1
|
Zhu J, Yan Z, Bošković F, Haynes CJE, Kieffer M, Greenfield JL, Wang J, Nitschke JR, Keyser UF. Fe II 4L 4 tetrahedron binds and aggregates DNA G-quadruplexes. Chem Sci 2021; 12:14564-14569. [PMID: 34881008 PMCID: PMC8580047 DOI: 10.1039/d1sc04430c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biological processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA–cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5′ end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, circular dichroism and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease. We find FeII4L4 binds to G-quadruplex and forms aggregates. G-quadruplex in the aggregates is protected from digestion by S1 nuclease.![]()
Collapse
Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Cally J E Haynes
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Marion Kieffer
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jake L Greenfield
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jin Wang
- Department of Chemistry and of Physics, State University of New York at Stony Brook Stony Brook New York 11794-3400 USA
| | - Jonathan R Nitschke
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
| |
Collapse
|
2
|
Zhang J, Qiu Z, Fan J, He F, Kang W, Yang S, Wang H, Huang J, Nie Z. Scan and Unlock: A Programmable DNA Molecular Automaton for Cell‐Selective Activation of Ligand‐Based Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015129] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Zongyang Qiu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Hangzhou 310024 P. R. China
- Institute of Biology Westlake Institute for Advanced Study 18 Shilongshan Road Hangzhou 310024 P. R. China
| | - Jiahui Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Fang He
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Hong‐Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Jing Huang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Hangzhou 310024 P. R. China
- Institute of Biology Westlake Institute for Advanced Study 18 Shilongshan Road Hangzhou 310024 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| |
Collapse
|
3
|
Zhang J, Qiu Z, Fan J, He F, Kang W, Yang S, Wang H, Huang J, Nie Z. Scan and Unlock: A Programmable DNA Molecular Automaton for Cell‐Selective Activation of Ligand‐Based Signaling. Angew Chem Int Ed Engl 2021; 60:6733-6743. [DOI: 10.1002/anie.202015129] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Jinghui Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Zongyang Qiu
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Hangzhou 310024 P. R. China
- Institute of Biology Westlake Institute for Advanced Study 18 Shilongshan Road Hangzhou 310024 P. R. China
| | - Jiahui Fan
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Fang He
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Wenyuan Kang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Hong‐Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| | - Jing Huang
- Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Hangzhou 310024 P. R. China
- Institute of Biology Westlake Institute for Advanced Study 18 Shilongshan Road Hangzhou 310024 P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics College of Chemistry and Chemical Engineering, College of Biology Hunan University Changsha 410082 P. R. China
| |
Collapse
|
4
|
Huang X, Song J, Yung BC, Huang X, Xiong Y, Chen X. Ratiometric optical nanoprobes enable accurate molecular detection and imaging. Chem Soc Rev 2018; 47:2873-2920. [PMID: 29568836 PMCID: PMC5926823 DOI: 10.1039/c7cs00612h] [Citation(s) in RCA: 446] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exploring and understanding biological and pathological changes are of great significance for early diagnosis and therapy of diseases. Optical sensing and imaging approaches have experienced major progress in this field. Particularly, an emergence of various functional optical nanoprobes has provided enhanced sensitivity, specificity, targeting ability, as well as multiplexing and multimodal capabilities due to improvements in their intrinsic physicochemical and optical properties. However, one of the biggest challenges of conventional optical nanoprobes is their absolute intensity-dependent signal readout, which causes inaccurate sensing and imaging results due to the presence of various analyte-independent factors that can cause fluctuations in their absolute signal intensity. Ratiometric measurements provide built-in self-calibration for signal correction, enabling more sensitive and reliable detection. Optimizing nanoprobe designs with ratiometric strategies can surmount many of the limitations encountered by traditional optical nanoprobes. This review first elaborates upon existing optical nanoprobes that exploit ratiometric measurements for improved sensing and imaging, including fluorescence, surface enhanced Raman scattering (SERS), and photoacoustic nanoprobes. Next, a thorough discussion is provided on design strategies for these nanoprobes, and their potential biomedical applications for targeting specific biomolecule populations (e.g. cancer biomarkers and small molecules with physiological relevance), for imaging the tumor microenvironment (e.g. pH, reactive oxygen species, hypoxia, enzyme and metal ions), as well as for intraoperative image guidance of tumor-resection procedures.
Collapse
Affiliation(s)
- Xiaolin Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China. and Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
| | - Jibin Song
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA. and MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou 350108, P. R. China
| | - Bryant C Yung
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
| | - Xiaohua Huang
- Department of Chemistry, University of Memphis, 213 Smith Chemistry Bldg., Memphis, TN 38152, USA
| | - Yonghua Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, P. R. China.
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
| |
Collapse
|
5
|
Song X, Eshra A, Dwyer C, Reif J. Renewable DNA seesaw logic circuits enabled by photoregulation of toehold-mediated strand displacement. RSC Adv 2017. [DOI: 10.1039/c7ra02607b] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We propose a scalable design and verifications for photoregulated renewable DNA seesaw logic circuits, which can be repeatedly reset to reliably process new inputs. Synchronized control of complex DNA reaction networks could be achieved efficiently.
Collapse
Affiliation(s)
- Xin Song
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
| | - Abeer Eshra
- Department of Computer Science
- Duke University
- Durham
- USA
- Department of Computer Science and Engineering
| | - Chris Dwyer
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
| | - John Reif
- Department of Electrical and Computer Engineering
- Duke University
- Durham
- USA
- Department of Computer Science
| |
Collapse
|
6
|
Yang ZH, Zhuo Y, Yuan R, Chai YQ. Highly Effective Protein Converting Strategy for Ultrasensitive Electrochemical Assay of Cystatin C. Anal Chem 2016; 88:5189-96. [DOI: 10.1021/acs.analchem.6b00210] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Zhe-Han Yang
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ying Zhuo
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ruo Yuan
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence
and Real-Time Analytic Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| |
Collapse
|
7
|
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.
Collapse
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).
| |
Collapse
|
8
|
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]
|
9
|
Wei Y, Zhang J, Wang X, Duan Y. Amplified fluorescent aptasensor through catalytic recycling for highly sensitive detection of ochratoxin A. Biosens Bioelectron 2014; 65:16-22. [PMID: 25461133 DOI: 10.1016/j.bios.2014.09.100] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/01/2014] [Accepted: 09/23/2014] [Indexed: 12/31/2022]
Abstract
This paper describes a novel approach utilizing nano-graphite-aptamer hybrid and DNase I for the amplified detection of ochratoxin A (OTA) for the first time. Nano-graphite can effectively quench the fluorescence of carboxyfluorescein (FAM) labeled OTA specific aptamer due to their strong π-π; stacking interactions; while upon OTA addition, it will bind with aptamer to fold into an OTA-aptamerG-quadruplex structure, which does not adsorb on the surface of nano-graphite and thus retains the dye fluorescence. Meanwhile, the G-quadruplex structure can be cleaved by DNase I, and in such case OTA is delivered from the complex. The released OTA then binds other FAM-labeled aptamers on the nano-graphite surface, and touches off another target recycling, resulting in the successive release of dye-labeled aptamers from the nano-graphite, which leads to significant amplification of the signal. Under the optimized conditions, the present amplified sensing system exhibits high sensitivity toward OTA with a limit of detection of 20nM (practical measurement), which is about 100-fold higher than that of traditional unamplified homogeneous assay. Our developed method also showed high selectivity against other interference molecules and can be applied for the detection of OTA in real red wine samples. The proposed assay is simple, cost-effective, and might open a door for the development of new assays for other biomolecules. This aptasensor is of great practical importance in food safety and could be widely extended to the detection of other toxins by replacing the sequence of the recognition aptamer.
Collapse
Affiliation(s)
- Yin Wei
- Research Center of Analytical Instrumentation, Analytical & Testing Center, Sichuan University, Chengdu, China
| | - Ji Zhang
- Research Center of Analytical Instrumentation, Analytical & Testing Center, Sichuan University, Chengdu, China
| | - Xu Wang
- Research Center of Analytical Instrumentation, Analytical & Testing Center, Sichuan University, Chengdu, China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, College of Life Science, Sichuan University, Chengdu, China.
| |
Collapse
|
10
|
Kamiya Y, Asanuma H. Light-driven DNA nanomachine with a photoresponsive molecular engine. Acc Chem Res 2014; 47:1663-72. [PMID: 24617966 DOI: 10.1021/ar400308f] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CONSPECTUS: DNA is regarded as an excellent nanomaterial due to its supramolecular property of duplex formation through A-T and G-C complementary pairs. By simply designing sequences, we can create any desired 2D or 3D nanoarchitecture with DNA. Based on these nanoarchitectures, motional DNA-based nanomachines have also been developed. Most of the nanomachines require molecular fuels to drive them. Typically, a toehold exchange reaction is applied with a complementary DNA strand as a fuel. However, repetitive operation of the machines accumulates waste DNA duplexes in the solution that gradually deteriorate the motional efficiency. Hence, we are facing an "environmental problem" even in the nanoworld. One of the direct solutions to this problem is to use clean energy, such as light. Since light does not contaminate the reaction system, a DNA nanomachine run by a photon engine can overcome the drawback of waste that is a problem with molecular-fueled engines. There are several photoresponsive molecules that convert light energy to mechanical motion through the change of geometry of the molecules; these include spiropyran, diarylethene, stilbene, and azobenzene. Although each molecule has both advantages and drawbacks, azobenzene derivatives are widely used as "molecular photon engines". In this Account, we review light-driven DNA nanomachines mainly focusing on the photoresponsive DNAs that we have developed for the past decade. The basis of our method is installation of an azobenzene into a DNA sequence through a d-threoninol scaffold. Reversible hybridization of the DNA duplex, triggered by trans-cis isomerization of azobenzene in the DNA sequences by irradiation with light, induces mechanical motion of the DNA nanomachine. Moreover we have successfully developed azobenzene derivatives that improve its photoisomerizaition properties. Use of these derivatives and techniques have allowed us to design various DNA machines that demonstrate sophisticated motion in response to lights of different wavelengths without a drop in photoregulatory efficiency. In this Account, we emphasize the advantages of our methods including (1) ease of preparation, (2) comprehensive sequence design of azobenzene-tethered DNA, (3) efficient photoisomerization, and (4) reversible photocontrol of hybridization by irradiation with appropriate wavelengths of light. We believe that photon-fueled DNA nanomachines driven by azobenzene-derivative molecular photon-fueled engines will be soon science rather than "science fiction".
Collapse
Affiliation(s)
- Yukiko Kamiya
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
- Ecotopia
Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate
School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 Japan
| |
Collapse
|
11
|
Zhang Z, Li S, Chen N, Yang C, Wang Y. Programmable display of DNA-protein chimeras for controlling cell-hydrogel interactions via reversible intermolecular hybridization. Biomacromolecules 2013; 14:1174-80. [PMID: 23452302 DOI: 10.1021/bm400096z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Extensive studies have been recently carried out to achieve dynamic control of cell-material interactions primarily through physicochemical stimulation. The purpose of this study was to apply reversible intermolecular hybridization to program cell-hydrogel interactions in physiological conditions based on DNA-antibody chimeras and complementary oligonucleotides. The results showed that DNA oligonucleotides could be captured to and released from the immobilizing DNA-functionalized hydrogels with high specificity via DNA hybridization. Accordingly, DNA-antibody chimeras were captured to the hydrogels, successfully inducing specific cell attachment. The cell attachment to the hydrogels reached the plateau at approximately half an hour after the functionalized hydrogels and the cells were incubated together. The attached cells were rapidly released from the bound hydrogels when triggering complementary oligonucleotides were introduced to the system. However, the capability of the triggering complementary oligonucleotides in releasing cells was affected by the length of intermolecular hybridization. The length needed to be at least more than 20 base pairs in the current experimental setting. Notably, because the procedure of intermolecular hybridization did not involve any harsh condition, the released cells maintained the same viability as that of the cultured cells. The functionalized hydrogels also exhibited the potential to catch and release cells repeatedly. Therefore, this study demonstrates that it is promising to regulate cell-material interactions dynamically through the DNA-programmed display of DNA-protein chimeras.
Collapse
Affiliation(s)
- Zhaoyang Zhang
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, Connecticut 06269, USA
| | | | | | | | | |
Collapse
|
12
|
Yan G, Wang Y, He X, Wang K, Liu J, Du Y. A highly sensitive label-free electrochemical aptasensor for interferon-gamma detection based on graphene controlled assembly and nuclease cleavage-assisted target recycling amplification. Biosens Bioelectron 2013; 44:57-63. [PMID: 23391707 DOI: 10.1016/j.bios.2013.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/05/2013] [Accepted: 01/07/2013] [Indexed: 11/15/2022]
Abstract
We report here a highly sensitive and label-free electrochemical aptasensing technology for detection of interferon-gamma (IFN-γ) based on graphene controlled assembly and enzyme cleavage-assisted target recycling amplification strategy. In this work, in the absence of IFN-γ, the graphene could not be assembled onto the 16-mercaptohexadecanoic acid (MHA) modified gold electrode because the IFN-γ binding aptamer was strongly adsorbed on the graphene due to the strong π-π interaction. Thus the electronic transmission was blocked (eT OFF). However, the presence of target IFN-γ and DNase I led to desorption of aptamer from the graphene surface and further cleavage of the aptamer, thereby releasing the IFN-γ. The released IFN-γ could then re-attack other aptamers on the graphene, resulting in the successive release of the aptamers from the graphene. At the same time, the "naked" graphene could be assembled onto the MHA modified gold electrode with hydrophobic interaction and π-conjunction, mediating the electron transfer between the electrode and the electroactive indicator. Then, measurable electrochemical signals were generated (eT ON), which was related to the concentration of the IFN-γ. By taking advantages of graphene and enzyme cleavage-assisted target recycling amplification, the developed label-free electrochemical aptasensing technology showed a linear response to concentration of IFN-γ range from 0.1 to 0.7 pM. The detection limit of IFN-γ was determined to be 0.065 pM. Moreover, this aptasensor shows good selectivity toward the target in the presence of other relevant proteins. Our strategy thus opens new opportunities for label-free and amplified detection of other kinds of proteins.
Collapse
Affiliation(s)
- Genping Yan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, PR China
| | | | | | | | | | | |
Collapse
|
13
|
Li F, Zhang H, Lai C, Li XF, Le XC. A molecular translator that acts by binding-induced DNA strand displacement for a homogeneous protein assay. Angew Chem Int Ed Engl 2012; 51:9317-20. [PMID: 22893418 DOI: 10.1002/anie.201202677] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 07/23/2012] [Indexed: 12/23/2022]
Affiliation(s)
- Feng Li
- Department of Chemistry, University of Alberta, Edmonton, T6G 2G3 Canada
| | | | | | | | | |
Collapse
|
14
|
Li F, Zhang H, Lai C, Li XF, Le XC. A Molecular Translator that Acts by Binding-Induced DNA Strand Displacement for a Homogeneous Protein Assay. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202677] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
15
|
Li N. Reversible regulation of aptamer activity with effector-responsive hairpin oligonucleotides. ACTA ACUST UNITED AC 2012; 18:77-84. [PMID: 22651934 DOI: 10.1177/2211068212448429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aptamers are oligonucleotides that can bind to various nonnucleic acid molecular targets in a high affinity and specificity. As an emerging class of therapeutic agents, aptamers offer an unparalleled advantage over other classes of therapeutic agents: the possibility to rationally regulate the therapeutic activity of aptamers. Most existing strategies for regulating the aptamer activity have a limited specificity and/or reversibility. Herein we report a simple, generic strategy to simultaneously achieve specificity and reversibility by exploiting the spontaneous conformational change of hairpin oligonucleotides upon the specific recognition of nucleic acid effectors. The effector-responsive hairpin oligonucleotide consists of a sensing loop that recognizes a particular nucleic acid effector, an aptamer stem that inhibits a certain therapeutic target, and an antidote stem that is complementary to the aptamer. Upon the introduction/removal of the effector, the hairpin oligonucleotide undergoes a conformational change that activates/deactivates the aptamer's inhibiting activity on the therapeutic target. This new strategy has been demonstrated with an anticoagulant aptamer that binds and inhibits human α-thrombin.
Collapse
Affiliation(s)
- Na Li
- Department of Mechanical & Aerospace Engineering, University of Miami, Coral Gables, FL 33146, USA.
| |
Collapse
|
16
|
Affiliation(s)
- Anthony J. Genot
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Jonathan Bath
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Andrew J. Turberfield
- Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| |
Collapse
|
17
|
de Puig H, Federici S, Baxamusa SH, Bergese P, Hamad-Schifferli K. Quantifying the nanomachinery of the nanoparticle-biomolecule interface. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2477-84. [PMID: 21692181 DOI: 10.1002/smll.201100530] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Indexed: 05/21/2023]
Abstract
A study is presented of the nanomechanical phenomena experienced by nanoparticle-conjugated biomolecules. A thermodynamic framework is developed to describe the binding of thrombin-binding aptamer (TBA) to thrombin when the TBA is conjugated to nanorods. Binding results in nanorod aggregation (viz. directed self-assembly), which is detectable by absorption spectroscopy. The analysis introduces the energy of aggregation, separating it into TBA-thrombin recognition and surface-work contributions. Consequently, it is demonstrated that self-assembly is driven by the interplay of surface work and thrombin-TBA recognition. It is shown that the work at the surface is about -10 kJ mol(-1) and results from the accumulation of in-plane molecular forces of pN magnitude and with a lifetime of <1 s, which arises from TBA nanoscale rearrangements fuelled by thrombin-directed nanorod aggregation. The obtained surface work can map aggregation regimes as a function of different nanoparticle surface conditions. Also, the thermodynamic treatment can be used to obtain quantitative information on surface effects impacting biomolecules on nanoparticle surfaces.
Collapse
Affiliation(s)
- Helena de Puig
- Department of Biological Engineering and the Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA; Institut Quimic de Sarrià, Universitat Ramon Llull Via Augusta 390, 08017 Barcelona, Spain
| | | | | | | | | |
Collapse
|
18
|
Tang D, Tang J, Li Q, Su B, Chen G. Ultrasensitive aptamer-based multiplexed electrochemical detection by coupling distinguishable signal tags with catalytic recycling of DNase I. Anal Chem 2011; 83:7255-9. [PMID: 21888312 DOI: 10.1021/ac201891w] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work reports an aptamer-based, disposable, and multiplexed sensing platform for simultaneous electrochemical determination of small molecules, employing adenosine triphosphate (ATP) and cocaine as the model target analytes. The multiplexed sensing strategy is based on target-induced release of distinguishable redox tag-conjugated aptamers from a magnetic graphene platform. The electronic signal of the aptasensors could be further amplified by coupling DNase I with catalytic recycling of self-produced reactants. The assay was based on the change in the current at the various peak potentials in the presence of the corresponding signal tags. Experimental results revealed that the multiplexed electrochemical aptasensor enabled the simultaneous monitoring of ATP and cocaine in a single run with wide working ranges and low detection limits (LODs: 0.1 pM for ATP and 1.5 pM for cocaine). This concept offers promise for rapid, simple, and cost-effective analysis of biological samples.
Collapse
|
19
|
Yang CJ, Cui L, Huang J, Yan L, Lin X, Wang C, Zhang WY, Kang H. Linear molecular beacons for highly sensitive bioanalysis based on cyclic Exo III enzymatic amplification. Biosens Bioelectron 2011; 27:119-24. [PMID: 21764287 DOI: 10.1016/j.bios.2011.06.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/11/2011] [Accepted: 06/21/2011] [Indexed: 12/21/2022]
Abstract
Sensitive analysis or monitoring of biomolecules and small molecules is very important for many biological researches, clinical diagnosis and forensic investigations. As a sequence-independent exonuclease, Exonuclease III (Exo III) has been widely used for amplified detection of proteins and nucleic acids where displacing probes or molecular beacons are used as the signaling probes. However, displacing probes suffer slow hybridization rate and high background signal and molecular beacons are difficult to design and prone to undesired nonspecific interactions. Herein, we report a new type of probes called linear molecular beacons (LMBs) for use in Exo III amplification assays to improve hybridization kinetics and reduce background noises. LMBs are linear oligonucleotide probes with a fluorophore and quencher attached to 3' terminal and penultimate nucleotides, respectively. Compared to conventional molecular beacons and displacing probes, LMBs are easy to design and synthesize. More importantly, LMBs have a much lower background noise and allow faster reaction rates. Using LMBs in cyclic Exo III amplification assay, ultrasensitive nucleic acid detection methods were developed with a detection limit of less than 120fM, which is 2 orders of magnitude lower than that of conventional molecular beacons or displacing probes-based Exo III amplification assays. Furthermore, LMBs can be extended as universal probes for detection of non-nucleic acid molecules such as cocaine with high sensitivity. These results demonstrate that the combination of Exo III amplification and LMB signaling provides a general method for ultrasensitive and selective detection of a wide range of targets.
Collapse
Affiliation(s)
- Chaoyong James Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, PR China.
| | | | | | | | | | | | | | | |
Collapse
|
20
|
Zhang H, Fang C, Zhang S. Ultrasensitive Electrochemical Analysis of Two Analytes by Using an Autonomous DNA Machine that Works in a Two-Cycle Mode. Chemistry 2011; 17:7531-7. [DOI: 10.1002/chem.201002767] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/06/2011] [Indexed: 01/12/2023]
|
21
|
Mok AK, Kedzierski NA, Chung PN, Lukeman PS. Positional photocleavage control of DNA-based nanoswitches. Chem Commun (Camb) 2011; 47:4905-7. [DOI: 10.1039/c1cc10292c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
22
|
Design of a Functional Nanomaterial with Recognition Ability for Constructing Light-Driven Nanodevices. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-3-642-18305-8_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
|
23
|
Shoshani S, Wolf S, Keinan E. Molecular computing with plant cell phenotype serving as quality controlled output. MOLECULAR BIOSYSTEMS 2011; 7:1113-20. [DOI: 10.1039/c0mb00226g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
24
|
A universal platform for sensitive and selective colorimetric DNA detection based on Exo III assisted signal amplification. Biosens Bioelectron 2010; 26:2796-800. [PMID: 21130640 DOI: 10.1016/j.bios.2010.11.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/13/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
Rapid growth of available sequence data has made the detection of nucleic acids critical to the development of modern life sciences. Many amplification methods based on gold nanoparticles and endonuclease for sensitive DNA detection have been developed. However, these approaches require specific target sequence for endonuclease recognition, which cannot be fulfilled in all systems. Replacing the restriction enzyme with a nuclease that does not require any specific recognition sequence may offer a universally adaptable system. Here we have developed a novel homogeneous, colorimetric DNA detection method, which consists of Exo III, a linker DNA, and two DNA-modified gold nanoparticles. This system is simple, low-cost, sensitive and selective. By coupling cyclic enzymatic cleavage and gold nanoparticle for signal amplification, our system provides a colorimetric detection limit of 15 pM, which is 3 orders of magnitude more sensitive than that of a general three-component sandwich assay format. Due to the intrinsic property of Exo III, our method shows excellent detection selectivity for single-base discrimination. More importantly, superior to other methods based on nicking and FokI endonuclease, our target sequence-independent platform is generally applicable for DNA sensing. This new approach could be widely applied to sensitive nucleic acids detection.
Collapse
|
25
|
Eckhoff G, Codrea V, Ellington AD, Chen X. Beyond allostery: Catalytic regulation of a deoxyribozyme through an entropy-driven DNA amplifier. ACTA ACUST UNITED AC 2010. [DOI: 10.1186/1759-2208-1-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
The programmability and replicability of RNA and DNA have respectively enabled the design and selection of a number of allosteric ribozymes and deoxyribozymes. These catalysts have been adapted to function as signal transducers in biosensors and biochemical reaction networks both in vitro and in vivo. However, allosteric control of nucleic acid catalysts is currently limited by the fact that one molecule of effector (input) generally regulates at most one molecule of ribozyme or deoxyribozyme (output). In consequence, allosteric control is usually inefficient when the concentration of input molecules is low. In contrast, catalytic regulation of protein enzymes, as in protein phosphorylation cascades, generally allows one input molecule (e.g., one kinase molecule) to regulate multiple output molecules (e.g., kinase substrates). Achieving such catalytic signal amplification would also be of great utility for nucleic acid circuits. Here we show that allosteric regulation of nucleic acid enzymes can be coupled to signal amplification in an entropy-driven DNA circuit. In this circuit, kinetically trapped DNA logic gates are triggered by a specific sequence, and upon execution generate a peroxidase deoxyribozyme that converts a colorless substrate (ABTS) into a green product (ABTS•+). This scheme provides a new paradigm for the design of enzyme-free biosensors for point-of-care diagnostics.
Collapse
|
26
|
Fletcher SJ, Phillips LW, Milligan AS, Rodda SJ. Toward specific detection of Dengue virus serotypes using a novel modular biosensor. Biosens Bioelectron 2010; 26:1696-700. [PMID: 20692150 DOI: 10.1016/j.bios.2010.07.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 07/08/2010] [Accepted: 07/13/2010] [Indexed: 10/19/2022]
Abstract
Arthropod-borne diseases affect a significant portion of the world's population. Dengue fever, a viral disease carried by the Aedes aegypti mosquito, is one of the most wide-spread, with many fatalities evident each year. To date, Dengue viral diagnostic technologies have been too complex, time-consuming and expensive to be widely deployed, particularly in developing countries where the disease is most prevalent. Here we demonstrate a modular biosensor that is able to rapidly identify sequences associated with the Dengue virus genome. The biosensor consists of an oligonucleotide linker module, an aptamer/restriction endonuclease signal transducer and a fluorescent signalling molecule. The linker molecule has a simple stem/loop conformation and comprises a target-complementary moiety within the loop and a trigger moiety within the stem. When bound to the target nucleic acid, the trigger strand of the denatured stem can bind to the aptamer within the signal transducer. Disruption of the aptamer releases the restriction endonuclease EcoRI from aptamer-mediated inhibition. Active EcoRI is able to rapidly cleave multiple signalling molecules to generate a detectable signal. The biosensor was able to detect sequences derived from each of the four Dengue virus serotypes with a great degree of specificity. Along with sequences specific to each serotype, a pan-Dengue sequence, common to all serotypes, was also detected.
Collapse
Affiliation(s)
- Stephen J Fletcher
- Lifeprint Australia Pty Ltd, Plant Genomics Centre, Hartley Grove, Urrbrae 5064, Australia.
| | | | | | | |
Collapse
|
27
|
Freeman R, Sharon E, Teller C, Willner I. Control of biocatalytic transformations by programmed DNA assemblies. Chemistry 2010; 16:3690-8. [PMID: 20151432 DOI: 10.1002/chem.200902559] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This study demonstrates the self-assembly of inhibitor/enzyme-tethered nucleic acid fragments or enzyme I-, enzyme II-modified nucleic acids into functional nanostructures that lead to the controlled inhibition of the enzyme or the activation of an enzyme cascade. In one system, the anti-cocaine aptamer subunits are modified with monocarboxy methylene blue (MB(+)) as the inhibitor and with choline oxidase (ChOx). The cocaine-induced self-assembly of the aptamer subunits complex results in the inhibition of ChOx by MB(+). In a further configuration, two nucleic acids of limited complementarity are functionalized at their 3' and 5' ends with glucose oxidase (GOx) and horseradish peroxidase (HRP), respectively, or with MB(+) and ChOx. In the presence of a target DNA sequence, synergistic complementary base-pairing occurs, thus leading to stable supramolecular Y-shaped nanostructures of the nucleic acid units. A GOx/HRP bienzyme cascade or the programmed inhibition of ChOx by MB(+) is demonstrated in the resulting nucleic acid nanostructures. A quantitative theoretical model that describes the nucleic acid assemblies and that results in the inhibition of ChOx by MB(+) or in the activation of the GOx/HRP cascade, respectively, is provided.
Collapse
Affiliation(s)
- Ronit Freeman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | | | |
Collapse
|
28
|
Wang X, Huang J, Zhou Y, Yan S, Weng X, Wu X, Deng M, Zhou X. Conformational Switching of G-Quadruplex DNA by Photoregulation. Angew Chem Int Ed Engl 2010; 49:5305-9. [DOI: 10.1002/anie.201002290] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
29
|
Wang X, Huang J, Zhou Y, Yan S, Weng X, Wu X, Deng M, Zhou X. Conformational Switching of G-Quadruplex DNA by Photoregulation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201002290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
30
|
Cui L, Ke G, Wang C, Yang CJ. A cyclic enzymatic amplification method for sensitive and selective detection of nucleic acids. Analyst 2010; 135:2069-73. [DOI: 10.1039/c0an00215a] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
31
|
Liang X, Nishioka H, Mochizuki T, Asanuma H. An interstrand-wedged duplex composed of alternating DNAbase pairs and covalently attached intercalators. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b915993b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
32
|
Zhang M, Huang J, Deng M, Weng X, Ma H, Zhou X. Sensitive and visual detection of adenosine by a rationally designed FokI-based biosensing strategy. Chem Asian J 2009; 4:1420-3. [PMID: 19591184 DOI: 10.1002/asia.200900200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ming Zhang
- College of Chemistry and Molecular Sciences, Ministry of Education, Key Lab Biomed, Wuhan University, Wuhan, Hubei, 430072, PR China
| | | | | | | | | | | |
Collapse
|
33
|
Picuri JM, Frezza BM, Ghadiri MR. Universal translators for nucleic acid diagnosis. J Am Chem Soc 2009; 131:9368-77. [PMID: 19566101 DOI: 10.1021/ja902490x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Defined broadly, molecular translators are constructs that can convert any designated molecular input into a unique output molecule. In particular, the development of universal nucleic acid translators would be of significant practical value in view of the expanding biomedical importance of gene diagnostics. Currently, diagnostic assays for nucleic acids must be individually developed and optimized for each new sequence because inputs for one assay are sequence-specific and are therefore incompatible with any other assay designed for the detection of a different nucleic acid. However, if a desired nucleic acid sequence could be translated in vitro into a predetermined nucleic acid output for which there is already a known diagnostic assay, then that single assay could be easily adapted to detect nearly any strand. Here we investigate PCR-independent isothermal molecular translation strategies that function without the need for post-translation purification and can be implemented with commercially available components. Translation yields up to 96% are obtained in 5 min at room temperature with minimal background reaction (<1%) and with discrimination of single nucleotide polymorphisms in the input sequence. Furthermore, we apply these translators to adapt a high-gain HIV diagnostic system for high-throughput detection of hepatitis C, avian influenza (H5N1), and smallpox without making changes to the underlying assay. Finally, we show the feasibility of translating small-molecule interactions into nucleic acid outputs by demonstrating the utility of a DNA aptamer for translating adenosine into a readily detectable output DNA sequence. Additionally, equilibrium expressions are described in order to facilitate rational engineering of aptameric translators for label-free detection of any molecule that an aptamer can recognize.
Collapse
Affiliation(s)
- John M Picuri
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | | | | |
Collapse
|
34
|
Liang X, Mochizuki T, Asanuma H. A supra-photoswitch involving sandwiched DNA base pairs and azobenzenes for light-driven nanostructures and nanodevices. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1761-1768. [PMID: 19572326 DOI: 10.1002/smll.200900223] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A supra-photoswitch is designed for complete ON/OFF switching of DNA hybridization by light irradiation for the purpose of using DNA as a material for building nanostructures. Azobenzenes, attached to D-threoninols that function as scaffolds, are introduced into each DNA strand after every two natural nucleotides (in the form (NNX)n where N and X represent the natural nucleotide and the azobenzene moiety, respectively). Hybridization of these two modified strands forms a supra-photoswitch consisting of alternating natural base pairs and azobenzene moieties. In this newly designed sequence, each base pair is sandwiched between two azobenzene moieties and all the azobenzene moieties are separated by base pairs. When the duplex is irradiated by visible light, the azobenzene moieties take the trans form and this duplex is surprisingly stable compared to the corresponding native duplex composed of only natural oligonucleotides. On the other hand, when the azobenzene moieties are isomerized to the cis form by UV light irradiation, the duplex is completely dissociated. Based on this design, a DNA hairpin structure is synthesized that should be closed by visible light irradiation and opened by UV light irradiation at the level of a single molecule. Indeed, perfect ON/OFF photoregulation is attained. This is a promising strategy for the design of supra-photoswitches such as photoresponsive sticky ends on DNA nanodevices and other nanostructures.
Collapse
Affiliation(s)
- Xingguo Liang
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | | | | |
Collapse
|
35
|
Shlyahovsky B, Li Y, Lioubashevski O, Elbaz J, Willner I. Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold. ACS NANO 2009; 3:1831-1843. [PMID: 19507821 DOI: 10.1021/nn900085x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes. This results in the respective translocation of the blocking nucleic acids to the footholds carrying the HRP-mimicking DNAzyme sequence, and the concomitant release of the respective DNAzyme. The released product-strands then self-assemble into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. The principle of the logic operation is, then, implemented as a possible paradigm for future nanomedicine. The nucleic acid inputs that bind to the blocked footholds result in the translocation of the blocking nucleic acids to the respective footholds carrying the antithrombin aptamer. The released aptamer inhibits, then, the hydrolytic activity of thrombin. The system demonstrates the regulation of a biocatalytic reaction by a translator system activated on a DNA scaffold.
Collapse
Affiliation(s)
- Bella Shlyahovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | | | | | |
Collapse
|
36
|
Elbaz J, Moshe M, Willner I. Coherent activation of DNA tweezers: a "SET-RESET" logic system. Angew Chem Int Ed Engl 2009; 48:3834-7. [PMID: 19378312 DOI: 10.1002/anie.200805819] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Open sesame: Aptamer-substrate complexes activate the coherent operation of two tweezers that act as a "SET-RESET" logic system. Each tweezer cycles between a fluorescent open state and a closed quenched state (Q = quencher, F = fluorophore) when triggered by adenosine monophosphate (AMP) and adenosine deaminase (AD).
Collapse
Affiliation(s)
- Johann Elbaz
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | | | | |
Collapse
|
37
|
Elbaz J, Moshe M, Willner I. Coherent Activation of DNA Tweezers: A “SET-RESET” Logic System. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805819] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
38
|
Modi S, M G S, Goswami D, Gupta GD, Mayor S, Krishnan Y. A DNA nanomachine that maps spatial and temporal pH changes inside living cells. NATURE NANOTECHNOLOGY 2009; 4:325-30. [PMID: 19421220 DOI: 10.1038/nnano.2009.83] [Citation(s) in RCA: 565] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 03/20/2009] [Indexed: 05/18/2023]
Abstract
DNA nanomachines are synthetic assemblies that switch between defined molecular conformations upon stimulation by external triggers. Previously, the performance of DNA devices has been limited to in vitro applications. Here we report the construction of a DNA nanomachine called the I-switch, which is triggered by protons and functions as a pH sensor based on fluorescence resonance energy transfer (FRET) inside living cells. It is an efficient reporter of pH from pH 5.5 to 6.8, with a high dynamic range between pH 5.8 and 7. To demonstrate its ability to function inside living cells we use the I-switch to map spatial and temporal pH changes associated with endosome maturation. The performance of our DNA nanodevices inside living systems illustrates the potential of DNA scaffolds responsive to more complex triggers in sensing, diagnostics and targeted therapies in living systems.
Collapse
Affiliation(s)
- Souvik Modi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore, 560065, India
| | | | | | | | | | | |
Collapse
|
39
|
|
40
|
|
41
|
Elbaz J, Tel-Vered R, Freeman R, Yildiz H, Willner I. Switchable Motion of DNA on Solid Supports. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
42
|
Elbaz J, Tel-Vered R, Freeman R, Yildiz H, Willner I. Switchable Motion of DNA on Solid Supports. Angew Chem Int Ed Engl 2008; 48:133-7. [DOI: 10.1002/anie.200802905] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
43
|
Liang X, Nishioka H, Takenaka N, Asanuma H. A DNA nanomachine powered by light irradiation. Chembiochem 2008; 9:702-5. [PMID: 18253940 DOI: 10.1002/cbic.200700649] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xingguo Liang
- Core Research for Evolution Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | | | | | | |
Collapse
|
44
|
Jungmann R, Renner S, Simmel FC. From DNA nanotechnology to synthetic biology. HFSP JOURNAL 2008; 2:99-109. [PMID: 19404476 DOI: 10.2976/1.2896331] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Indexed: 01/16/2023]
Abstract
Attempts to construct artificial systems from biological molecules such as DNA and RNA by self-assembly are compatible with the recent development of synthetic biology. Genetic mechanisms can be used to produce or control artificial structures made from DNA and RNA, and these structures can in turn be used as artificial gene regulatory elements, in vitro as well as in vivo. Artificial biochemical circuits can be incorporated into cell-like reaction compartments, which opens up the possibility to operate them permanently out of equilibrium. In small systems, stochastic effects become noticeable and will have to be accounted for in the design of future systems.
Collapse
Affiliation(s)
- Ralf Jungmann
- Physics Department E14, Technical University Munich, James-Franck-Strasse, 85748 Garching, Germany
| | | | | |
Collapse
|
45
|
Abstract
DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated.
Collapse
Affiliation(s)
- Friedrich C Simmel
- Technical University Munich, Physics Department E14, James-Franck-Straße D-85748 Garching, Germany
| |
Collapse
|
46
|
Tagawa M, Shohda KI, Fujimoto K, Sugawara T, Suyama A. Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2'-deoxyuridine. Nucleic Acids Res 2007; 35:e140. [PMID: 17982178 PMCID: PMC2175349 DOI: 10.1093/nar/gkm872] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.
Collapse
Affiliation(s)
- Miho Tagawa
- Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, Japan
| | | | | | | | | |
Collapse
|
47
|
Kossoy E, Lavid N, Soreni-Harari M, Shoham Y, Keinan E. A Programmable Biomolecular Computing Machine with Bacterial Phenotype Output. Chembiochem 2007; 8:1255-60. [PMID: 17562552 DOI: 10.1002/cbic.200700180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The main advantage of autonomous biomolecular computing devices over electronic computers is their ability to interact directly with biological systems. No interface is required since all components of molecular computers, including hardware, software, input, and output are molecules that interact in solution along a cascade of programmable chemical events. Here, we demonstrate for the first time that the output of a computation preduced by a molecular finite automaton can be a visible bacterial phenotype. Our 2-symbol-2-state finite automaton utilized linear double-stranded DNA inputs that were prepared by inserting a string of six base pair symbols into the lacZ gene on the pUC18 plasmid. The computation resulted in a circular plasmid that differed from the original pUC18 by either a 9 base pair (accepting state) or 11 base pair insert (unaccepting state) within the lacZ alpha region gene. Upon transformation and expression of the resultant plasmids in E. coli, the accepting state was represented by production of functional beta-galactosidase and formation of blue colonies on X-gal medium. In contrast, the unaccepting state was represented by white colonies due to a shift in the open reading frame of lacZ.
Collapse
Affiliation(s)
- Elizaveta Kossoy
- Schulich Faculty of Chemistry and Institute of Catalysis Science and Technology, Technion--Israel Institute of Technology, Technion City, Haifa 32000, Israel
| | | | | | | | | |
Collapse
|
48
|
Weizmann Y, Beissenhirtz MK, Cheglakov Z, Nowarski R, Kotler M, Willner I. A virus spotlighted by an autonomous DNA machine. Angew Chem Int Ed Engl 2007; 45:7384-8. [PMID: 17036292 DOI: 10.1002/anie.200602754] [Citation(s) in RCA: 250] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yossi Weizmann
- Institute of Chemistry, The Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | | | | | | | | |
Collapse
|
49
|
Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007; 25:795-801. [PMID: 17515909 DOI: 10.1038/nbt1307] [Citation(s) in RCA: 336] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 04/19/2007] [Indexed: 11/09/2022]
Abstract
Molecular automata that combine sensing, computation and actuation enable programmable manipulation of biological systems. We use RNA interference (RNAi) in human kidney cells to construct a molecular computing core that implements general Boolean logic to make decisions based on endogenous molecular inputs. The state of an endogenous input is encoded by the presence or absence of 'mediator' small interfering RNAs (siRNAs). The encoding rules, combined with a specific arrangement of the siRNA targets in a synthetic gene network, allow direct evaluation of any Boolean expression in standard forms using siRNAs and indirect evaluation using endogenous inputs. We demonstrate direct evaluation of expressions with up to five logic variables. Implementation of the encoding rules through sensory up- and down-regulatory links between the inputs and siRNA mediators will allow arbitrary Boolean decision-making using these inputs.
Collapse
Affiliation(s)
- Keller Rinaudo
- FAS Center for Systems Biology, Harvard University, 7 Divinity Ave., Cambridge, Massachusetts 02138 USA
| | | | | | | | | | | |
Collapse
|
50
|
Abstract
We are learning to build synthetic molecular machinery from DNA. This research is inspired by biological systems in which individual molecules act, singly and in concert, as specialized machines: our ambition is to create new technologies to perform tasks that are currently beyond our reach. DNA nanomachines are made by self-assembly, using techniques that rely on the sequence-specific interactions that bind complementary oligonucleotides together in a double helix. They can be activated by interactions with specific signalling molecules or by changes in their environment. Devices that change state in response to an external trigger might be used for molecular sensing, intelligent drug delivery or programmable chemical synthesis. Biological molecular motors that carry cargoes within cells have inspired the construction of rudimentary DNA walkers that run along self-assembled tracks. It has even proved possible to create DNA motors that move autonomously, obtaining energy by catalysing the reaction of DNA or RNA fuels.
Collapse
Affiliation(s)
- Jonathan Bath
- University of Oxford, Department of Physics, Clarendon Laboratory, Parks Road, Oxford OX1 3PU, UK
| | | |
Collapse
|