new mode of automatic and logical sensing and analyzing subtle molecular information for clinical diagnosis, as well as guiding personalized medication.
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Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tingting Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Junyan Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaoyan Teng
- Department of Laboratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 201306, China
| | - Yanyan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Hsiao-Chu Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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3
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Zhang C, Zheng T, Ma Q, Yang L, Zhang M, Wang J, Teng X, Miao Y, Lin H, Yang Y, Han D. Logical Analysis of Multiple Single‐Nucleotide‐Polymorphisms with Programmable DNA Molecular Computation for Clinical Diagnostics. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Chao Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Tingting Zheng
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Qian Ma
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Linlin Yang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Mingzhi Zhang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Junyan Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Xiaoyan Teng
- Department of Laboratory Medicine Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai 201306 China
| | - Yanyan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Hsiao‐chu Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
| | - Yang Yang
- Department of Thoracic Surgery Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai 200433 China
| | - Da Han
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai 200127 China
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4
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Gomes de Oliveira AG, Dubovichenko MV, ElDeeb AA, Wanjohi J, Zablotskaya S, Kolpashchikov DM. RNA-Cleaving DNA Thresholder Controlled by Concentrations of miRNA Cancer Marker. Chembiochem 2021; 22:1750-1754. [PMID: 33433948 DOI: 10.1002/cbic.202000769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/30/2020] [Indexed: 11/10/2022]
Abstract
Oligonucleotide gene therapy (OGT) agents suppress specific mRNAs in cells and thus reduce the expression of targeted genes. The ability to unambiguously distinguish cancer from healthy cells can solve the low selectivity problem of OGT agents. Cancer RNA markers are expressed in both healthy and cancer cells with a higher expression level in cancer cells. We have designed a DNA-based construct, named DNA thresholder (DTh) that cleaves targeted RNA only at high concentrations of cancer marker RNA and demonstrates low cleavage activity at low marker concentrations. The RNA-cleaving activity can be adjusted within one order of magnitude of the cancer marker RNA concentration by simply redesigning DTh. Importantly, DTh recognizes cancer marker RNA, while cleaving targeted RNA; this offers a possibility to suppress vital genes exclusively in cancer cells, thus triggering their death. DTh is a prototype of computation-inspired molecular device for controlling gene expression and cancer treatment.
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Affiliation(s)
- Andrey Giovanni Gomes de Oliveira
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation
| | - Mikhail V Dubovichenko
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation
| | - Ahmed A ElDeeb
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation
| | - Joseph Wanjohi
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation
| | - Sofia Zablotskaya
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation
| | - Dmitry M Kolpashchikov
- SCAMT institute, Laboratory of Molecular Robotics and Biosensor Materials, ITMO University, 9 Lomonosova Str., 191002, St. Petersburg, Russian Federation.,Chemistry Department, University of Central Florida, 32816-2366, Orlando, FL, USA.,Burnett School of Biomedical Sciences, University of Central Florida, 32816, Orlando, FL, USA
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5
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Molden TA, Grillo MC, Kolpashchikov DM. Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors. Chemistry 2020; 27:2421-2426. [DOI: 10.1002/chem.202003959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/30/2020] [Indexed: 01/27/2023]
Affiliation(s)
- Tatiana A. Molden
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
| | - Marcella C. Grillo
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
| | - Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida 4111 Libra Drive, Physical Sciences 255 Orlando FL 32816-2366 USA
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6
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Wei W, Li J, Yao H, Shi K, Liu H. A versatile molecular logic system based on Eu(III) coordination polymer film electrodes combined with multiple properties of NADH. Phys Chem Chem Phys 2020; 22:22746-22757. [PMID: 33020777 DOI: 10.1039/d0cp03020a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein, a new type of lanthanide coordination polymer film made up of europium (Eu(iii)) and poly(N-methacryloylglycine) (Eu(iii)-PMAG) was prepared on an ITO electrode surface driven by the coordination between N-methacryloylglycine (MAG) and Eu(iii) through a single-step polymerization process. The fluorescence signal of Eu(iii)-PMAG films at 617 nm originating from Eu(iii) could be well retained in the buffer solution but was regulated by the concentration of Cu(ii) and the complexing agent EDTA. The switching of fluorescence by Cu(ii) was attributed to the inhibition of the "antenna effect" between Eu(iii) and the MAG ligand in the films. The coexistence of reduced β-nicotinamide adenine dinucleotide (NADH) in the solution can apparently quench the fluorescence of Eu(iii)-PMAG films through the internal filtration effect of UV absorbance overlapping the excitation wavelength, but itself exhibiting a fluorescence emission at 468 nm. In addition, the electrocatalytic oxidation of NADH with the help of the ferrocenedicarboxylic acid (FcDA) probe demonstrated a cyclic voltammetry (CV) signal at 0.45 V (vs. SCE). Based on various reversible stimulus-responsive behaviours, a 4-input/10-output logic network was built using Cu(ii), EDTA, NADH and FcDA as inputs and the signals of fluorescence from Eu(iii)-PMAG (617 nm) and NADH (468 nm), the CV response from FcDA and the UV-vis absorbance from the Cu(ii)-EDTA complex as outputs. Meanwhile, 6 different functional logic devices were constructed based on the same versatile platform, including a 2-to-1 encoder, a 1-to-2 decoder, a 1-to-2 demultiplexer, a parity checker, a transfer gate and a reprogrammable 3-input/2-output keypad lock. Combined with the new type of lanthanide coordination polymer film, NADH played central roles in designing sophisticated computing systems with its fluorescence, UV and electrocatalytic properties. This work might provide a novel avenue to develop intelligent multi-analyte sensing and information processing at the molecular level based on one single platform.
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Affiliation(s)
- Wenting Wei
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China.
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7
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Biswas PK, Saha S, Gaikwad S, Schmittel M. Reversible Multicomponent AND Gate Triggered by Stoichiometric Chemical Pulses Commands the Self-Assembly and Actuation of Catalytic Machinery. J Am Chem Soc 2020; 142:7889-7897. [DOI: 10.1021/jacs.0c01315] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Pronay Kumar Biswas
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Suchismita Saha
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Sudhakar Gaikwad
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and Engineering, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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8
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Huang D, Guo C, Miao J, Zhang Y, Lin X, Chen D, Yang S, Yang Q, Tang Y. Construction of a novel DNA-based comparator and its application in intelligent analysis. NANOSCALE 2019; 11:16241-16244. [PMID: 31454010 DOI: 10.1039/c9nr05270d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this work, a novel and general comparator was constructed based on cascaded strand displacement reactions and DNA hybridization and its potential in intelligently weighing the quantitative predominance of two targets was explored in a complex biological matrix, which not only enriches the information processing mode of DNA computation but also provides an instructive way to deal with quantitative analyzing tasks in further DNA-based logic sensors.
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Affiliation(s)
- Dan Huang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Chen Guo
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Jiarong Miao
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yi Zhang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Xiao Lin
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Die Chen
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Shu Yang
- West China School of Pharmacy, Sichuan University, Chengdu, 610041, China.
| | - Qianfan Yang
- College of Chemistry, Sichuan University, Chengdu 610064, Sichuan, China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Centre for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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9
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Abstract
Hybridization probes are RNA or DNA oligonucleotides or their analogs that bind to specific nucleotide sequences in targeted nucleic acids (analytes) via Watson-Crick base pairs to form probe-analyte hybrids. Formation of a stable hybrid would indicate the presence of a DNA or RNA fragment complementary to the known probe sequence. Some of the well-known technologies that rely on nucleic acid hybridization are TaqMan and molecular beacon (MB) probes, fluorescent in situ hybridization (FISH), polymerase chain reaction (PCR), antisense, siRNA, and CRISPR/cas9, among others. Although invaluable tools for DNA and RNA recognition, hybridization probes suffer from several common disadvantages including low selectivity under physiological conditions, low affinity to folded single-stranded RNA and double-stranded DNA, and high cost of dye-labeled and chemically modified probes. Hybridization probes are evolving into multifunctional molecular devices (dubbed here "multicomponent probes", "DNA machines", and "DNA robots") to satisfy complex and often contradictory requirements of modern biomedical applications. In the definition used here, "multicomponent probes" are DNA probes that use more than one oligonucleotide complementary to an analyzed sequence. A "DNA machine" is an association of a discrete number of DNA strands that undergoes structural rearrangements in response to the presence of a specific analyte. Unlike multicomponent probes, DNA machines unify several functional components in a single association even in the absence of a target. DNA robots are DNA machines equipped with computational (analytic) capabilities. This Account is devoted to an overview of the ongoing evolution of hybridization probes to DNA machines and robots. The Account starts with a brief excursion to historically significant and currently used instantaneous probes. The majority of the text is devoted to the design of (i) multicomponent probes and (ii) DNA machines for nucleic acid recognition and analysis. The fundamental advantage of both designs is their ability to simultaneously address multiple problems of RNA/DNA analysis. This is achieved by modular design, in which several specialized functional components are used simultaneously for recognition of RNA or DNA analytes. The Account is concluded with the analysis of perspectives for further evolution of DNA machines into DNA robots.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Department of Chemistry, University of Central Florida, 4111 Libra Drive, Physical Sciences
255, Orlando, Florida 32816-2366, United States
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10
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Sun SC, Lee CC, Chuang MC. Polymerase-assisted fluorescence resonance energy transfer (FRET) assay for simultaneous detection of binary viral sequences. Anal Chim Acta 2018; 1030:148-155. [DOI: 10.1016/j.aca.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/01/2018] [Indexed: 12/20/2022]
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11
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Connelly RP, Morozkin ES, Gerasimova YV. Alphanumerical Visual Display Made of DNA Logic Gates for Drug Susceptibility Testing of Pathogens. Chembiochem 2018; 19:203-206. [PMID: 29206338 PMCID: PMC5962014 DOI: 10.1002/cbic.201700626] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics of drug-resistant pathogens require the analysis of point mutations in bacterial or viral genomes, which is usually performed by trained professionals and/or by sophisticated computer algorithms. We have developed a DNA-based logic system that autonomously analyzes mutations found in the genome of Mycobacterium tuberculosis complex (MTC) bacteria and communicates the output to a human user as alphanumeric characters read by the naked eye. The five-gate system displays "O" ("no infection") for the absence of MTC infection and "P" or "F" for passing or failing a drug-susceptibility test, respectively.
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Affiliation(s)
- Ryan P Connelly
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Evgeny S Morozkin
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4111 Libra Drive, Orlando, FL, 32816, USA
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12
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Simultaneous detections of genetic fragment and single nucleotide mutation with a three-tiered output for tuberculosis diagnosis. Anal Chim Acta 2017; 1007:1-9. [PMID: 29405982 DOI: 10.1016/j.aca.2017.12.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/30/2017] [Accepted: 12/11/2017] [Indexed: 01/08/2023]
Abstract
Tuberculosis (TB) remains one of the major infectious diseases worldwide. The pathogenic bacterium, Mycobacterium tuberculosis (M.tb), continuously evolves strains carrying drug-resistance genes, thus posing a growing challenge to TB prevention and treatment. We report a diagnostic system that uses a molecular beacon probe and an assistant strand as the core to simultaneously interact with an M.tb-specific fragment (in IS6110) and a single nucleotide substitution (SNS)-encoded segment (in rpoB) associated with drug resistance. A single fluorescent output in three-tiered levels was produced for combinatorial interpretations based on formation of a four-way DNA junction (4WJ). The SNS caused the 4WJ to partially dissociate, thus resulting in medium-level fluorescence. By contrast, high- and low-level fluorescence, represented the complete complementary complex and absence of either targeted fragments, respectively. Manipulating the length of the analyte-binding arm realized the medium output. The thermodynamics and kinetics of 4WJ construction were investigated to maximize the tiered-output performance. Biocatalytic amplification driven by the Klenow Fragment and Nt.AlwI was incorporated into the method to enhance the signal 64-fold and ensure long-term stability of the three-tiered output. The detection accuracy of the sensing system was verified using unpurified amplicons with templates of extracted DNA and boiled bacterial solutions. The tiered-output mechanism was usable at bacterial loads ranging from 4 × 100 to 4 × 103 CFU per reaction. The interference caused by nontuberculous mycobacteria was minimal. The results demonstrated the integrity of the sensing method as an alternative strategy for rapid screening of M.tb and detecting rifampin-resistance.
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13
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Kamar O, Sun SC, Lin CH, Chung WY, Lee MS, Liao YC, Kolpashchikov DM, Chuang MC. A mutation-resistant deoxyribozyme OR gate for highly selective detection of viral nucleic acids. Chem Commun (Camb) 2017; 53:10592-10595. [PMID: 28900642 PMCID: PMC5645154 DOI: 10.1039/c7cc05576e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Highly selective probes hybridize only to fully complementary DNA or RNA sequences and, therefore, often fail to recognize mutated viral genomes. Here we designed a probe that possesses two seemingly incompatible properties: it tolerates some point mutations in genome, while it remains selective towards others. An OR deoxyribozyme logic gate was designed to fluorescently report the sequences of enterovirus 71 (EV71) covering ∼90% of all known EV71 strains. Importantly, sequences of closely related coxsackieviruses that differed by single nucleotides were reliably differentiated in 7 out of 8 cases.
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Affiliation(s)
- Ola Kamar
- Chemistry Department, University of Central Florida, Orlando, 32816, Florida, USA.
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14
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Campbell EA, Peterson E, Kolpashchikov DM. Self-Assembling Molecular Logic Gates Based on DNA Crossover Tiles. Chemphyschem 2017; 18:1730-1734. [PMID: 28234410 DOI: 10.1002/cphc.201700109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Indexed: 02/02/2023]
Abstract
DNA-based computational hardware has attracted ever-growing attention due to its potential to be useful in the analysis of complex mixtures of biological markers. Here we report the design of self-assembling logic gates that recognize DNA inputs and assemble into crossover tiles when the output signal is high; the crossover structures disassemble to form separate DNA stands when the output is low. The output signal can be conveniently detected by fluorescence using a molecular beacon probe as a reporter. AND, NOT, and OR logic gates were designed. We demonstrate that the gates can connect to each other to produce other logic functions.
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Affiliation(s)
- Eleanor A Campbell
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Evan Peterson
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, College of Medicine and National Center for Forensic Science, University of Central Florida, Orlando, FL, 32816, USA)An invited contribution to a Special Issue on Molecular Logic
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15
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Gamella M, Zakharchenko A, Guz N, Masi M, Minko S, Kolpashchikov DM, Iken H, Poghossian A, Schöning MJ, Katz E. DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array. ELECTROANAL 2017; 29:398-408. [PMID: 29379265 PMCID: PMC5786385 DOI: 10.1002/elan.201600389] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 12/23/2022]
Abstract
An array of four independently wired indium tin oxide (ITO) electrodes was used for electrochemically stimulated DNA release and activation of DNA-based Identity, AND and XOR logic gates. Single-stranded DNA molecules were loaded on the mixed poly(N,N-di-methylaminoethyl methacrylate) (PDMAEMA)/poly-(methacrylic acid) (PMAA) brush covalently attached to the ITO electrodes. The DNA deposition was performed at pH 5.0 when the polymer brush is positively charged due to protonation of tertiary amino groups in PDMAE-MA, thus resulting in electrostatic attraction of the negatively charged DNA. By applying electrolysis at -1.0 V(vs. Ag/AgCl reference) electrochemical oxygen reduction resulted in the consumption of hydrogen ions and local pH increase near the electrode surface. The process resulted in recharging the polymer brush to the negative state due to dissociation of carboxylic groups of PMAA, thus repulsing the negatively charged DNA and releasing it from the electrode surface. The DNA release was performed in various combinations from different electrodes in the array assembly. The released DNA operated as input signals for activation of the Boolean logic gates. The developed system represents a step forward in DNA computing, combining for the first time DNA chemical processes with electronic input signals.
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Affiliation(s)
- Maria Gamella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Andrey Zakharchenko
- Nanostructured Materials Lab, The University of Georgia, Athens, GA 30602, USA
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Madeline Masi
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
| | - Sergiy Minko
- Nanostructured Materials Lab, The University of Georgia, Athens, GA 30602, USA
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Heiko Iken
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
| | - Arshak Poghossian
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
- Institute of Bio- and Nanosystems, Research Centre Jülich, GmbH, D-52425 Jülich Germany
| | - Michael J. Schöning
- Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Jülich, Heinrich-Muβmann-Str. 1, D-52428 Jülich, Germany
- Institute of Bio- and Nanosystems, Research Centre Jülich, GmbH, D-52425 Jülich Germany
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA, http://people.clarkson.edu/~ekatz/
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16
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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17
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015; 55:164-8. [DOI: 10.1002/anie.201507249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/15/2015] [Indexed: 12/21/2022]
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18
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Tam DY, Dai Z, Chan MS, Liu LS, Cheung MC, Bolze F, Tin C, Lo PK. A Reversible DNA Logic Gate Platform Operated by One- and Two-Photon Excitations. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507249] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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19
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Guo Y, Yao W, Xie Y, Zhou X, Hu J, Pei R. Logic gates based on G-quadruplexes: principles and sensor applications. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1633-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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20
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O'Steen MR, Cornett EM, Kolpashchikov DM. Nuclease-containing media for resettable operation of DNA logic gates. Chem Commun (Camb) 2015; 51:1429-31. [PMID: 25493931 DOI: 10.1039/c4cc09283j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We designed and tested a system that allows DNA logic gates to respond multiple times to the addition of oligonucleotide inputs. After producing an output signal, the system spontaneously resets to the background state. This system does not require any operator action to achieve reset of a DNA logic gate, and may become useful for construction of reusable DNA-based computational devices.
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Affiliation(s)
- Martin R O'Steen
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA.
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21
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Engström A. Fighting an old disease with modern tools: characteristics and molecular detection methods of drug-resistant Mycobacterium tuberculosis. Infect Dis (Lond) 2015; 48:1-17. [PMID: 26167849 DOI: 10.3109/23744235.2015.1061205] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis (TB) is an ancient disease, but not a disease of the past. The increasing prevalence of drug-resistant strains of Mycobacterium tuberculosis, the causative agent of TB, demands new measures to combat the situation. Rapid and accurate detection of the pathogen, and its drug susceptibility pattern, is essential for timely initiation of treatment, and ultimately, control of the disease. Molecular-based methods offer a great chance to improve detection of drug-resistant TB; however, their development and usage should be accompanied with a profound understanding of drug resistance mechanisms and circulating M. tuberculosis strains in specific settings, as otherwise, the usefulness of such tests may be limited. This review gives an overview of the history of TB treatment and drug resistance, drug resistance mechanisms for the most commonly used drugs and molecular methods designed to detect drug-resistant strains.
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Affiliation(s)
- Anna Engström
- a From the Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden and Molecular Mycobacteriology, Research Center Borstel , Borstel , Germany
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22
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Lai YH, Liao YC, Mu JJ, Kuo TM, Hsu YH, Chuang MC. Biomolecular logic gate for analysis of the New Delhi metallo-β-lactamase (NDM)-coding gene with concurrent determination of its drug resistance-encoding fragments. Chem Commun (Camb) 2015; 50:12018-21. [PMID: 24835410 DOI: 10.1039/c4cc01108b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We herein exploit a newly schemed logic gate to superiorly facilitate analysis of long and highly structured nucleic acids. This strategy uniquely enables the identification of NDM-specific genes and concurrent screening of two active site-encoded fragments, which is promising for evaluating microbial drug resistance.
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Affiliation(s)
- Yu-Hsuan Lai
- Department of Chemistry, Tunghai University, Taichung, Taiwan.
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23
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Mailloux S, Gerasimova YV, Guz N, Kolpashchikov DM, Katz E. Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems. Angew Chem Int Ed Engl 2015; 54:6562-6. [PMID: 25864379 PMCID: PMC4495919 DOI: 10.1002/anie.201411148] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/06/2015] [Indexed: 11/09/2022]
Abstract
Molecular computing based on enzymes or nucleic acids has attracted a great deal of attention due to the perspectives of controlling living systems in the way we control electronic computers. Enzyme-based computational systems can respond to a great variety of small molecule inputs. They have the advantage of signal amplification and highly specific recognition. DNA computing systems are most often controlled by oligonucleotide inputs/outputs and are capable of sophisticated computing as well as controlling gene expressions. Here, we developed an interface that enables communication of otherwise incompatible nucleic-acid and enzyme-computational systems. The enzymatic system processes small molecules as inputs and produces NADH as an output. The NADH output triggers electrochemical release of an oligonucleotide, which is accepted by a DNA computational system as an input. This interface is universal because the enzymatic and DNA computing systems are independent of each other in composition and complexity.
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Affiliation(s)
- Shay Mailloux
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810 (USA)
| | - Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366 (USA)
| | - Nataliia Guz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810 (USA)
| | - Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366 (USA).
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810 (USA).
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24
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Lee CC, Liao YC, Lai YH, Lee CCD, Chuang MC. Recognition of dual targets by a molecular beacon-based sensor: subtyping of influenza A virus. Anal Chem 2015; 87:5410-6. [PMID: 25879394 DOI: 10.1021/acs.analchem.5b00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular beacon (MB)-based sensor to offer a decisive answer in combination with information originated from dual-target inputs is designed. The system harnesses an assistant strand and thermodynamically favored designation of unpaired nucleotides (UNs) to process the binary targets in "AND-gate" format and report fluorescence in "off-on" mechanism via a formation of a DNA four-way junction (4WJ). By manipulating composition of the UNs, the dynamic fluorescence difference between the binary targets-coexisting circumstance and any other scenario was maximized. Characteristic equilibrium constant (K), change of entropy (ΔS), and association rate constant (k) between the association ("on") and dissociation ("off") states of the 4WJ were evaluated to understand unfolding behavior of MB in connection to its sensing capability. Favorable MB and UNs were furthermore designed toward analysis of genuine genetic sequences of hemagglutinin (HA) and neuraminidase (NA) in an influenza A H5N2 isolate. The MB-based sensor was demonstrated to yield a linear calibration range from 1.2 to 240 nM and detection limit of 120 pM. Furthermore, high-fidelity subtyping of influenza virus was implemented in a sample of unpurified amplicons. The strategy opens an alternative avenue of MB-based sensors for dual targets toward applications in clinical diagnosis.
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Affiliation(s)
- Chun-Ching Lee
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | - Yu-Chieh Liao
- ‡Institute of Population Health Science, National Health Research Institutes, Zhunan, Miaoli County 35053, Taiwan
| | - Yu-Hsuan Lai
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
| | | | - Min-Chieh Chuang
- †Department of Chemistry, Tunghai University, Taichung 40704, Taiwan
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25
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Mailloux S, Gerasimova YV, Guz N, Kolpashchikov DM, Katz E. Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411148] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Wu L, Ren J, Qu X. Target-responsive DNA-capped nanocontainer used for fabricating universal detector and performing logic operations. Nucleic Acids Res 2014; 42:gku858. [PMID: 25249622 PMCID: PMC4245965 DOI: 10.1093/nar/gku858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 01/28/2023] Open
Abstract
Nucleic acids have become a powerful tool in nanotechnology because of their controllable diverse conformational transitions and adaptable higher-order nanostructure. Using single-stranded DNA probes as the pore-caps for various target recognition, here we present an ultrasensitive universal electrochemical detection system based on graphene and mesoporous silica, and achieve sensitivity with all of the major classes of analytes and simultaneously realize DNA logic gate operations. The concept is based on the locking of the pores and preventing the signal-reporter molecules from escape by target-induced the conformational change of the tailored DNA caps. The coupling of 'waking up' gatekeeper with highly specific biochemical recognition is an innovative strategy for the detection of various targets, able to compete with classical methods which need expensive instrumentation and sophisticated experimental operations. The present study has introduced a new electrochemical signal amplification concept and also adds a new dimension to the function of graphene-mesoporous materials hybrids as multifunctional nanoscale logic devices. More importantly, the development of this approach would spur further advances in important areas, such as point-of-care diagnostics or detection of specific biological contaminations, and hold promise for use in field analysis.
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Affiliation(s)
- Li Wu
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100039, China
| | - Jinsong Ren
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Xiaogang Qu
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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27
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Gerasimova YV, Kolpashchikov DM. Divide and control: split design of multi-input DNA logic gates. Chem Commun (Camb) 2014; 51:870-2. [PMID: 25513764 DOI: 10.1039/c4cc08241a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Logic gates made of DNA have received significant attention as biocompatible building blocks for molecular circuits. The majority of DNA logic gates, however, are controlled by the minimum number of inputs: one, two or three. Here we report a strategy to design a multi-input logic gate by splitting a DNA construct.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, Orlando, FL 32816, USA
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28
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Biosensors with built-in biomolecular logic gates for practical applications. BIOSENSORS-BASEL 2014; 4:273-300. [PMID: 25587423 PMCID: PMC4264359 DOI: 10.3390/bios4030273] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 01/20/2023]
Abstract
Molecular logic gates, designs constructed with biological and chemical molecules, have emerged as an alternative computing approach to silicon-based logic operations. These molecular computers are capable of receiving and integrating multiple stimuli of biochemical significance to generate a definitive output, opening a new research avenue to advanced diagnostics and therapeutics which demand handling of complex factors and precise control. In molecularly gated devices, Boolean logic computations can be activated by specific inputs and accurately processed via bio-recognition, bio-catalysis, and selective chemical reactions. In this review, we survey recent advances of the molecular logic approaches to practical applications of biosensors, including designs constructed with proteins, enzymes, nucleic acids, nanomaterials, and organic compounds, as well as the research avenues for future development of digitally operating “sense and act” schemes that logically process biochemical signals through networked circuits to implement intelligent control systems.
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29
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Pu F, Ren J, Qu X. "Plug and play" logic gates based on fluorescence switching regulated by self-assembly of nucleotide and lanthanide ions. ACS APPLIED MATERIALS & INTERFACES 2014; 6:9557-9562. [PMID: 24830828 DOI: 10.1021/am501949t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Molecular logic gates in response to chemical, biological, or optical input signals at a molecular level have received much interest over the past decade. Herein, we construct "plug and play" logic systems based on the fluorescence switching of guest molecules confined in coordination polymer nanoparticles generated from nucleotide and lanthanide ions. In the system, the addition of new modules directly enables new logic functions. PASS 0, YES, PASS 1, NOT, IMP, OR, and AND gates are successfully constructed in sequence. Moreover, different logic gates (AND, INH, and IMP) can be constructed using different guest molecules and the same input combinations. The work will be beneficial to the future logic design and expand the applications of coordination polymers.
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Affiliation(s)
- Fang Pu
- Laboratory of Chemical Biology and State Key laboratory of Rare Earth Resources Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, People's Republic of China
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30
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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31
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Guo Y, Cheng J, Wang J, Zhou X, Hu J, Pei R. Label-free logic modules and two-layer cascade based on stem-loop probes containing a G-quadruplex domain. Chem Asian J 2014; 9:2397-401. [PMID: 24909844 DOI: 10.1002/asia.201402199] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 11/08/2022]
Abstract
A simple, versatile, and label-free DNA computing strategy was designed by using toehold-mediated strand displacement and stem-loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two-layer logic cascade were constructed. The probes contain a G-quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light-up fluorescent signal of G-quadruplex/NMM complex was used as the output readout. The inputs are the disease-specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label-free and modular strategy might be adapted in multi-target diagnosis through DNA hybridization and aptamer-target interaction.
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Affiliation(s)
- Yahui Guo
- Suzhou Key Laboratory of Nanotheranostics, Division of Nanobiomedicine, Collaborative Innovation Center of Suzhou Nano Science and Technology, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123 (P.R. China); Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry & Molecular Sciences, Wuhan University, Wuhan, 430072 (P.R. China)
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32
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Zhu K, Dietrich R, Didier A, Acar G, Märtlbauer E. Versatile antibody-sensing Boolean logic for the simultaneous detection of multiple bacterial toxins. Chem Commun (Camb) 2014; 49:9314-6. [PMID: 23999916 DOI: 10.1039/c3cc45370g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present an OR gate based on monoclonal antibodies for the simultaneous detection of multiple toxins in a single tube. To further simplify the operating procedure, the Boolean rule of simplification was used to guide the selection of a marker toxin among the natural toxin profiles.
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Affiliation(s)
- Kui Zhu
- Department of Veterinary Sciences, Ludwig-Maximilians-University Munich, Schönleutnerstr. 8, 85764 Oberschleissheim, Germany.
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33
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Pu F, Ju E, Ren J, Qu X. Multiconfigurable logic gates based on fluorescence switching in adaptive coordination polymer nanoparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1111-1117. [PMID: 24243760 DOI: 10.1002/adma.201304109] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/06/2013] [Indexed: 06/02/2023]
Abstract
Fluorescence switching of guest molecules confined in coordination polymer nanoparticles (CPNs) generated from nucleotides and lanthanide ions are used to construct multiconfigurable logic gates. Moreover, the potential of the material as fluorescent probe with large Stokes shift is demonstrated for cellular imaging. In this work the logic gate is integrated into the therapeutic agent and this will be highly beneficial in future molecular computing.
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Affiliation(s)
- Fang Pu
- State Key Laboratory of Rare Earth Resource Utilization and Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, (P. R. China)
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34
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Busseron E, Ruff Y, Moulin E, Giuseppone N. Supramolecular self-assemblies as functional nanomaterials. NANOSCALE 2013; 5:7098-140. [PMID: 23832165 DOI: 10.1039/c3nr02176a] [Citation(s) in RCA: 496] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.
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Affiliation(s)
- Eric Busseron
- SAMS Research Group, University of Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84087, 67034 Strasbourg Cedex 2, France
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35
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Cornett EM, O’Steen MR, Kolpashchikov DM. Operating Cooperatively (OC) sensor for highly specific recognition of nucleic acids. PLoS One 2013; 8:e55919. [PMID: 23441157 PMCID: PMC3575382 DOI: 10.1371/journal.pone.0055919] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/03/2013] [Indexed: 11/18/2022] Open
Abstract
Molecular Beacon (MB) probes have been extensively used for nucleic acid analysis because of their ability to produce fluorescent signal in solution instantly after hybridization. The indirect binding of MB probe to a target analyte offers several advantages, including: improved genotyping accuracy and the possibility to analyse folded nucleic acids. Here we report on a new design for MB-based sensor, called ‘Operating Cooperatively’ (OC), which takes advantage of indirect binding of MB probe to a target analyte. The sensor consists of two unmodified DNA strands, which hybridize to a universal MB probe and a nucleic acid analyte to form a fluorescent complex. OC sensors were designed to analyze two human SNPs and E.coli 16S rRNA. High specificity of the approach was demonstrated by the detection of true analyte in over 100 times excess amount of single base substituted analytes. Taking into account the flexibility in the design and the simplicity in optimization, we conclude that OC sensors may become versatile and efficient tools for instant DNA and RNA analysis in homogeneous solution.
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Affiliation(s)
- Evan M. Cornett
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Martin R. O’Steen
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Dmitry M. Kolpashchikov
- Chemistry Department, College of Sciences, University of Central Florida, Orlando, Florida, United States of America
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
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36
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Rao S, Guo Z, Liang D, Chen D, Wei Y, Xiang Y. A proteorhodopsin-based biohybrid light-powering pH sensor. Phys Chem Chem Phys 2013; 15:15821-4. [DOI: 10.1039/c3cp52894d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Abstract
Analysis of single-nucleotide polymorphisms (SNPs) is important for diagnosis of infectious and genetic diseases, for environment and population studies, as well as in forensic applications. Herein is a detailed description to design an "operating cooperatively" (OC) sensor for highly specific SNP analysis. OC sensors use two unmodified DNA adaptor strands and a molecular beacon probe to detect a nucleic acid targets with exceptional specificity towards SNPs. Genotyping can be accomplished at room temperature in a homogenous assay. The approach is easily adaptable for any nucleic acid target, and has been successfully used for analysis of targets with complex secondary structures. Additionally, OC sensors are an easy-to-design and cost-effective method for SNP analysis and nucleic acid detection.
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