1
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Choi W, Park E, Bae S, Choi KH, Han S, Son KH, Lee DY, Cho IJ, Seong H, Hwang KS, Nam JM, Choi J, Lee H, Choi N. Multiplex SNP Genotyping Using SWITCH: Sequence-Specific Nanoparticle with Interpretative Toehold-Mediated Sequence Decoding in Hydrogel. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105538. [PMID: 34923738 DOI: 10.1002/smll.202105538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Single nucleotide polymorphisms (SNPs) that can alter phenotypes of individuals play a pivotal role in disease development and, more importantly, responses to therapy. However, SNP genotyping has been challenging due to the similarity of SNP alleles and their low concentration in biological samples. Sequence-specific nanoparticle with interpretative toehold-mediated sequence decoding in hydrogel (SWITCH) for multiplex SNP genotyping is presented. The encoding with gold nanoparticle probes transduces each SNP target to ≈1000 invaders with prominently different sequences between wild and mutant types, featuring polymerase chain reaction (PCR)-free amplification. Subsequently, the toehold-mediated DNA replacement in hydrogel microparticles decodes the invaders via SNP-specific fluorescence signals. The 4-plex detection of the warfarin-associated SNP targets spiked in commercially validated human serum (S1-100ML, Merck) is successfully demonstrated with excellent specificity. This work is the first technology development presenting PCR-free, multiplex SNP genotyping with a single reporting fluorophore, to the best of knowledge.
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Affiliation(s)
- Woongsun Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Eunhye Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Seojin Bae
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | | | - Sangeun Han
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Kuk-Hui Son
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Incheon, 21936, Korea
| | - Do Young Lee
- OPTOLANE Technologies, Inc., Seongnam, 13494, Korea
| | - Il-Joo Cho
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Yonsei-KIST Convergence Research Institute, Yonsei University, Seoul, 03722, Korea
- School of Electrical and Electronics Engineering, Yonsei University, Seoul, 03722, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Hyejeong Seong
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | - Kyo Seon Hwang
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Jungkyu Choi
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Korea
| | - Hyojin Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
| | - Nakwon Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology (UST), Seoul, 02792, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
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2
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Rajendran A, Shigi N, Sumaoka J, Komiyama M. Affinity Isolation of Defined Genomic Fragments Cleaved by Nuclease S1-based Artificial Restriction DNA Cutter. ACTA ACUST UNITED AC 2019; 76:e76. [PMID: 30753751 DOI: 10.1002/cpnc.76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The human genome is highly susceptible to various modifications, lesions, and damage. To analyze lesions and proteins bound to a defined region of the human genome, the genome should be fragmented at desired sites and the region of interest should be isolated. The few available methods for isolating a desired region of the human genome have serious drawbacks and can only be applied to specific sequences or require tedious experimental procedures. We have recently developed a novel method to isolate a desired fragment of the genome released by site-specific scission of DNA using a pair of pseudo-complementary peptide nucleic acids (pcPNAs) and S1 nuclease. When conjugated to biotin, one of the pcPNAs can be used to affinity purify the cleavage product. Here we report a detailed protocol to isolate defined kilobase-length DNA fragments that can be applied to plasmid or genomic DNA and is not limited by sequence. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Arivazhagan Rajendran
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan.,Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,Department of Applied Chemistry, School of Engineering, Tokyo University of Technology, Tokyo, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, Ibaraki, Japan.,College of Food Science and Engineering, Ocean University of China, Qingdao, China
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3
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Rajendran A, Shigi N, Sumaoka J, Komiyama M. One-Pot Isolation of a Desired Human Genome Fragment by Using a Biotinylated pcPNA/S1 Nuclease Combination. Biochemistry 2018; 57:2908-2912. [PMID: 29722525 DOI: 10.1021/acs.biochem.8b00202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Scission of the human genome at predetermined sites and isolation of a particular fragment are of great interest for the analysis of lesion/modification sites, in proteomics, and for gene therapy. However, methods for human genome scission and specific fragment isolation are limited. Here, we report a novel one-pot method for the site-specific scission of DNA by using a biotinylated pcPNA/S1 nuclease combination and isolation of a desired fragment by streptavidin-coated magnetic beads. The proof of concept was initially demonstrated for the clipping of plasmid DNA and isolation of the required fragment. Our method was then successfully applied for the isolation of a fragment from the cell-derived human genome.
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Affiliation(s)
- Arivazhagan Rajendran
- Life Science Center of Tsukuba Advanced Research Alliance , University of Tsukuba , 1-1-1 Tennoudai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance , University of Tsukuba , 1-1-1 Tennoudai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance , University of Tsukuba , 1-1-1 Tennoudai , Tsukuba , Ibaraki 305-8577 , Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance , University of Tsukuba , 1-1-1 Tennoudai , Tsukuba , Ibaraki 305-8577 , Japan
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4
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Isogawa A, Fuchs RP, Fujii S. Versatile and efficient chromatin pull-down methodology based on DNA triple helix formation. Sci Rep 2018; 8:5925. [PMID: 29651103 PMCID: PMC5897567 DOI: 10.1038/s41598-018-24417-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022] Open
Abstract
The goal of present paper is to develop a reliable DNA-based method for isolation of protein complexes bound to DNA (Isolation of DNA Associated Proteins: IDAP). We describe a robust and versatile procedure to pull-down chromatinized DNA sequences-of-interest by formation of a triple helix between a sequence tag present in the DNA and a complementary triple helix forming oligonucleotide (TFO) coupled to a desthiobiotin residue. Following optimization to insure efficient recovery of native plasmids via TFO probe in vitro, the procedure is shown to work under various experimental situations. For instance, it allows capture proteins associated to plasmids hosted in E. coli, and is also successfully applied to recovering nucleosomes in vitro opening many possibilities to study post translational modifications of histones in a genuine nucleosome context. Incubation in human nuclear extracts of a plasmid carrying a NF-κB model promoter is shown to pull-down a specific transcription factor. Finally, isolation of a specific locus from human genomic chromatin has been successfully achieved (Chromatin-of-Interest Fragment Isolation: CoIFI). In conclusion, the methodology can be implemented for capturing proteins that specifically bind to any sequence-of-interest, DNA adduct or secondary structure provided a short sequence tag for triple helix formation is located nearby.
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Affiliation(s)
- Asako Isogawa
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France.,Inserm, U1068, CRCM, Marseille, F-13009, France.,Institut Paoli-Calmettes, Marseille, F-13009, France.,Aix-Marseille University, UM 105, F-13284, Marseille, France
| | - Robert P Fuchs
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France. .,Inserm, U1068, CRCM, Marseille, F-13009, France. .,Institut Paoli-Calmettes, Marseille, F-13009, France. .,Aix-Marseille University, UM 105, F-13284, Marseille, France. .,Harvard Medical School, Boston, MA, 02115, USA.
| | - Shingo Fujii
- DNA Damage Tolerance CNRS, UMR7258, Marseille, F-13009, France. .,Inserm, U1068, CRCM, Marseille, F-13009, France. .,Institut Paoli-Calmettes, Marseille, F-13009, France. .,Aix-Marseille University, UM 105, F-13284, Marseille, France.
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5
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Hartono YD, Xu Y, Karshikoff A, Nilsson L, Villa A. Modeling p K Shift in DNA Triplexes Containing Locked Nucleic Acids. J Chem Inf Model 2018. [PMID: 29537270 DOI: 10.1021/acs.jcim.7b00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (LNA), is widely used in triplex forming oligonucleotides to target sites in the human genome. In this study, the parameters for LNA are developed in line with the CHARMM nucleic acid force field and validated toward the available structural experimental data. In conjunction, two computational methods were used to calculate the protonation state of the third strand cytidine in various DNA triplex environments: λ-dynamics and multiple pH regime. Both approaches predict p K of this cytidine shifted above physiological pH when cytidine is in the third strand in a triplex environment. Both methods show an upshift due to cytidine methylation, and a small downshift when the sugar configuration is locked. The predicted p K values for cytidine in DNA triplex environment can inform the design of better-binding oligonucleotides.
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Affiliation(s)
- Yossa Dwi Hartono
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden.,Division of Structural Biology and Biochemistry, School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551
| | - You Xu
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Andrey Karshikoff
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
| | - Alessandra Villa
- Department of Biosciences and Nutrition , Karolinska Institutet , SE-141 83 Huddinge , Sweden
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6
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Maruyama T, Ishizu N, Eguchi Y, Hosogi T, Goto M. Liquid-liquid extraction of enzymatically synthesized functional RNA oligonucleotides using reverse micelles with a DNA-surfactant. Chem Commun (Camb) 2018; 52:12376-12379. [PMID: 27711339 DOI: 10.1039/c6cc06985a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We successfully implemented solvent extraction of short, single-stranded RNA using reverse micelles (water-in-oil microemulsions) with a DNA-surfactant. A thrombin-binding RNA aptamer was enzymatically synthesized and purified by extraction using the reverse micellar system. The extracted RNA aptamer retained thrombin-binding activity after the extraction procedure.
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Affiliation(s)
- Tatsuo Maruyama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan.
| | - Naoki Ishizu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan.
| | - Yuka Eguchi
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe 657-8501, Japan.
| | - Takuya Hosogi
- Department of Applied Chemistry, Graduate School of Engineering and Center for Future Chemistry, Kyushu University, 744 Moto-oka, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering and Center for Future Chemistry, Kyushu University, 744 Moto-oka, Fukuoka 819-0395, Japan
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7
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Hu Q, Wang Q, Kong J, Li L, Zhang X. Electrochemically mediated in situ growth of electroactive polymers for highly sensitive detection of double-stranded DNA without sequence-preference. Biosens Bioelectron 2017; 101:1-6. [PMID: 29031128 DOI: 10.1016/j.bios.2017.09.045] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/10/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022]
Abstract
The ability to directly detect double-stranded DNA (dsDNA) without sequence-preference continues to be a major challenge. Herein, we report an electrochemical method for the direct, highly sensitive detection of dsDNA based on the strand replacement of dsDNA by peptide nucleic acid (PNA) and the in situ growth of electroactive polymers through the surface-initiated electrochemically mediated atom transfer radical polymerization (SI-eATRP). Thiolated PNA molecules are firstly self-assembled onto gold electrode surface for the specific recognition of target dsDNA (dsDNA-T), which in turn leads to the formation of a high density of PNA/DNA heteroduplexes on the electrode surface for the subsequent attachment of ATRP initiators via the phosphate-Zr4+-carboxylate chemistry. By applying a negative potential to the electrode, the air-stable CuII deactivators can be reduced into the CuI activators so as to trigger the surface-initiated polymerization for the in situ growth of electroactive polymers. Due to the strand replacement of dsDNA by PNA, dsDNA can be directly detected without sequence-preference. Besides, the growth of polymers enables the modification of numerous electroactive probes, thereby greatly improving the electrochemical signal. Under optimal conditions, a good linearity between the electrochemical signal and the logarithm of dsDNA-T concentration over the range from 1.0 fM to 1.0nM, with a detection limit of 0.47 fM, can be obtained. Results indicate that it is highly selective, and holds high anti-interference capability in the presence of human serum samples. Therefore, this method offers great promises in providing a universal and efficient solution for the direct detection of dsDNA.
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Affiliation(s)
- Qiong Hu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Qiangwei Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng 252000, PR China
| | - Xueji Zhang
- Chemistry Department, College of Arts and Sciences, University of South Florida, East Fowler Ave, Tampa, FL 33620-4202, United States.
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8
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Applications of PNA-Based Artificial Restriction DNA Cutters. Molecules 2017; 22:molecules22101586. [PMID: 28934140 PMCID: PMC6151779 DOI: 10.3390/molecules22101586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 09/16/2017] [Accepted: 09/18/2017] [Indexed: 12/14/2022] Open
Abstract
More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In this article, recent progress of these man-made tools have been reviewed. By cutting the human genome site-selectively, desired fragments can be clipped from either the termini of chromosomes (telomeres) or from the middle of genome. These fragments should provide important information on the biological functions of complicated genome system. DNA/RNA hybrid duplexes, which are formed in living cells, are also site-selectively hydrolyzed by these cutters. In order to further facilitate the applications of the artificial DNA cutters, various chemical modifications have been attempted. One of the most important successes is preparation of PNA derivatives which can form double-duplex invasion complex even under high salt conditions. This is important for in vivo applications, since the inside of living cells is abundant of metal ions. Furthermore, site-selective DNA cutters which require only one PNA strand, in place of a pair of pcPNA strands, are developed. This progress has opened a way to new fields of PNA-based biochemistry and biotechnology.
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9
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Hartono Y, Pabon-Martinez YV, Uyar A, Wengel J, Lundin KE, Zain R, Smith CIE, Nilsson L, Villa A. Role of Pseudoisocytidine Tautomerization in Triplex-Forming Oligonucleotides: In Silico and in Vitro Studies. ACS OMEGA 2017; 2:2165-2177. [PMID: 30023656 PMCID: PMC6044803 DOI: 10.1021/acsomega.7b00347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/02/2017] [Indexed: 06/08/2023]
Abstract
Pseudoisocytidine (ΨC) is a synthetic cytidine analogue that can target DNA duplex to form parallel triplex at neutral pH. Pseudoisocytidine has mainly two tautomers, of which only one is favorable for triplex formation. In this study, we investigated the effect of sequence on ΨC tautomerization using λ-dynamics simulation, which takes into account transitions between states. We also performed in vitro binding experiments with sequences containing ΨC and furthermore characterized the structure of the formed triplex using molecular dynamics simulation. We found that the neighboring methylated or protonated cytidine promotes the formation of the favorable tautomer, whereas the neighboring thymine or locked nucleic acid has a poor effect, and consecutive ΨC has a negative influence. The deleterious effect of consecutive ΨC in a triplex formation was confirmed using in vitro binding experiments. Our findings contribute to improving the design of ΨC-containing triplex-forming oligonucleotides directed to target G-rich DNA sequences.
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Affiliation(s)
- Yossa
Dwi Hartono
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
- Division
of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Y. Vladimir Pabon-Martinez
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Arzu Uyar
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Jesper Wengel
- Department
of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, 5230 Odense M, Denmark
| | - Karin E. Lundin
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Rula Zain
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
- Department
of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - C. I. Edvard Smith
- Department
of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, SE-141 86 Huddinge, Sweden
| | - Lennart Nilsson
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
| | - Alessandra Villa
- Department
of Biosciences and Nutrition, Karolinska
Institutet, SE-141 83 Huddinge, Sweden
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10
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Kalinichenko SV, Shepelev MV, Korobko IV. A gel-less isolation of untagged plasmid DNA insert from vector backbone in homogeneous format. Anal Biochem 2017; 521:28-30. [PMID: 28082218 DOI: 10.1016/j.ab.2017.01.006] [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: 10/27/2016] [Revised: 01/06/2017] [Accepted: 01/07/2017] [Indexed: 11/24/2022]
Abstract
Agarose gel electrophoresis with subsequent DNA extraction from gel is routinely used for DNA fragment isolation after plasmid DNA digestion. We describe a gel-less method for DNA fragment isolation after plasmid DNA digestion which is based on in-solution negative selection through depletion of vector backbone bearing LoxP sites by sorption on solid phase-immobilized mutated Cre recombinase. The method might be especially useful in preparation of DNA fragments for transgenic animal generation where residual agarose presence is a concern, and DNA fragments are frequently large in size and thus might be mechanically damaged during purification with conventional affinity-based gel extraction methods.
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Affiliation(s)
- Svetlana V Kalinichenko
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia
| | - Mikhail V Shepelev
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia
| | - Igor V Korobko
- Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov street, Moscow 119334, Russia.
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11
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Fujita T, Yuno M, Fujii H. Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells 2016; 21:370-7. [PMID: 26848818 DOI: 10.1111/gtc.12341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for various biological applications, including genome editing. We developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR to isolate target genomic regions from cells for their biochemical characterization. In this study, we developed 'in vitro enChIP' using recombinant CRISPR ribonucleoproteins (RNPs) to isolate target genomic regions. in vitro enChIP has the great advantage over conventional enChIP of not requiring expression of CRISPR complexes in cells. We first showed that in vitro enChIP using recombinant CRISPR RNPs can be used to isolate target DNA from mixtures of purified DNA in a sequence-specific manner. In addition, we showed that this technology can be used to efficiently isolate target genomic regions, while retaining their intracellular molecular interactions, with negligible contamination from irrelevant genomic regions. Thus, in vitro enChIP technology is of potential use for sequence-specific isolation of DNA, as well as for identification of molecules interacting with genomic regions of interest in vivo in combination with downstream analysis.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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12
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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13
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Dai R, Zhang B, Zhao G, Ding X. Site-specific recombination for cloning of large DNA fragments in vitro. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Ruixue Dai
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
| | - Bo Zhang
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
- Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology; Shanghai Institute for Biological Science, Chinese Academy of Science; Shanghai P. R. China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics; Chinese National Human Genome Centre at Shanghai; Shanghai P. R. China
| | - Xiaoming Ding
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
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14
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Hou XH, Guo XY, Chen Y, He CY, Chen ZY. Increasing the minicircle DNA purity using an enhanced triplex DNA technology to eliminate DNA contaminants. Mol Ther Methods Clin Dev 2015; 1:14062. [PMID: 26052527 PMCID: PMC4449018 DOI: 10.1038/mtm.2014.62] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/24/2014] [Indexed: 12/01/2022]
Abstract
DNA vectors for human gene therapy have to meet the efficacy and safety requirements. Minicircles (MCs), a class of optimized DNA vectors free of plasmid backbone (PB) DNAs, have emerged as promising candidates because of their superior transgene expression profiles. However, the existence of impure DNAs, including the unrecombined MC producing plasmid (PP) and PB circle, in the MC products made using the current technologies exceed the safety limit. Here, we report the development of an enhanced triplex DNA (TriD) technology to eliminate almost all the impure DNAs from the MC products. To do this, a pair of optimized TriD forming sequences was placed to flank the kanamycin resistance gene in the PP. The MC products were incubated with a biotinylated TriD forming DNA oligonucleotide (olig), and the resulted TriDs were removed by binding to streptovidin-coated magnetic beads. Consequently, the residual impure DNAs were 0.03% or less in the final MC products. The reproducibility of this technique was confirmed with MCs of various transgene expression cassettes, sizes, and quantities, suggesting its great potential in making high quality MC for human gene therapy.
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Affiliation(s)
- Xiaohu H Hou
- The Laboratory for Gene and Cell Therapy, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoyan Y Guo
- The Laboratory for Gene and Cell Therapy, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yusheng Chen
- The Laboratory for Gene and Cell Therapy, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Cheng-Yi He
- The Laboratory for Gene and Cell Therapy, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhi-Ying Chen
- The Laboratory for Gene and Cell Therapy, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N. Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area. J Phys Chem B 2014; 118:9583-94. [DOI: 10.1021/jp505107g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | - Shigenori Tanaka
- Graduate
School of System Informatics, Department of Computational Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
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16
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Oana H, Nishikawa K, Matsuhara H, Yamamoto A, Yamamoto TG, Haraguchi T, Hiraoka Y, Washizu M. Non-destructive handling of individual chromatin fibers isolated from single cells in a microfluidic device utilizing an optically driven microtool. LAB ON A CHIP 2014; 14:696-704. [PMID: 24356711 DOI: 10.1039/c3lc51111a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report a novel method for the non-destructive handling of, and biochemical experiments with, individual intact chromatin fibers, as well as their isolation from single cells, utilizing a specifically designed microfluidic device with an optically driven microtool under the microscope. Spheroplasts of recombinant fission yeast cells expressing fluorescent protein-tagged core histones were employed, and isolation of chromatin fibers was conducted by cell bursting via changing from isotonic conditions to hypotonic conditions in the microfluidic device. The isolation of chromatin fibers was confirmed by the fluorescent protein-tagged core histones involved in the chromatin fibers. For the non-destructive handling of the isolated chromatin fibers in the microfluidic device, we developed antibody-conjugated microspheres, which had affinity to the fluorescent protein-tagged core histones, and the microspheres were manipulated using optical tweezers, which functioned as optically driven microtools. With the aid of the microtool, isolated chromatin fibers were handled non-destructively and were tethered at the microstructures fabricated in the microfluidic device with straightened conformation by the flow. Immunofluorescence staining was carried out as a demonstrative biochemical experiment with the individual native chromatin fibers isolated in the microfluidic device, and specific fluorescent spots were visualized along the tethered chromatin fibers. Thus, the potential application of this method for epigenetic analyses of intact chromatin fibers isolated from single cells is demonstrated.
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Affiliation(s)
- Hidehiro Oana
- Department of Mechanical Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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Mikhaĭlov VS, Potapov VK, Amirkhanov RN, Amirkhanov NV, Bulanenkova SS, Akopov SB, Zarytova VF, Nikolaev LG, Sverdlov ED. [Affinity capture of specific DNA fragments with the use of short synthetic sequences]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:81-6. [PMID: 23844509 DOI: 10.1134/s106816201301007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ability of short peptide nucleic acid (PNA) oligomers and oligonucleotides containing modified residues of 5-methylcitidine, 2-aminoadenosine and 5-propynyl-2'-deoxyuridine (strong binding oligonucleotides, SBO) to affinity capture the target double-stranded DNA fragment from mixture by means of the end invasion was compared. Both types of probes were highly effective at the conditions used. The SBO-based probes may represent a handy and easily prepared alternative to PNA for selection of target DNA fragments from mixtures.
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18
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Cho H, Alcantara D, Yuan H, Sheth RA, Chen HH, Huang P, Andersson SB, Sosnovik DE, Mahmood U, Josephson L. Fluorochrome-functionalized nanoparticles for imaging DNA in biological systems. ACS NANO 2013; 7:2032-41. [PMID: 23373524 PMCID: PMC3800685 DOI: 10.1021/nn305962n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Attaching DNA binding fluorochromes to nanoparticles (NPs) provides a way of obtaining NPs that bind to DNA through fluorochrome mediated interactions. To obtain a nanoparticle (NP) that bound to the DNA in biological systems, we attached the DNA binding fluorochrome, TO-PRO 1 (TO), to the surface of the Feraheme (FH) NP, to obtain a fluorochrome-functionalized NP denoted TO-FH. When reacted with DNA in vitro, TO-FH formed microaggregates that were characterized by fluorescence, light scattering, and T2 changes. The formation of DNA/TO-FH microaggregates was also characterized by AFM, with microaggregates exhibiting a median size of 200 nm, and consisting of DNA and multiple TO-FH NPs whose individual diameters were only 25-35 nm. TO-FH failed to bind normal cells in culture, but treatment with chemotherapeutic agents or detergents yielded necrotic cells that bound TO-FH and vital fluorochromes similarly. The uptake of TO-FH by HT-29 xenografts (treated with 5-FU and oxaliplatin) was evident by surface fluorescence and MRI. Attaching multiple DNA binding fluorochromes to magnetic nanoparticles provides a way of generating DNA binding NPs that can be used to detect DNA detection by microaggregate formation in vitro, for imaging the DNA of necrotic cells in culture, and for imaging the DNA of a tumor treated with a chemotherapeutic agent. Fluorochrome functionalized NPs are a multimodal (magnetic and fluorescent), highly multivalent (n ≈ 10 fluorochromes/NP) nanomaterials useful for imaging the DNA of biological systems.
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Affiliation(s)
- Hoonsung Cho
- Center for Translational Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - David Alcantara
- Instituto de Nanociencia de Aragon, Universidad de Zaragoza, Spain
| | - Hushan Yuan
- Center for Translational Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Rahul A. Sheth
- Division of Nuclear Medicine & Molecular Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Howard H. Chen
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Peng Huang
- Department of Mechanical Engineering, Boston University, Massachusetts 02215, United States
| | - Sean B. Andersson
- Department of Mechanical Engineering, Boston University, Massachusetts 02215, United States
- Division of Systems Engineering, Boston University, Massachusetts 02215, United States
| | - David E. Sosnovik
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Umar Mahmood
- Center for Translational Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
- Division of Nuclear Medicine & Molecular Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
| | - Lee Josephson
- Center for Translational Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, Massachusetts 02129, United States
- Address correspondence to
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19
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Current trends in separation of plasmid DNA vaccines: A review. Anal Chim Acta 2013; 760:1-15. [DOI: 10.1016/j.aca.2012.11.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/22/2012] [Accepted: 11/06/2012] [Indexed: 11/20/2022]
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20
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Development and characterization of 18 microsatellite loci from the endemic elongate loach (Leptobotia elongata). CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9806-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 2012; 30:440-6. [PMID: 22544021 DOI: 10.1038/nbt.2183] [Citation(s) in RCA: 316] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/16/2012] [Indexed: 11/09/2022]
Abstract
Functional analysis of genome sequences requires methods for cloning DNA of interest. However, existing methods, such as library cloning and screening, are too demanding or inefficient for high-throughput application to the wealth of genomic data being delivered by massively parallel sequencing. Here we describe direct DNA cloning based on the discovery that the full-length Rac prophage protein RecE and its partner RecT mediate highly efficient linear-linear homologous recombination mechanistically distinct from conventional recombineering mediated by Redαβ from lambda phage or truncated versions of RecET. We directly cloned all ten megasynthetase gene clusters (each 10–52 kb in length) from Photorhabdus luminescens into expression vectors and expressed two of them in a heterologous host to identify the metabolites luminmycin A and luminmide A/B. We also directly cloned cDNAs and exactly defined segments from bacterial artificial chromosomes. Direct cloning with full-length RecE expands the DNA engineering toolbox and will facilitate bioprospecting for natural products.
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Affiliation(s)
- Jun Fu
- Technische Universitaet Dresden, Genomics, BioInnovationsZentrum, Dresden, Germany
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22
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Alcantara D, Guo Y, Yuan H, Goergen CJ, Chen HH, Cho H, Sosnovik DE, Josephson L. Fluorochrome-Functionalized Magnetic Nanoparticles for High-Sensitivity Monitoring of the Polymerase Chain Reaction by Magnetic Resonance. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Ongkudon CM, Chew JH, Liu B, Danquah MK. Chromatographic Removal of Endotoxins: A Bioprocess Engineer's Perspective. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/649746] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Gram-negative bacteria are widely used for the production of gene-based products such as DNA vaccines and bio-drugs, where endotoxin contamination can occur at any point within the process and its removal is of great concern. In this article, we review the structures of endotoxin and the effects that it causes in vivo. The endotoxin removal strategies are also discussed in the light of the different interaction mechanisms involved between endotoxins and bioproducts particularly plasmid DNA and proteins. For most cases, endotoxin removal is favoured at a highly ionic or acidic condition. Various removal methods particularly chromatography-based techniques are covered in this article according to the relevant applications.
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Affiliation(s)
- Clarence M. Ongkudon
- Bio Engineering Laboratory, Department of Chemical Engineering, Monash University, Wellington Road, Clayton, VIC 3800, Australia
- Biotechnology Research Institute, University Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Jia Han Chew
- Bio Engineering Laboratory, Department of Chemical Engineering, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Boyin Liu
- Bio Engineering Laboratory, Department of Chemical Engineering, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Michael K. Danquah
- Bio Engineering Laboratory, Department of Chemical Engineering, Monash University, Wellington Road, Clayton, VIC 3800, Australia
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Alcantara D, Guo Y, Yuan H, Goergen CJ, Chen HH, Cho H, Sosnovik DE, Josephson L. Fluorochrome-functionalized magnetic nanoparticles for high-sensitivity monitoring of the polymerase chain reaction by magnetic resonance. Angew Chem Int Ed Engl 2012; 51:6904-7. [PMID: 22684680 DOI: 10.1002/anie.201201661] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/04/2012] [Indexed: 11/10/2022]
Abstract
Easy to find: magnetic nanoparticles bearing fluorochromes (red) that intercalate with DNA (green) form microaggregates with DNA generated by the polymerase chain reaction (PCR). These aggregates can be detected at low cycle numbers by magnetic resonance (MR).
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Affiliation(s)
- David Alcantara
- Center for Translational Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, Charlestown, 02129, USA
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25
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Xu N, Yang H, Cui M, Wan C, Liu S. High-performance liquid chromatography-electrospray ionization-mass spectrometry ligand fishing assay: a method for screening triplex DNA binders from natural plant extracts. Anal Chem 2012; 84:2562-8. [PMID: 22220694 DOI: 10.1021/ac202796v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel ligand fishing assay was established to screen triplex DNA binders from complicated samples by a combination of immobilization of triplex DNA on agarose beads and high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS). The biotinylated oligodeoxynucleotides were first bound to the streptavidin agarose beads and then incubated with the duplex DNA as the baits for ligand fishing. This assay was validated by the testing ligand library consisting of coralyne, ethidium bromide, vitexin, and formononetin. The binding affinities of ligands to target DNA were also obtained based on the calibration curves of ligands. Two components (berberine and palmatine) in the extract of Phellodendron chinense Schneid cortexes were fished out as triplex DNA binders by this assay, which indicated its feasibility for screening triplex DNA binders from complicated samples. This preliminary assay can be used for not only screening binders of triplex DNA from natural products extracts but also can obtain their binding affinity information.
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Affiliation(s)
- Niusheng Xu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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26
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Alvira M, Eritja R. Triplex-stabilizing properties of parallel clamps carrying LNA derivatives at the Hoogsteen strand. Chem Biodivers 2010; 7:376-82. [PMID: 20151386 DOI: 10.1002/cbdv.200900230] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA Parallel clamps with a polypurine strand linked to a polypyrimidine Hoogsteen strand containing locked nucleic acids bind their corresponding polypyrimidine targets with high affinity.
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Affiliation(s)
- Margarita Alvira
- Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, ES-08028 Barcelona, Spain
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Gfrörer A, Schnetter ME, Wolfrum J, Greulich KO. Double and Triple Helices of Nucleic Acid Polymers, Studied by UV-Resonance Raman Spectroscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19930970203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Schneider UV, Severinsen JK, Géci I, Okkels LM, Jøhnk N, Mikkelsen ND, Klinge T, Pedersen EB, Westh H, Lisby G. A novel FRET pair for detection of parallel DNA triplexes by the LightCycler. BMC Biotechnol 2010; 10:4. [PMID: 20102641 PMCID: PMC2823659 DOI: 10.1186/1472-6750-10-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melting temperature of DNA structures can be determined on the LightCycler using quenching of FAM. This method is very suitable for pH independent melting point (Tm) determination performed at basic or neutral pH, as a high throughput alternative to UV absorbance measurements. At acidic pH quenching of FAM is not very suitable, since the fluorescence of FAM is strongly pH dependent and drops with acidic pH.Hoogsteen based parallel triplex helix formation requires protonation of cytosines in the triplex forming strand. Therefore, nucleic acid triplexes show strong pH dependence and are stable only at acidic pH. This led us to establish a new pH independent fluorophore based measuring system on the LightCycler for thermal stability studies of parallel triplexes. RESULTS A novel LightCycler FRET pair labelled with ATTO495 and ATTO647N was established for parallel triplex detection with antiparallel duplex as a control for the general applicability of these fluorophores for Tm determination. The ATTO fluorophores were pH stable from pH 4.5 to 7.5. Melting of triplex and duplex structures were accompanied by a large decrease in fluorescence intensity leading to well defined Tm and high reproducibility. Validation of Tm showed low intra- and inter-assay coefficient of variation; 0.11% and 0.14% for parallel triplex and 0.19% and 0.12% for antiparallel duplex. Measurements of Tm and fluorescence intensity over time and multiple runs showed great time and light stability of the ATTO fluorophores. The variance on Tm determinations was significant lower on the LightCycler platform compared to UV absorbance measurements, which enable discrimination of DNA structures with very similar Tm. Labelling of DNA probes with ATTO fluorophore increased Tm of antiparallel duplexes significantly, but not Tm of parallel triplexes. CONCLUSIONS We have established a novel pH independent FRET pair with high fluorescence signals on the LightCycler platform for both antiparallel duplex and parallel triplex formation. The method has been thoroughly validated, and is characterized by an excellent accuracy and reproducibility. This FRET pair is especially suitable for DeltaTm and Tm determinations of pH dependent parallel triplex formation.
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Affiliation(s)
- Uffe V Schneider
- QuantiBact Inc, Department of Clinical Microbiology, Hvidovre Hospital, Kettegaards Alle 30, 2650 Hvidovre, Denmark.
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Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB. The triple helix: 50 years later, the outcome. Nucleic Acids Res 2008; 36:5123-38. [PMID: 18676453 PMCID: PMC2532714 DOI: 10.1093/nar/gkn493] [Citation(s) in RCA: 265] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA. They are not only used as biotechnological tools but also to induce modifications on DNA with the aim to control gene expression, such as by site-directed mutagenesis or DNA recombination. Here, we report the state of art of the triplex-based anti-gene strategy 50 years after the discovery of such a structure, and we show the importance of the actual applications and the main challenges that we still have ahead of us.
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Affiliation(s)
- Maria Duca
- LCMBA CNRS UMR6001, University of Nice-Sophia Antipolis, Parc Valrose, 06108 NICE Cedex 2, France
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30
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Voß C. Downstream Processing of Plasmid DNA for Gene Therapy and Genetic Vaccination. Chem Eng Technol 2008. [DOI: 10.1002/ceat.200800069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC PLANT BIOLOGY 2008; 8:55. [PMID: 18482440 PMCID: PMC2416452 DOI: 10.1186/1471-2229-8-55] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 05/15/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. RESULTS A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. CONCLUSION Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.
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Affiliation(s)
- Luu M Cuc
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- Agriculture Genetics Institute, Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Hanoi, Vietnam
| | - Emma S Mace
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- Department of Primary Industries & Fisheries, Hermitage Research Station, 604 Yangan Road, Warwick, QLD 4370, Australia
| | - Jonathan H Crouch
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- International Wheat and Maize Improvement Centre (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico
| | - Vu D Quang
- Agriculture Genetics Institute, Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Hanoi, Vietnam
| | - Tran D Long
- Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Ha Noi, Vietnam
| | - Rajeev K Varshney
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
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Maruyama T, Hosogi T, Goto M. Sequence-selective extraction of single-stranded DNA using DNA-functionalized reverse micelles. Chem Commun (Camb) 2007:4450-2. [DOI: 10.1039/b708082d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nadal A, Coll A, Aviñó A, Esteve T, Eritja R, Pla M. Efficient Sequence‐Specific Purification of
Listeria innocua
mRNA Species by Triplex Affinity Capture with Parallel Tail‐Clamps. Chembiochem 2006; 7:1039-47. [PMID: 16729343 DOI: 10.1002/cbic.200500519] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Parallel clamps can interact in a sequence-specific manner with homopyrimidine DNA and RNA oligonucleotides to form triplexes. For longer nucleic acids, we have previously demonstrated the inhibitory effect of DNA-target secondary structures on triplex formation. We further designed a modification of these molecules-that is, tail-clamps formed by addition of a tail sequence to the parallel clamp-and proved efficient binding of the molecules with structured single-stranded DNA targets. Here we explore the possible application of the tail-clamp strategy for triplex formation with RNA targets, which are typically found as strongly folded single-stranded molecules. Efficient and specific binding of a tail-clamp designed to form a parallel triplex with Listeria innocua iap mRNA sequences has been verified by UV melting curves and triplex affinity capture techniques. Furthermore, we show for the first time the formation of stable complexes of mRNA with tail-clamps not only under acidic but also under neutral and slightly basic pH conditions. These results signify a further step towards the possible applications of triplexes with mRNA molecules; research, analytical, and therapeutic uses can be envisaged. As an example, our tail-clamp-based triplex affinity capture assay allowed the specific capture and recovery of iap mRNA molecules from an L. innocua total RNA solution with 45 % yield.
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Affiliation(s)
- Anna Nadal
- Institute of Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (Edif. Politècnica 1), Spain
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Shang H, Chang WS, Kan S, Majetich SA, Lee GU. Synthesis and characterization of paramagnetic microparticles through emulsion-templated free radical polymerization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:2516-22. [PMID: 16519449 DOI: 10.1021/la052636f] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
A novel method is described for the preparation of high-magnetization paramagnetic microparticles functionalized with a controlled density of poly(ethylene glycol) (PEG) and carboxyl groups. These microparticles were synthesized using four steps: (1) creation of an oil-in-water emulsion in which hydrophobic iron oxide nanoparticles and a UV-activated initiator were distributed in hexane; (2) formation of uniform microparticles through emulsion homogenization and evaporation of hexane; (3) functionalization of the microparticle with a PEG-functionalized surfactant and acrylic acid; and (4) polymerization of the microparticles. Characterization of the microparticles with electron microscopy and light scattering revealed that they were composed of densely packed iron oxide nanoparticles and that the size of the microparticles may be controlled through the pore size of the membrane used to homogenize the emulsion. The concentration of surfactant and acrylic acid used in the third processing step was found to determine the surface chemistry, iron content, and magnetization of the microparticles. Increasing the PEG surfactant to acrylic acid ratio resulted in higher PEG surface densities, lower iron content, and lower magnetization. The resulting microparticles were readily functionalized with antibodies and showed a low propensity for nonspecific protein adsorption. We believe that these microparticles will be useful for magnetic tweezers measurements and bioanalytical devices that require microparticles with a high magnetization.
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Affiliation(s)
- Hao Shang
- School of Chemical Engineering, Forney Hall, Purdue University, West Lafayette, Indiana 47907-1283, USA
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36
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Forde GM, Ghose S, Slater NKH, Hine AV, Darby RAJ, Hitchcock AG. LacO-LacI interaction in affinity adsorption of plasmid DNA. Biotechnol Bioeng 2006; 95:67-75. [PMID: 16646090 DOI: 10.1002/bit.20955] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Current approaches for purifying plasmids from bacterial production systems exploit the physiochemical properties of nucleic acids in non-specific capture systems. In this study, an affinity system for plasmid DNA (pDNA) purification has been developed utilizing the interaction between the lac operon (lacO) sequence contained in the pDNA and a 64mer synthetic peptide representing the DNA-binding domain of the lac repressor protein, LacI. Two plasmids were evaluated, the native pUC19 and pUC19 with dual lacO3/lacOs operators (pUC19(lacO3/lacOs)), where the lacOs operator is perfectly symmetrical. The DNA-protein affinity interaction was evaluated by surface plasmon resonance using a Biacore system. The affinity capture of DNA in a chromatography system was evaluated using LacI peptide that had been immobilized to Streamline adsorbent. The KD-values for double stranded DNA (dsDNA) fragments containing lacO1 and lacO3 and lacOS and lacO3 were 5.7 +/- 0.3 x 10(-11) M and 4.1 +/- 0.2 x 10(-11) M respectively, which compare favorably with literature reports of 5 x 10(-10)-1 x 10(-9) M for native lacO1 and 1-1.2 x 10(-10) M for lacO1 in a saline buffer. Densitometric analysis of the gel bands from the affinity chromatography run clearly showed a significant preference for capture of the supercoiled fraction from the feed pDNA sample. The results indicate the feasibility of the affinity approach for pDNA capture and purification using native protein-DNA interaction.
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Affiliation(s)
- Gareth M Forde
- Department of Chemical Engineering, Cambridge Unit for Bioscience Engineering (CUBE), Pembroke Street, University of Cambridge, Cambridge CB2 3RA, UK
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37
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Ferreira GNM. Chromatographic Approaches in the Purification of Plasmid DNA for Therapy and Vaccination. Chem Eng Technol 2005. [DOI: 10.1002/ceat.200500158] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Nadal A, Eritja R, Esteve T, Pla M. "Parallel" and "antiparallel tail-clamps" increase the efficiency of triplex formation with structured DNA and RNA targets. Chembiochem 2005; 6:1034-42. [PMID: 15880676 DOI: 10.1002/cbic.200400358] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sequence-specific triple-helix structures can be formed by parallel and antiparallel DNA clamps interacting with single-stranded DNA or RNA targets. Single-stranded nucleic acid molecules are known to adopt secondary structures that might interfere with intermolecular interactions. We demonstrate the correlation between a secondary structure involving the target--a stable stem predicted by in silico folding and experimentally confirmed by thermal stability and competition analyses--and an inhibitory effect on triplex formation. We overcame structural impediments by designing a new type of clamp: "tail-clamps". A combination of gel-shift, kinetic analysis, UV thermal melting and thermodynamic techniques was used to demonstrate that tail-clamps efficiently form triple helices with a structured target sequence. The performance of parallel and antiparallel tail-clamps was compared: antiparallel tail-clamps had higher binding efficiencies than parallel tail-clamps both with structured DNA and RNA targets. In addition, the reported triplex-stabilizing property of 8-aminopurine residues was confirmed for tail-clamps. Finally, we discuss the possible use of this improved triplex technology as a new tool for applications in molecular biology.
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Affiliation(s)
- Anna Nadal
- Departament de Genètica Molecular, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona 18-26, 08034 Barcelona, Spain
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39
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Abstract
Liquid chromatography plays a central role in process-scale manufacturing of therapeutic plasmid DNA (pDNA) for gene therapy and DNA vaccination. Apart from its use as a preparative purification step, it is also very useful as an analytical tool to monitor and control pDNA quality during processing and in final formulations. This paper gives an overview of the use of pDNA chromatography. The specificity of pDNA purification and the consequent limitations to the performance of chromatography are described. Strategies currently used to overcome those limitations, as well as other possible solutions are presented. Applications of the different types of chromatography to the purification of therapeutic pDNA are reviewed, and the main advantages and disadvantages behind each technique highlighted.
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Affiliation(s)
- M M Diogo
- Centro de Engenharia Biológica e Química, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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40
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Wang Z, Yuan Z, Hengge UR. Processing of plasmid DNA with ColE1-like replication origin. Plasmid 2004; 51:149-61. [PMID: 15109822 DOI: 10.1016/j.plasmid.2003.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Revised: 11/06/2003] [Indexed: 12/22/2022]
Abstract
With the increasing utilization of plasmid DNA as a biopharmaceutical drug, there is a rapidly growing need for high quality plasmid DNA for drug applications. Although there are several different kinds of replication origins, ColE1-like replication origin is the most extensively used origin in biotechnology. This review addresses problems in upstream and downstream processing of plasmid DNA with ColE1-like origin as drug applications. In upstream processing of plasmid DNA, regulation of replication of ColE1-like origin was discussed. In downstream processing of plasmid DNA, we analyzed simple, robust, and scalable methods, which can be used in the efficient production of pharmaceutical-grade plasmid DNA.
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Affiliation(s)
- Zhijun Wang
- Key Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 200032 Shanghai, People's Republic of China.
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41
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Potaman VN. Applications of triple-stranded nucleic acid structures to DNA purification, detection and analysis. Expert Rev Mol Diagn 2003; 3:481-96. [PMID: 12877387 DOI: 10.1586/14737159.3.4.481] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Regions of double-stranded (duplex) DNA with purine bases predominantly in one strand and pyrimidine bases in the other may bind oligonucleotides of an appropriate sequence to form triple-stranded (triplex) structures. Oligonucleotide analogs and mimics, such as peptide nucleic acid, may also form stable complexes with duplex DNA. Triplex formation enables the specific targeting of duplex domains. The principles of triplex structures and recent developments in the gene therapeutic and biotechnological applications are briefly reviewed. Adaptations of triplex methodology to molecular diagnostics (DNA purification, detection and analysis) are reviewed in greater detail.
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Affiliation(s)
- Vladimir N Potaman
- Institute of Biosciences & Technology, Texas A&M University Health Sciences Center, Houston 77030-3303, USA.
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42
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Costioli MD, Fisch I, Garret-Flaudy F, Hilbrig F, Freitag R. DNA purification by triple-helix affinity precipitation. Biotechnol Bioeng 2003; 81:535-45. [PMID: 12514802 DOI: 10.1002/bit.10497] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent advances in DNA-based medicine (gene therapy, genetic vaccination) have intensified the necessity for pharmaceutical-grade plasmid DNA purification at comparatively large scales. In this contribution triple-helix affinity precipitation is introduced for this purpose. A short, single-stranded oligonucleotide sequence (namely (CTT)(7)), which is capable of recognizing a complementary sequence in the double-stranded target (plasmid) DNA, is linked to a thermoresponsive N-isopropylacrylamide oligomer to form a so-called affinity macroligand (AML). At 4 degrees C, i.e., below its critical solution temperature, the AML binds specifically to the target molecule in solution; by raising the temperature to 40 degrees C, i.e., beyond the critical solution temperature of the AML, the complex can be precipitated quantitatively. After redissolution of the complex at lower temperature, the target DNA can be released by a pH shift to slightly alkaline conditions (pH 9.0). Yields of highly pure (plasmid) DNA were routinely between 70% and 90%. Non-specific co- precipitation of either the target molecule by the non-activated AML precursor or of contaminants by the AML were below 7% and presumably due to physical entrapment of these molecules in the wet precipitate. Ligand efficiencies were at least 1 order of magnitude higher than in triple-helix affinity chromatography.
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Affiliation(s)
- Matteo D Costioli
- Center of Biotechnology, Swiss Federal Institute of Technology Lausanne, 1015 Ecublens, Switzerland
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43
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Cheng DW, Armstrong KC. Direct capture and cloning of receptor kinase and peroxidase genes from genomic DNA. Genome 2002; 45:977-83. [PMID: 12416632 DOI: 10.1139/g02-055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A direct DNA capture and cloning procedure with magnetic bead separation was used to isolate receptor kinase like and peroxidase genes from oat (Avena sativa) and wheat (Triticum aestivum L.) genomic DNA, respectively. In this procedure, the digoxigenin-labeled probe DNA and target genomic DNA fragments were mixed, denatured, and hybridized. The double-helix complexes formed were captured with anti-digoxigenin immunoglobulin-coated magnetic beads and then cloned into either the lambdaBlueSTAR or pUC18 vector. The effectiveness of this procedure was demonstrated by using two specific DNA probes to capture receptor-like kinase genes and surrounding sequences from oat genomic DNA and a peroxidase gene from wheat genomic DNA.
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Affiliation(s)
- Davis W Cheng
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
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44
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Mace ES, Godwin ID. Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta). Genome 2002; 45:823-32. [PMID: 12416614 DOI: 10.1139/g02-045] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.
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Affiliation(s)
- Emma S Mace
- M.S. Swaminathan Applied Genomics Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Andhra Pradesh, India.
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45
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Demidov VV. Scholar, inventor and businessman: Charles R. Cantor at his 60th anniversary. Drug Discov Today 2002. [DOI: 10.1016/s1359-6446(02)02420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Abstract
A concise survey of the emerging PD-loop technology is presented, which outlines several exemplary methods with robust DNA diagnostic potential: duplex DNA capture, topological DNA labeling, nondenaturing DNA sequencing and hybridization of molecular beacons to double-stranded DNA. Advantages of these new PNA-based assays over existing techniques for sequence-specific detection and manipulation of DNA duplexes are discussed. Future prospects for the further development of PD-loop technology are highlighted.
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Affiliation(s)
- V V Demidov
- Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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47
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Mori T, Umeno D, Maeda M. Sequence-specific affinity precipitation of oligonucleotide using poly(N-isopropylacrylamide)-oligonucleotide conjugate. Biotechnol Bioeng 2001; 72:261-8. [PMID: 11135195 DOI: 10.1002/1097-0290(20010205)72:3<261::aid-bit2>3.0.co;2-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this study we develop a sequence-specific precipitation separation system of oligonucleotide (ODN) using a conjugate between poly(N-isopropylacrylamide) (PNIPAM) and ODN. PNIPAM is known as a thermoresponsive polymer and dehydrates to precipitate above its phase transition temperature in an aqueous milieu. The principal advantage of this separation system using the conjugate is that the hybridization reaction between the conjugate and oligonucleotide is conducted in homogeneous solution. The conjugate was prepared by copolymerization between N-isopropylacrylamide and a vinyl-derivatized (dT)(8). The obtained conjugate efficiently precipitated (dA)(8) from solution when the solution contained more than 1.5 M NaCl. The conjugate containing 3 nmol of (dT)(8) residue was able to precipitate 1.4 nmol of (dA)(8), suggesting that the (dT)(8) residue of the conjugate formed a triple helix with (dA)(8). From an equimolar mixture of (dA)(8) and its one point mutant, the conjugate selectively precipitated (dA)(8): the highest selectivity was obtained for the isolation of (dA)(8) from the mixture consisting of (dA)(4)dT(dA)(3) and (dA)(8). When the conjugate was applied for the precipitation of five oligo(dA)s having different chain lengths, the longer oligo(dA)s tended to be precipitated by the conjugate more efficiently than the shorter ones. The conjugate could be used repeatedly for precipitation of (dA)(8) without showing any loss in precipitation efficiency.
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Affiliation(s)
- T Mori
- Department of Materials Physics and Chemistry, Graduate School of Engineering, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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48
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Ljunglöf A, Bergvall P, Bhikhabhai R, Hjorth R. Direct visualisation of plasmid DNA in individual chromatography adsorbent particles by confocal scanning laser microscopy. J Chromatogr A 1999; 844:129-35. [PMID: 10399329 DOI: 10.1016/s0021-9673(99)00386-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Confocal microscopy was used for the measurement of plasmid DNA adsorbed to individual adsorbent particles intended for anion-exchange and triple helix affinity chromatography. Plasmid DNA was visualized with the fluorescent dye YOYO-1, that forms a highly fluorescent complex with double stranded DNA. Confocal images were translated into fluorescence intensity profiles and the distribution of plasmid DNA in the particles was measured. The results that adsorption of plasmid DNA mainly takes place in an outer layer of the particles. The described procedure can also be advantageously used to demonstrate triple helix formation between plasmid DNA and immobilized oligonucleotides.
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Affiliation(s)
- A Ljunglöf
- Amersham Pharmacia Biotech, Uppsala, Sweden.
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49
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Broude NE, Storm N, Malpel S, Graber JH, Lukyanov S, Sverdlov E, Smith CL. PCR based targeted genomic and cDNA differential display. GENETIC ANALYSIS : BIOMOLECULAR ENGINEERING 1999; 15:51-63. [PMID: 10191986 DOI: 10.1016/s1050-3862(98)00038-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We previously described a targeted genomic differential display method (TGDD: Broude NE, Chandra A, Smith CL. Differential display of genomic subsets containing specific interspersed repeats. Proc. Natl. Acad. Sci. USA 1997;94:4548-53). In that method, presently characterized as method I, targeting was accomplished by capturing DNA fragments containing specific a sequence by hybridization with complementary single-stranded DNA. The captured fragments were amplified by PCR. Here, we describe method II where targeting is accomplished by PCR using primers specific to the target sequence. Method II takes advantage of PCR suppression to eliminate fragments not containing the target sequence (Siebert PDA, Chenchik A, Kellogg DE, Lukyanov KA and Lukyanov SA. An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res 1995;23:1087-1088). Targeting focuses analysis on and around interesting areas and additionally serves to reduce the complexity of the amplified subset. These approaches are useful to amplify genome subsets containing a variety of targets including various conserved sequences coding for cis-acting elements or protein motifs.
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Affiliation(s)
- N E Broude
- Center for Advanced Biotechnology, Boston University, MA 02215, USA
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50
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Roweis S, Winfree E, Burgoyne R, Chelyapov NV, Goodman MF, Rothemund PW, Adleman LM. A sticker-based model for DNA computation. J Comput Biol 1999; 5:615-29. [PMID: 10072080 DOI: 10.1089/cmb.1998.5.615] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We introduce a new model of molecular computation that we call the sticker model. Like many previous proposals it makes use of DNA strands as the physical substrate in which information is represented and of separation by hybridization as a central mechanism. However, unlike previous models, the stickers model has a random access memory that requires no strand extension and uses no enzymes; also (at least in theory), its materials are reusable. The paper describes computation under the stickers model and discusses possible means for physically implementing each operation. Finally, we go on to propose a specific machine architecture for implementing the stickers model as a microprocessor-controlled parallel robotic workstation. In the course of this development a number of previous general concerns about molecular computation (Smith, 1996; Hartmanis, 1995; Linial et al., 1995) are addressed. First, it is clear that general-purpose algorithms can be implemented by DNA-based computers, potentially solving a wide class of search problems. Second, we find that there are challenging problems, for which only modest volumes of DNA should suffice. Third, we demonstrate that the formation and breaking of covalent bonds is not intrinsic to DNA-based computation. Fourth, we show that a single essential biotechnology, sequence-specific separation, suffices for constructing a general-purpose molecular computer. Concerns about errors in this separation operation and means to reduce them are addressed elsewhere (Karp et al., 1995; Roweis and Winfree, 1999). Despite these encouraging theoretical advances, we emphasize that substantial engineering challenges remain at almost all stages and that the ultimate success or failure of DNA computing will certainly depend on whether these challenges can be met in laboratory investigations.
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Affiliation(s)
- S Roweis
- Laboratory for Molecular Science, University of Southern California, Los Angeles 90089, USA
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