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Calle-Casteñeda S, Winden E, Vasquez-Echeverri A, Schickling M, Browning E, Hernandez Ortiz JP, Schwartz DC. 'Gel-Stacks' gently confine or reversibly immobilize arrays of single DNA molecules for manipulation and study. Biotechniques 2024. [PMID: 38655877 DOI: 10.2144/btn-2023-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Large DNA molecules (>20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be 'rescued' as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed 'Gel-Stacks.' Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion.
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Affiliation(s)
- Susana Calle-Casteñeda
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eamon Winden
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alejandro Vasquez-Echeverri
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew Schickling
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Evelyn Browning
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Juan Pablo Hernandez Ortiz
- GHI One Health Colombia & One Health Genomic Laboratory, Universidad Nacional de Colombia - Medellín, Medellín, 050034, Colombia
- Departamento de Materiales y Nanotecnología, Universidad Nacional de Colombia - Medellín, Medellín, 050034, Colombia
| | - David C Schwartz
- Laboratory for Molecular & Computational Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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2
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Ye JC, Tang G. Optical Genome Mapping: A Machine-Based Platform in Cytogenomics. Methods Mol Biol 2024; 2825:113-124. [PMID: 38913305 DOI: 10.1007/978-1-0716-3946-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Optical genome mapping (OGM) has generated excitement following decades of research and development. Now, commercially available technical platforms have been used to compare various other cytogenetic and cytogenomic technologies, including karyotype, microarrays, and DNA sequencing, with impressive results. In this chapter, using OGM as a case study, we advocate for a new trend in future cytogenomics, emphasizing the power of machine automation to deliver higher-quality cytogenomic data. By briefly discussing OGM, along with its major advantages and limitations, we underscore the importance of karyotype-based genomic research, from both a theoretical framework and a new technology perspective. We also call for the encouragement of further technological platform development for the future of cytogenetics and cytogenomics.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Guilin Tang
- Department of Hematopathology, Division of Pathology-Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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3
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Rau S, Huynh T, Larsen A, Kounovsky-Shafer KL. Concentration of lambda concatemers using a 3D printed device. Electrophoresis 2023; 44:744-751. [PMID: 36799437 PMCID: PMC10121831 DOI: 10.1002/elps.202200200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/18/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Abstract
Identifying significant variations in genomes can be cumbersome, as the variations span a multitude of base pairs and can make genome assembly difficult. However, large DNA molecules that span the variation aid in assembly. Due to the DNA molecule's large size, routine molecular biology techniques can break DNA. Therefore, a method is required to concentrate large DNA. A bis-acrylamide roadblock was cured in a proof-of-principle 3D printed device to concentrate DNA at the interface between the roadblock and solution. Lambda concatemer DNA was stained with YOYO-1 and loaded into the 3D printed device. A dynamic range of voltages and acrylamide concentrations were tested to determine how much DNA was concentrated and recovered. The fluorescence of the original solution and the concentrated solution was measured, the recovery was 37% of the original sample, and the volume decreased by a factor of 3 of the original volume.
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Affiliation(s)
- Samantha Rau
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
| | - Thi Huynh
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
| | - Alex Larsen
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
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4
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Yamamoto K, Ota N, Tanaka Y. Nanofluidic Devices and Applications for Biological Analyses. Anal Chem 2021; 93:332-349. [PMID: 33125221 DOI: 10.1021/acs.analchem.0c03868] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Koki Yamamoto
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobutoshi Ota
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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5
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Masters C, Dolphin J, Maschmann A, McGill K, Moore M, Thompson D, Kounovsky-Shafer KL. Development of 3D printed mesofluidic devices to elute and concentrate DNA. Electrophoresis 2018; 40:810-816. [PMID: 30367503 DOI: 10.1002/elps.201800309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 11/08/2022]
Abstract
To understand structural variation for personal genomics, an extensive ensemble of large DNA molecules will be required to span large structural variations. Nanocoding, a whole-genome analysis platform, can analyze large DNA molecules for the construction of physical restriction maps of entire genomes. However, handling of large DNA is difficult and a system is needed to concentrate large DNA molecules, while keeping the molecules intact. Insert technology was developed to protect large DNA molecules during routine cell lysis and molecular biology techniques. However, eluting and concentrating DNA molecules has been difficult in the past. Utilizing 3D printed mesofluidic device, a proof of principle system was developed to elute and concentrate lambda DNA molecules at the interface between a solution and a poly-acrylamide roadblock. The matrix allowed buffer solution to move through the pores in the matrix; however, it slowed down the progression of DNA in the matrix, since the molecules were so large and the pore size was small. Using fluorescence intensity of the insert, 84% of DNA was eluted from the insert and 45% of DNA was recovered in solution from the eluted DNA. DNA recovered was digested with a restriction enzyme to determine that the DNA molecules remained full length during the elution and concentration of DNA.
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Affiliation(s)
- Cody Masters
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Jocelyn Dolphin
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - April Maschmann
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Keegan McGill
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Matthew Moore
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Drew Thompson
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
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6
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Maschmann A, Masters C, Davison M, Lallman J, Thompson D, Kounovsky-Shafer KL. Determining if DNA Stained with a Cyanine Dye Can Be Digested with Restriction Enzymes. J Vis Exp 2018. [PMID: 29443093 DOI: 10.3791/57141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Visualization of DNA for fluorescence microscopy utilizes a variety of dyes such as cyanine dyes. These dyes are utilized due to their high affinity and sensitivity for DNA. In order to determine if the DNA molecules are full length after the completion of the experiment, a method is required to determine if the stained molecules are full length by digesting DNA with restriction enzymes. However, stained DNA may inhibit the enzymes, so a method is needed to determine what enzymes one could use for fluorochrome stained DNA. In this method, DNA is stained with a cyanine dye overnight to allow the dye and DNA to equilibrate. Next, stained DNA is digested with a restriction enzyme, loaded into a gel and electrophoresed. The experimental DNA digest bands are compared to an in silico digest to determine the restriction enzyme activity. If there is the same number of bands as expected, then the reaction is complete. More bands than expected indicate partial digestion and less bands indicate incomplete digestion. The advantage of this method is its simplicity and it uses equipment that a scientist would need for a restriction enzyme assay and gel electrophoresis. A limitation of this method is that the enzymes available to most scientists are commercially available enzymes; however, any restriction enzymes could be used.
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Affiliation(s)
| | - Cody Masters
- Department of Chemistry, University of Nebraska - Kearney
| | | | - Joshua Lallman
- Department of Chemistry, University of Nebraska - Kearney
| | - Drew Thompson
- Department of Chemistry, University of Nebraska - Kearney
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7
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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8
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Abstract
Repeated sequences make up approximately two-thirds of the human genome, which become fully accountable when very large DNA molecules are analyzed. Long, single DNA molecules are problematic using common experimental techniques and fluidic devices because of mechanical considerations that include breakage, dealing with the massive size of these coils, or the huge length of stretched DNAs. Accordingly, we harness analyte “issues” as exploitable advantages by invention and characterization of the “molecular gate,” which controls and synchronizes formation of stretched molecules as DNA dumbbells within nanoslit geometries that may also offer new routes to separation. This was accomplished by theoretical studies and experiments leveraging a series of electrical forces acting on DNA molecules, device walls, and the fluid flows within our devices. Very large DNA molecules enable comprehensive analysis of complex genomes, such as human, cancer, and plants because they span across sequence repeats and complex somatic events. When physically manipulated, or analyzed as single molecules, long polyelectrolytes are problematic because of mechanical considerations that include shear-mediated breakage, dealing with the massive size of these coils, or the length of stretched DNAs using common experimental techniques and fluidic devices. Accordingly, we harness analyte “issues” as exploitable advantages by our invention and characterization of the “molecular gate,” which controls and synchronizes formation of stretched DNA molecules as DNA dumbbells within nanoslit geometries. Molecular gate geometries comprise micro- and nanoscale features designed to synergize very low ionic strength conditions in ways we show effectively create an “electrostatic bottle.” This effect greatly enhances molecular confinement within large slit geometries and supports facile, synchronized electrokinetic loading of nanoslits, even without dumbbell formation. Device geometries were considered at the molecular and continuum scales through computer simulations, which also guided our efforts to optimize design and functionalities. In addition, we show that the molecular gate may govern DNA separations because DNA molecules can be electrokinetically triggered, by varying applied voltage, to enter slits in a size-dependent manner. Lastly, mapping the Mesoplasmaflorum genome, via synchronized dumbbell formation, validates our nascent approach as a viable starting point for advanced development that will build an integrated system capable of large-scale genome analysis.
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9
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Lallman J, Flaugh R, Kounovsky-Shafer KL. Determination of electroosmotic and electrophoretic mobility of DNA and dyes in low ionic strength solutions. Electrophoresis 2017; 39:862-868. [PMID: 28834563 DOI: 10.1002/elps.201700281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 11/10/2022]
Abstract
Nanocoding, a genome analysis platform, relies on very low ionic strength conditions to elongate DNA molecules up to 1.06 (fully stretched DNA = 1). Understanding how electroosmotic and electrophoretic forces vary, as ionic strength decreases, will enable better Nanocoding devices, or other genome analysis platforms, to be developed. Using gel electrophoresis to determine overall mobility (includes contributions from electrophoretic and electroosmotic forces) in different ionic strength conditions, linear DNA molecules (pUC19 (2.7 kb), pBR322 (4.4 kb), ΦX174 (5.4 kb), and PSNAPf-H2B (6.2 kb)) were analyzed in varying gel concentrations (1.50, 1.25, 1.00, 0.75, and 0.50%). Additionally, buffer concentration (Tris-EDTA, TE) was varied to determine free solution mobility at different ionic strength solutions. As ionic strength decreased from 13.8 to 7.3 mM, overall mobility increased. As TE buffer decreased (< 7.3 mM), overall mobility drastically decreased as ionic strength decreased. Rhodamine B dye was utilized to determine the electroosmotic mobility. As the ionic strength decreased, electroosmotic mobility increased. The experimental electrophoretic mobility was compared to theoretical considerations for electrophoretic mobility (Pitts and Debye-Hückel-Onsager). Electroosmotic forces decreased the overall mobility of DNA molecules and bromophenol blue migration in a gel matrix as ionic strength decreased.
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Affiliation(s)
- Joshua Lallman
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
| | - Rachel Flaugh
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, USA
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10
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Abstract
In optical DNA mapping technologies sequence-specific intensity variations (DNA barcodes) along stretched and stained DNA molecules are produced. These “fingerprints” of the underlying DNA sequence have a resolution of the order one kilobasepairs and the stretching of the DNA molecules are performed by surface adsorption or nano-channel setups. A post-processing challenge for nano-channel based methods, due to local and global random movement of the DNA molecule during imaging, is how to align different time frames in order to produce reproducible time-averaged DNA barcodes. The current solutions to this challenge are computationally rather slow. With high-throughput applications in mind, we here introduce a parameter-free method for filtering a single time frame noisy barcode (snap-shot optical map), measured in a fraction of a second. By using only a single time frame barcode we circumvent the need for post-processing alignment. We demonstrate that our method is successful at providing filtered barcodes which are less noisy and more similar to time averaged barcodes. The method is based on the application of a low-pass filter on a single noisy barcode using the width of the Point Spread Function of the system as a unique, and known, filtering parameter. We find that after applying our method, the Pearson correlation coefficient (a real number in the range from -1 to 1) between the single time-frame barcode and the time average of the aligned kymograph increases significantly, roughly by 0.2 on average. By comparing to a database of more than 3000 theoretical plasmid barcodes we show that the capabilities to identify plasmids is improved by filtering single time-frame barcodes compared to the unfiltered analogues. Since snap-shot experiments and computational time using our method both are less than a second, this study opens up for high throughput optical DNA mapping with improved reproducibility.
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11
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Maschmann A, Kounovsky-Shafer KL. Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:406-417. [PMID: 28362164 DOI: 10.1080/15257770.2017.1300665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.
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Affiliation(s)
- April Maschmann
- a Department of Chemistry , University of Nebraska-Kearney , Kearney , NE , USA
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12
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Niman CS, Zuckermann MJ, Balaz M, Tegenfeldt JO, Curmi PMG, Forde NR, Linke H. Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke. NANOSCALE 2014; 6:15008-15019. [PMID: 25367216 DOI: 10.1039/c4nr04701j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.
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Affiliation(s)
- Cassandra S Niman
- Division of Solid State Physics, Lund University, Box 118, 22100 Lund, Sweden.
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13
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Zarkov A, Vasilev A, Deligeorgiev T, Stoynov S, Nedelcheva-Veleva M. Novel Fluorescent Dyes for Single DNA Molecule Techniques. Mol Imaging 2013. [DOI: 10.2310/7290.2012.00018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Alexander Zarkov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Aleksey Vasilev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Todor Deligeorgiev
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Stoyno Stoynov
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
| | - Marina Nedelcheva-Veleva
- From the Institute of Molecular Biology “Roumen Tsanev,” Bulgarian Academy of Sciences, and Faculty of Chemistry, University of Sofia, Sofia, Bulgaria
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14
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Abstract
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
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15
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Schatz MC, Witkowski J, McCombie WR. Current challenges in de novo plant genome sequencing and assembly. Genome Biol 2013; 13:243. [PMID: 22546054 DOI: 10.1186/gb4015] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community.
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Affiliation(s)
- Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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16
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Luzzietti N, Knappe S, Richter I, Seidel R. Nicking enzyme-based internal labeling of DNA at multiple loci. Nat Protoc 2012; 7:643-53. [PMID: 22402634 DOI: 10.1038/nprot.2012.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The labeling of biomolecules has become standard practice in molecular biosciences. Modifications are used for detection, sorting and isolation of small molecules, complexes and entire cells. We have recently reported a method for introducing internal chemical and structural modifications into kbp-sized DNA target substrates that are frequently used in single-molecule experiments. It makes use of nicking enzymes that create single-stranded DNA gaps, which can be subsequently filled with labeled oligonucleotides. Here we provide a detailed protocol and further expand this method. We show that modifications can be introduced at distant loci within one molecule in a simple one-pot reaction. In addition, we achieve labeling on both strands at a specific locus, as demonstrated by Förster resonance energy transfer (FRET) experiments. The protocol requires an initial cloning of the target substrate (3-5 d), whereas the labeling itself takes 4-6 h. More elaborate purification and verification of label incorporation requires 2 h for each method.
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Affiliation(s)
- Nicholas Luzzietti
- Biotechnology Center, Dresden University of Technology, Dresden, Germany
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17
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Niedringhaus TP, Milanova D, Kerby MB, Snyder MP, Barron AE. Landscape of next-generation sequencing technologies. Anal Chem 2011; 83:4327-41. [PMID: 21612267 DOI: 10.1021/ac2010857] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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Luzzietti N, Brutzer H, Klaue D, Schwarz FW, Staroske W, Clausing S, Seidel R. Efficient preparation of internally modified single-molecule constructs using nicking enzymes. Nucleic Acids Res 2010; 39:e15. [PMID: 21071409 PMCID: PMC3035433 DOI: 10.1093/nar/gkq1004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Investigations of enzymes involved in DNA metabolism have strongly benefited from the establishment of single molecule techniques. These experiments frequently require elaborate DNA substrates, which carry chemical labels or nucleic acid tertiary structures. Preparing such constructs often represents a technical challenge: long modified DNA molecules are usually produced via multi-step processes, involving low efficiency intermolecular ligations of several fragments. Here, we show how long stretches of DNA (>50 bp) can be modified using nicking enzymes to produce complex DNA constructs. Multiple different chemical and structural modifications can be placed internally along DNA, in a specific and precise manner. Furthermore, the nicks created can be resealed efficiently yielding intact molecules, whose mechanical properties are preserved. Additionally, the same strategy is applied to obtain long single-strand overhangs subsequently used for efficient ligation of ss- to dsDNA molecules. This technique offers promise for a wide range of applications, in particular single-molecule experiments, where frequently multiple internal DNA modifications are required.
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Affiliation(s)
- Nicholas Luzzietti
- Biotechnology Center, Technische Universität Dresden, D-01062 Dresden, Germany
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19
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Chan SH, Stoddard BL, Xu SY. Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity. Nucleic Acids Res 2010; 39:1-18. [PMID: 20805246 PMCID: PMC3017599 DOI: 10.1093/nar/gkq742] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Restriction endonucleases (REases) are highly specific DNA scissors that have facilitated the development of modern molecular biology. Intensive studies of double strand (ds) cleavage activity of Type IIP REases, which recognize 4–8 bp palindromic sequences, have revealed a variety of mechanisms of molecular recognition and catalysis. Less well-studied are REases which cleave only one of the strands of dsDNA, creating a nick instead of a ds break. Naturally occurring nicking endonucleases (NEases) range from frequent cutters such as Nt.CviPII (^CCD; ^ denotes the cleavage site) to rare-cutting homing endonucleases (HEases) such as I-HmuI. In addition to these bona fida NEases, individual subunits of some heterodimeric Type IIS REases have recently been shown to be natural NEases. The discovery and characterization of more REases that recognize asymmetric sequences, particularly Types IIS and IIA REases, has revealed recognition and cleavage mechanisms drastically different from the canonical Type IIP mechanisms, and has allowed researchers to engineer highly strand-specific NEases. Monomeric LAGLIDADG HEases use two separate catalytic sites for cleavage. Exploitation of this characteristic has also resulted in useful nicking HEases. This review aims at providing an overview of the cleavage mechanisms of Types IIS and IIA REases and LAGLIDADG HEases, the engineering of their nicking variants, and the applications of NEases and nicking HEases.
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Teague B, Waterman MS, Goldstein S, Potamousis K, Zhou S, Reslewic S, Sarkar D, Valouev A, Churas C, Kidd JM, Kohn S, Runnheim R, Lamers C, Forrest D, Newton MA, Eichler EE, Kent-First M, Surti U, Livny M, Schwartz DC. High-resolution human genome structure by single-molecule analysis. Proc Natl Acad Sci U S A 2010; 107:10848-53. [PMID: 20534489 PMCID: PMC2890719 DOI: 10.1073/pnas.0914638107] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Variation in genome structure is an important source of human genetic polymorphism: It affects a large proportion of the genome and has a variety of phenotypic consequences relevant to health and disease. In spite of this, human genome structure variation is incompletely characterized due to a lack of approaches for discovering a broad range of structural variants in a global, comprehensive fashion. We addressed this gap with Optical Mapping, a high-throughput, high-resolution single-molecule system for studying genome structure. We used Optical Mapping to create genome-wide restriction maps of a complete hydatidiform mole and three lymphoblast-derived cell lines, and we validated the approach by demonstrating a strong concordance with existing methods. We also describe thousands of new variants with sizes ranging from kb to Mb.
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Affiliation(s)
- Brian Teague
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Michael S. Waterman
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Steven Goldstein
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Konstantinos Potamousis
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Shiguo Zhou
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Susan Reslewic
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Deepayan Sarkar
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
| | - Anton Valouev
- Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910
| | - Christopher Churas
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Jeffrey M. Kidd
- Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195-5065
| | - Scott Kohn
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Rodney Runnheim
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Casey Lamers
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Dan Forrest
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
| | - Michael A. Newton
- Department of Statistics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
- Department of Biostatistics and Medical Informatics, University of Wisconsin, 1300 University Avenue, Madison, WI 53706-1510
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195-5065
| | - Marijo Kent-First
- Department of Animal Science, Department of Biological Sciences, Mississippi State University, 130 Harned Hall, Lee Boulevard, Mississippi State, MS 39762-9698
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, PA 15213-2536; and
| | - Miron Livny
- Department of Computer Sciences, University of Wisconsin, 1210 West Dayton Street, Madison, WI 53706-1685
| | - David C. Schwartz
- The Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics and Biotechnology Center, University of Wisconsin, 425 Henry Mall, Madison, WI 53706-1580
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