1
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Garcia-Etxarri A, Yuste R. Time for NanoNeuro. Nat Methods 2021; 18:1287-1293. [PMID: 34663955 DOI: 10.1038/s41592-021-01270-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 08/12/2021] [Indexed: 11/09/2022]
Abstract
The study of electronic properties of materials at the nanoscale has unveiled physical laws and generated materials such as nanoparticles, quantum dots, nanodiamonds, nanoelectrodes, and nanoprobes. Independently, large-scale public and private neuroscience programs have been launched to develop methods to measure and manipulate neural circuits in living animals and humans. Here, we review an upcoming field, NanoNeuro, defined as the intersection of nanoscience and neuroscience, that aims to develop nanoscale methods to record and stimulate neuronal activity. Because of their unique physical properties, nanomaterials have intrinsic advantages as biosensors and actuators, and they may be applicable to humans without the need for genetic modifications. Thus, nanoscience could make major methodological contributions to the future of neuroscience and, more generally, to biomedical sciences.
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Affiliation(s)
- Aitzol Garcia-Etxarri
- Donostia International Physics Center, Donostia-San Sebastián, Spain. .,IKERBASQUE, Bilbao, Spain.
| | - Rafael Yuste
- Donostia International Physics Center, Donostia-San Sebastián, Spain. .,IKERBASQUE, Bilbao, Spain. .,Kavli Institute of Brain Sciences, Dept. Biological Sciences, Columbia University, New York, USA.
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2
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KK S, Lin YL, Sewunet T, Wrande M, Sandegren L, Giske CG, Westerlund F. A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids. MICROMACHINES 2021; 12:1234. [PMID: 34683285 PMCID: PMC8538381 DOI: 10.3390/mi12101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.
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Affiliation(s)
- Sriram KK
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Marie Wrande
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
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3
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Wang X, Liu Z, Gao P, Li Y, Qu X. Surface functionalized quantum dots as biosensor for highly selective and sensitive detection of ppb level of propafenone. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 227:117709. [PMID: 31699588 DOI: 10.1016/j.saa.2019.117709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Monodispersed CdTe quantum dots (QDs) were prepared by using thioglycolic acid as surfactants in aqueous solution. The thioglycolic acid was chemically adsorbed on the surface of CdTe QDs that enables the QDs positively charged. In week acidic media, propafenone is positively charged, which can combine with the CdTe QDs to form larger ion-association complex via electrostatic attraction and hydrogen bond. Moreover, the formed ion-association complex could increase the intensity of resonance Rayleigh scattering (RRS), second-order scattering (SOS) and frequency doubling-scattering (FDS) of CdTe QDs, and quench the CdTe QDs fluorescence. Importantly, under optimal experimental conditions, the increased RRS, SOS and FDS intensity, and quenched fluorescence intensity of CdTe QDs were in direct proportion to the propafenone concentration in a certain range, respectively. Among them, the RRS method exhibited the highest sensitivity. In a wide concentration range of propafenone from 0.003 to 7.0 μg mL-1, the detection limit could reach 0.96 ng mL-1, which was much lower than previously reported methods. To simulate practical applications, the possible foreign interfering substances were also investigated, such as common ions, amino acid, and glucide. The proposed method here is rapid, sensitive and shows promising application for detection of ppb level of propafenone in human serum.
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Affiliation(s)
- Xiaodan Wang
- Department of Mining and Metallurgical Engineering, Baiyin Institute of Mining and Metallurgy, Chengxin Road No.2, Baiyin, Gansu Province, 730900, China
| | - Zhengqing Liu
- Frontier Institute of Science and Technology Jointly with College of Science, State Key Laboratory for Mechanical Behavior of Materials, Xi'an Jiaotong University, 99 Yanxiang Road, Yanta District, Xi'an, Shaanxi Province, 710054, China
| | - Pengfei Gao
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, PR China
| | - Yanjie Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing, 400716, PR China
| | - Xiaoyan Qu
- Frontier Institute of Science and Technology, Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, State Key Laboratory for Manufacturing Systems Engineering, Instrument Analysis Center, Xi'an Jiaotong University, Xi'an, 710000, China.
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4
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Yeh JW, Szeto K. Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits. BIOMICROFLUIDICS 2017; 11:044108. [PMID: 28794818 PMCID: PMC5526712 DOI: 10.1063/1.4996340] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/16/2017] [Indexed: 05/16/2023]
Abstract
Stretching single chromosomal DNA fibers in nanofluidic devices has become a valuable tool for studying the genome and more recently the epigenome. Although nanofluidic technology has been extensively used in single molecular DNA analysis, compared to bare DNA, much less work has been done to elongate chromatin, and only a few studies utilize more biologically relevant samples such as native eukaryotic chromatin. Here, we provide a method for stretching and imaging individual chromatin fibers within a micro- and nanofluidic device. This device was used to electrophoretically stretch and image single native chromatin fibers extracted from human cancer cells (HeLa cells) by attaching the chromatin to microspheres held at the entrance of a nanoslit. To further demonstrate the potential of this device in epigenetics, histone modification H3k79me2 was optically detected by fluorescence microscopy.
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Affiliation(s)
- Jia-Wei Yeh
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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5
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Kim KI, Lee S, Jin X, Kim SJ, Jo K, Lee JH. DNA Binding Peptide Directed Synthesis of Continuous DNA Nanowires for Analysis of Large DNA Molecules by Scanning Electron Microscope. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1601926. [PMID: 27813273 DOI: 10.1002/smll.201601926] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Synthesis of smooth and continuous DNA nanowires, preserving the original structure of native DNA, and allowing its analysis by scanning electron microscope (SEM), is demonstrated. Gold nanoparticles densely assembled on the DNA backbone via thiol-tagged DNA binding peptides work as seeds for metallization of DNA. This method allows whole analysis of DNA molecules with entangled 3D features.
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Affiliation(s)
- Kyung-Il Kim
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Xuelin Jin
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Su Ji Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 04107, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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6
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Lee J, Kim Y, Lee S, Jo K. Visualization of large elongated DNA molecules. Electrophoresis 2015; 36:2057-71. [PMID: 25994517 DOI: 10.1002/elps.201400479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/08/2015] [Accepted: 04/27/2015] [Indexed: 12/26/2022]
Abstract
Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Yongkyun Kim
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Mapogu, Seoul, Republic of Korea
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7
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Reinhart WF, Reifenberger JG, Gupta D, Muralidhar A, Sheats J, Cao H, Dorfman KD. Distribution of distances between DNA barcode labels in nanochannels close to the persistence length. J Chem Phys 2015; 142:064902. [PMID: 25681938 PMCID: PMC4327924 DOI: 10.1063/1.4907552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/25/2015] [Indexed: 11/14/2022] Open
Abstract
We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension.
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Affiliation(s)
- Wesley F Reinhart
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeff G Reifenberger
- BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA
| | - Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Han Cao
- BioNano Genomics, 9640 Towne Centre Dr., Ste. 100, San Diego, California 92121, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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8
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Sriram KK, Chang CL, Rajesh Kumar U, Chou CF. DNA combing on low-pressure oxygen plasma modified polysilsesquioxane substrates for single-molecule studies. BIOMICROFLUIDICS 2014; 8:052102. [PMID: 25332730 PMCID: PMC4189429 DOI: 10.1063/1.4892515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/28/2014] [Indexed: 05/21/2023]
Abstract
Molecular combing and flow-induced stretching are the most commonly used methods to immobilize and stretch DNA molecules. While both approaches require functionalization steps for the substrate surface and the molecules, conventionally the former does not take advantage of, as the latter, the versatility of microfluidics regarding robustness, buffer exchange capability, and molecule manipulation using external forces for single molecule studies. Here, we demonstrate a simple one-step combing process involving only low-pressure oxygen (O2) plasma modified polysilsesquioxane (PSQ) polymer layer to facilitate both room temperature microfluidic device bonding and immobilization of stretched single DNA molecules without molecular functionalization step. Atomic force microscopy and Kelvin probe force microscopy experiments revealed a significant increase in surface roughness and surface potential on low-pressure O2 plasma treated PSQ, in contrast to that with high-pressure O2 plasma treatment, which are proposed to be responsible for enabling effective DNA immobilization. We further demonstrate the use of our platform to observe DNA-RNA polymerase complexes and cancer drug cisplatin induced DNA condensation using wide-field fluorescence imaging.
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Affiliation(s)
| | - Chun-Ling Chang
- Institute of Physics , Academia Sinica, Taipei 11529, Taiwan
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9
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Jauffred L, Kyrsting A, Arnspang EC, Reihani SNS, Oddershede LB. Sub-diffraction positioning of a two-photon excited and optically trapped quantum dot. NANOSCALE 2014; 6:6997-7003. [PMID: 24839080 DOI: 10.1039/c4nr01319k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal quantum dots are luminescent long-lived probes that can be two-photon excited and manipulated by a single laser beam. Therefore, quantum dots can be used for simultaneous single molecule visualization and force manipulation using an infra-red laser. Here, we show that even a single optically trapped quantum dot, performing restricted Brownian motion within the focal volume, can be two-photon excited by the trapping laser beam and its luminescence can be detected by a camera. After two-photon excitation for a time long enough, the emitted light from the quantum dot is shown to blueshift. A quantum dot is much smaller than a diffraction limited laser focus and by mapping out the intensity of the focal volume and overlaying this with the positions visited by a quantum dot, a quantum dot is shown often to explore regions of the focal volume where the intensity is too low to render two-photon absorption likely. This is in accordance with the observation that a trapped quantum dot is only fluorescing 5-10 percent of the time. The results are important for realizing nano-scale quantum dot control and visualization and for correct interpretation of experiments using two-photon excited quantum dots as markers.
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10
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Sriram KK, Yeh JW, Lin YL, Chang YR, Chou CF. Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices. Nucleic Acids Res 2014; 42:e85. [PMID: 24753422 PMCID: PMC4041428 DOI: 10.1093/nar/gku254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites.
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Affiliation(s)
- K K Sriram
- Nano Science and Technology Program, Taiwan International Graduate Program, Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Department of Engineering and System Science, National Tsing Hua University, ESS New Building, 101, Sec. 2, Kuang-Fu Road, Hsinchu 30013, Taiwan Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Jia-Wei Yeh
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Yii-Lih Lin
- Nano Science and Technology Program, Taiwan International Graduate Program, Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Department of Chemistry, National Taiwan University, 1, Sec. 4, Roosevelt Road, Daan, Taipei 10617, Taiwan
| | - Yi-Ren Chang
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Research Centre for Applied Sciences, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Genomic Research Centre, Academia Sinica, 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan
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11
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Michaeli Y, Shahal T, Torchinsky D, Grunwald A, Hoch R, Ebenstein Y. Optical detection of epigenetic marks: sensitive quantification and direct imaging of individual hydroxymethylcytosine bases. Chem Commun (Camb) 2014; 49:8599-601. [PMID: 23756466 DOI: 10.1039/c3cc42543f] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein we report the specific labelling of the epigenetic modification 5-hydroxymethyl-cytosine along genomic DNA molecules with a fluorescent reporter molecule. Enzymatic glucosylation followed by a click chemistry reaction enables single molecule detection as well as global quantification of 5hmC in genomic DNA.
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Affiliation(s)
- Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel.
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12
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Levy-Sakin M, Grunwald A, Kim S, Gassman NR, Gottfried A, Antelman J, Kim Y, Ho S, Samuel R, Michalet X, Lin RR, Dertinger T, Kim AS, Chung S, Colyer RA, Weinhold E, Weiss S, Ebenstein Y. Toward single-molecule optical mapping of the epigenome. ACS NANO 2014; 8:14-26. [PMID: 24328256 PMCID: PMC4022788 DOI: 10.1021/nn4050694] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The past decade has seen an explosive growth in the utilization of single-molecule techniques for the study of complex systems. The ability to resolve phenomena otherwise masked by ensemble averaging has made these approaches especially attractive for the study of biological systems, where stochastic events lead to inherent inhomogeneity at the population level. The complex composition of the genome has made it an ideal system to study at the single-molecule level, and methods aimed at resolving genetic information from long, individual, genomic DNA molecules have been in use for the last 30 years. These methods, and particularly optical-based mapping of DNA, have been instrumental in highlighting genomic variation and contributed significantly to the assembly of many genomes including the human genome. Nanotechnology and nanoscopy have been a strong driving force for advancing genomic mapping approaches, allowing both better manipulation of DNA on the nanoscale and enhanced optical resolving power for analysis of genomic information. During the past few years, these developments have been adopted also for epigenetic studies. The common principle for these studies is the use of advanced optical microscopy for the detection of fluorescently labeled epigenetic marks on long, extended DNA molecules. Here we will discuss recent single-molecule studies for the mapping of chromatin composition and epigenetic DNA modifications, such as DNA methylation.
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Affiliation(s)
- Michal Levy-Sakin
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Assaf Grunwald
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Soohong Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Natalie R. Gassman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Anna Gottfried
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Josh Antelman
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Younggyu Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sam Ho
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Robin Samuel
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Ron R. Lin
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Thomas Dertinger
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Andrew S. Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Sangyoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Ryan A. Colyer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
- Corresponding authors: (Y. Ebenstein), (S. Weiss)
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel
- Corresponding authors: (Y. Ebenstein), (S. Weiss)
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13
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Zeng QH, Zhang XW, Xu KP, Jiang JG. Application of fluorescently labeled tracer technique for detection of natural active macromolecules in Chinese medicine. Drug Metab Rev 2013; 46:57-71. [DOI: 10.3109/03602532.2013.839699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. Curr Opin Biotechnol 2013; 24:690-8. [DOI: 10.1016/j.copbio.2013.01.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/20/2013] [Accepted: 01/22/2013] [Indexed: 12/25/2022]
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15
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Wang Y, Hu R, Lin G, Roy I, Yong KT. Functionalized quantum dots for biosensing and bioimaging and concerns on toxicity. ACS APPLIED MATERIALS & INTERFACES 2013; 5:2786-2799. [PMID: 23394295 DOI: 10.1021/am302030a] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Considerable efforts have been devoted to the development of novel functionalized nanomaterials for bio-oriented applications. With unique optical properties and molar scale production, colloidal photoluminescent quantum dots (QDs) have been properly functionalized with controlled interfaces as new class of optical probes with extensive use in biomedical research. In this review, we present a brief summary on the current research interests of using fine engineered QDs as a nanoplatform for biomedical sensing and imaging applications. In addition, recent concerns on the potential toxic effects of QDs are described as a general guidance for the development on QD formulations in future studies.
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Affiliation(s)
- Yucheng Wang
- School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore
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16
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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17
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Kimura Y, Goto Y, Oana H, Washizu M. Optical sequence probing with the homologous recombination protein RecA. J Biotechnol 2013; 164:254-9. [DOI: 10.1016/j.jbiotec.2012.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 07/23/2012] [Accepted: 08/19/2012] [Indexed: 12/01/2022]
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18
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Rasmussen TE, Jauffred L, Brewer J, Vogel S, Torbensen ER, Lagerholm BC, Oddershede L, Arnspang EC. Single Molecule Applications of Quantum Dots. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/jmp.2013.411a2002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Zhang Y, Hu Z, Qin H, Wei X, Cheng K, Liu F, Wu R, Zou H. Highly Efficient Extraction of Cellular Nucleic Acid Associated Proteins in Vitro with Magnetic Oxidized Carbon Nanotubes. Anal Chem 2012; 84:10454-62. [DOI: 10.1021/ac302695u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Ren’an Wu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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20
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Wang Y, Reinhart WF, Tree DR, Dorfman KD. Resolution limit for DNA barcodes in the Odijk regime. BIOMICROFLUIDICS 2012; 6:14101-141019. [PMID: 22299023 PMCID: PMC3269310 DOI: 10.1063/1.3672691] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 12/06/2011] [Indexed: 05/21/2023]
Abstract
We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of the DNA, simulations indicate that the theoretical predictions are reasonably accurate for channel widths up to two-thirds of the persistence length. Our results quantify the conjecture that DNA barcoding has kilobase pair resolution-provided the nanochannel lies in the Odijk regime.
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21
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Kim S, Gottfried A, Lin RR, Dertinger T, Kim AS, Chung S, Colyer RA, Weinhold E, Weiss S, Ebenstein Y. Enzymatically incorporated genomic tags for optical mapping of DNA-binding proteins. Angew Chem Int Ed Engl 2012; 51:3578-81. [PMID: 22344826 DOI: 10.1002/anie.201107714] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 12/19/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Soohong Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, USA
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22
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Kim S, Gottfried A, Lin RR, Dertinger T, Kim AS, Chung S, Colyer RA, Weinhold E, Weiss S, Ebenstein Y. Enzymatically Incorporated Genomic Tags for Optical Mapping of DNA-Binding Proteins. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107714] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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23
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Bailes J, Soloviev M. The application of semiconductor quantum dots for enhancing peptide desorption, improving peak resolution and sensitivity of detection in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Methods Mol Biol 2012; 906:211-217. [PMID: 22791435 DOI: 10.1007/978-1-61779-953-2_16] [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: 06/01/2023]
Abstract
The interest in quantum dots (QD) and a number of reported life sciences applications increased dramatically over the last decade. The popularity of QDs stems from better photostability, higher extinction -co-efficients, and unique optical properties such as superior light absorption. Here we report methods for improving matrix-assisted laser desorption/ionization desorption of crude tryptic protein digests by using CdSe/ZnS QDs. The addition of QDs to the matrix improves the signal-to-noise ratio, peak quality and increases the number of detected peptides and the overall sequence coverage.
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Affiliation(s)
- Julian Bailes
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, UK
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24
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Hu B, Zhang LP, Chen ML, Chen ML, Wang JH. The inhibition of fluorescence resonance energy transfer between quantum dots for glucose assay. Biosens Bioelectron 2011; 32:82-8. [PMID: 22192453 DOI: 10.1016/j.bios.2011.11.031] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 02/07/2023]
Abstract
Fluorescence resonance energy transfer (FRET) between two quantum dots of different sizes causes fluorescence quenching. Hereby a binding site pre-blocking approach is proposed to avoid this effect. Pre-binding of glucose on the donor occupies the binding sites and thus blocks resonance energy transfer between the two quantum dots, protecting the fluorescence from being quenched. A glucose assay is developed based on this approach. The glucose content is correlated with the fluorescence difference in the absence and in the presence of glucose. In practice, Green QDs-Con A conjugates are used as donors and Red QDs-NH(2)-glu conjugates as acceptors to form FRET system. The inhibition of fluorescence quenching is then measured in the presence of glucose. A linear calibration graph is achieved within 0.1-2.0 mmolL(-1), along with a detection limit of 0.03 mmolL(-1) and a RSD of 2.1% (1.0 mmolL(-1)). 91-105% of glucose in serum and urine samples is recovered. It is worth mentioning that the present glucose assay approach also generates a fluorescence chromatic difference imaging, and the color display clearly identifies the glucose contents by visual detection with a distinguishing ability of ca. 0.5 mmolL(-1). The present approach can potentially be used for the clinical determination of glucose in biological samples which can be further developed into a glucose sensor.
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Affiliation(s)
- Bo Hu
- Research Center for Analytical Sciences, Northeastern University, Box 332, Shenyang 110819, China
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25
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Zohar H, Muller SJ. Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA. NANOSCALE 2011; 3:3027-39. [PMID: 21734993 PMCID: PMC3322637 DOI: 10.1039/c1nr10280j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review is a practical guide for experimentalists interested in specifically labeling internal sequences on double-stranded (ds) DNA molecules for single-molecule experiments. We describe six labeling approaches demonstrated in a single-molecule context and discuss the merits and drawbacks of each approach with particular attention to the amount of specialized training and reagents required. By evaluating each approach according to criteria relevant to single-molecule experiments, including labeling yield and compatibility with cofactors such as Mg(2+), we provide a simple reference for selecting a labeling method for given experimental constraints. Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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26
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Iyer G, Pinaud F, Xu J, Ebenstein Y, Li J, Chang J, Dahan M, Weiss S. Aromatic aldehyde and hydrazine activated peptide coated quantum dots for easy bioconjugation and live cell imaging. Bioconjug Chem 2011; 22:1006-11. [PMID: 21553893 DOI: 10.1021/bc100593m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We present a robust scheme for preparation of semiconductor quantum dots (QDs) and cognate partners in a conjugation ready format. Our approach is based on bis-aryl hydrazone bond formation mediated by aromatic aldehyde and hydrazinonicotinate acetone hydrazone (HyNic) activated peptide coated quantum dots. We demonstrate controlled preparation of antibody--QD bioconjugates for specific targeting of endogenous epidermal growth factor receptors in breast cancer cells and for single QD tracking of transmembrane proteins via an extracellular epitope. The same approach was also used for optical mapping of RNA polymerases bound to combed genomic DNA in vitro.
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Affiliation(s)
- Gopal Iyer
- Department of Chemistry and Biochemistry, California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California 90095, United States.
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27
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Ali Z, Abbasi AZ, Zhang F, Arosio P, Lascialfari A, Casula MF, Wenk A, Kreyling W, Plapper R, Seidel M, Niessner R, Knöll J, Seubert A, Parak WJ. Multifunctional nanoparticles for dual imaging. Anal Chem 2011; 83:2877-82. [PMID: 21413785 DOI: 10.1021/ac103261y] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
For imaging with different modalities, labels, which provide contrast for all modalities, are required. Colloidal nanoparticles composed out of an inorganic core and a polymer shell offer progress in this direction. Both, the core and the polymer shell, can be synthesized to be fluorescent, magnetic, or radioactive. When different cores are combined with different polymer shells, different types of particles for dual imaging can be obtained, as for example, fluorescent cores with radioactive polymer shells. Properties and perspectives of such nanoparticles for multimodal imaging are discussed.
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Affiliation(s)
- Z Ali
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften, Philipps Universität Marburg, Marburg, Germany
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28
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Dolatabadi JEN, Mashinchian O, Ayoubi B, Jamali AA, Mobed A, Losic D, Omidi Y, de la Guardia M. Optical and electrochemical DNA nanobiosensors. Trends Analyt Chem 2011. [DOI: 10.1016/j.trac.2010.11.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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29
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Xu W, Muller SJ. Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping. LAB ON A CHIP 2011; 11:435-42. [PMID: 21072428 PMCID: PMC3322636 DOI: 10.1039/c0lc00176g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate the feasibility of a single-molecule microfluidic approach to both sequence detection and obtaining kinetic information for restriction endonucleases on dsDNA. In this method, a microfluidic stagnation point flow is designed to trap, hold, and linearize double-stranded (ds) genomic DNA to which a restriction endonuclease has been pre-bound sequence-specifically. By introducing the cofactor magnesium, we determine the binding location of the enzyme by the cleavage process of dsDNA as in optical restriction mapping, however here the DNA need not be immobilized on a surface. We note that no special labeling of the enzyme is required, which makes it simpler than our previous scheme using stagnation point flows for sequence detection. Our accuracy in determining the location of the recognition site is comparable to or better than other single molecule techniques due to the fidelity with which we can control the linearization of the DNA molecules. In addition, since the cleavage process can be followed in real time, information about the cleavage kinetics, and subtle differences in binding and cleavage frequencies among the recognition sites, may also be obtained. Data for the five recognition sites for the type II restriction endonuclease EcoRI on λ-DNA are presented as a model system. While the roles of the varying fluid velocity and tension along the chain backbone on the measured kinetics remain to be determined, we believe this new method holds promise for a broad range of studies of DNA-protein interactions, including the kinetics of other DNA cleavage processes, the dissociation of a restriction enzyme from the cleaved substrate, and other macromolecular cleavage processes.
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Affiliation(s)
- Weilin Xu
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, U.S.A
| | - Susan J. Muller
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, CA 94720, U.S.A
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30
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Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies. Methods Mol Biol 2011; 745:447-61. [PMID: 21660710 DOI: 10.1007/978-1-61779-129-1_26] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule studies of protein-DNA interactions continue to yield new information on numerous DNA processing pathways. For example, optical microscopy-based techniques permit the real-time observation of proteins that interact with DNA substrates, which in turn allows direct insight into reaction mechanisms. However, these experiments remain technically challenging and are limited by the paucity of stable chromophores and the difficulty of acquiring statistically significant observations. In this protocol, we describe a novel, high-throughput, nanofabricated experimental platform enabling real-time imaging of hundreds of individual protein-DNA complexes over hour timescales.
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31
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Zohar H, Hetherington CL, Bustamante C, Muller SJ. Peptide nucleic acids as tools for single-molecule sequence detection and manipulation. NANO LETTERS 2010; 10:4697-701. [PMID: 20923183 PMCID: PMC3322611 DOI: 10.1021/nl102986v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The ability to strongly and sequence-specifically attach modifications such as fluorophores and haptens to individual double-stranded (ds) DNA molecules is critical to a variety of single-molecule experiments. We propose using modified peptide nucleic acids (PNAs) for this purpose and implement them in two model single-molecule experiments where individual DNA molecules are manipulated via microfluidic flow and optical tweezers, respectively. We demonstrate that PNAs are versatile and robust sequence-specific tethers.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical Engineering, California Institute for Quantitative Biosciences, and Howard Hughes Medical InstituteUniversity of California, Berkeley, California 94720, United States
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32
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Dylla-Spears R, Townsend JE, Jen-Jacobson L, Sohn LL, Muller SJ. Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point. LAB ON A CHIP 2010; 10:1543-9. [PMID: 20358051 PMCID: PMC3322643 DOI: 10.1039/b926847b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate the use of a microfluidic stagnation point flow to trap and extend single molecules of double-stranded (ds) genomic DNA for detection of target sequences along the DNA backbone. Mutant EcoRI-based fluorescent markers are bound sequence-specifically to fluorescently labeled ds lambda-DNA. The marker-DNA complexes are introduced into a microfluidic cross slot consisting of flow channels that intersect at ninety degrees. Buffered solution containing the marker-DNA complexes flows in one channel of the cross slot, pure buffer flows in the opposing channel at the same flow rate, and fluid exits the two channels at ninety degrees from the inlet channels. This creates a stagnation point at the center of a planar extensional flow, where marker-DNA complexes may be trapped and elongated along the outflow axis. The degree of elongation can be controlled using the flow strength (i.e., a non-dimensional flow rate) in the device. Both the DNA backbone and the markers bound along the stretched DNA are observed directly using fluorescence microscopy, and the location of the markers along the DNA backbone is measured. We find that our method permits detection of each of the five expected target site positions to within 1.5 kb with standard deviations of <1.5 kb. We compare the method's precision and accuracy at molecular extensions of 68% and 88% of the contour length to binding distributions from similar data obtained via molecular combing. We also provide evidence that increased mixing of the sample during binding of the marker to the DNA improves binding to internal target sequences of dsDNA, presumably by extending the DNA and making the internal binding sites more accessible.
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33
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Jauffred L, Oddershede LB. Two-photon quantum dot excitation during optical trapping. NANO LETTERS 2010; 10:1927-30. [PMID: 20402477 DOI: 10.1021/nl100924z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A single CW infrared laser beam can simultaneously trap and excite an individual colloidal quantum dot. Though the laser light is relatively weak, the excitation occurs through two-photon absorption. This finding eliminates the demand for an excitation light source in addition to a trapping laser in nanoscale experiments with simultaneous force-manipulation and quantum dot visualization. Also, we demonstrate that optical trapping efficiencies of individual quantum dots do not correlate with their emission wavelength or physical size.
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34
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North SH, Lock EH, Taitt CR, Walton SG. Critical aspects of biointerface design and their impact on biosensor development. Anal Bioanal Chem 2010; 397:925-33. [PMID: 20349179 DOI: 10.1007/s00216-010-3637-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/04/2010] [Accepted: 03/07/2010] [Indexed: 11/29/2022]
Abstract
The stable integration of a biological recognition element on a transducing substrate surface is the single most important step in the creation of a high-functioning sensor surface. The key factors affecting biotic and abiotic functionalities at the biointerface are both chemical and physical. Understanding the interactions between biomolecules and surfaces, and their emergent complexity, is critical for biointerface implementation for sensing applications. In this overview, we highlight materials and methods typically used for biosensor development. Particular emphasis has been given to the experimental evaluation of biointerfacial properties and functionality. Promising research directions for application of biointerfaces to biosensing are suggested.
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Affiliation(s)
- Stella H North
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, 4555 Overlook Ave. SW, Washington, DC 20375, USA
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35
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LI CY, LI Q, LIU HT, ZHANG J, Aletangaole DAMIRIN. Hot Topic and Challenge of Semiconductor Quantum Dots as Fluorescence Labels*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2009.00342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Dylla-Spears R, Townsend JE, Sohn LL, Jen-Jacobson L, Muller SJ. Fluorescent marker for direct detection of specific dsDNA sequences. Anal Chem 2010; 81:10049-54. [PMID: 19908852 DOI: 10.1021/ac9019895] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have created a fluorescent marker using a mutant EcoRI restriction endonuclease (K249C) that enables prolonged, direct visualization of specific sequences on genomic lengths of double-stranded (ds) DNA. The marker consists of a biotinylated enzyme, attached through the biotin-avidin interaction to a fluorescent nanosphere. Control over biotin position with respect to the enzyme's binding pocket is achieved by biotinylating the mutant EcoRI at the mutation site. Biotinylated enzyme is incubated with dsDNA and NeutrAvidin-coated, fluorescent nanospheres under conditions that allow enzyme binding but prevent cleavage. Marker-laden DNA is then fluorescently stained and stretched on polylysine-coated glass slides so that the positions of the bound markers along individual DNA molecules can be measured. We demonstrate the marker's ability to bind specifically to its target sequence using both bulk gel-shift assays and single-molecule methods.
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Affiliation(s)
- Rebecca Dylla-Spears
- Department of Chemical Engineering, University of California, Berkeley, Berkeley, California, USA
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37
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Bioconjugated quantum dots as fluorescent probes for bioanalytical applications. Anal Bioanal Chem 2009; 396:229-40. [DOI: 10.1007/s00216-009-3033-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 07/24/2009] [Accepted: 07/30/2009] [Indexed: 10/20/2022]
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38
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Antelman J, Wilking-Chang C, Weiss S, Michalet X. Nanometer distance measurements between multicolor quantum dots. NANO LETTERS 2009; 9:2199-205. [PMID: 19374434 PMCID: PMC2748936 DOI: 10.1021/nl901163k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Quantum dot dimers made of short double-stranded DNA molecules labeled with different color quantum dots at each end were imaged using multicolor stage-scanning confocal microscopy. This approach eliminates chromatic aberration and color registration issues usually encountered in other multicolor imaging techniques. We demonstrate nanometer accuracy in individual distance measurement by suppression of quantum dot blinking and thoroughly characterize the contribution of different effects to the variability observed between measurements. Our analysis opens the way to accurate structural studies of biomolecules and biomolecular complexes using multicolor quantum labeling.
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Affiliation(s)
| | | | | | - Xavier Michalet
- CORRESPONDING AUTHOR FOOTNOTE. Correspondence should be address to XM (, Ph: 310 794-6693, Fax: 310 267-4672)
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