1
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Sun Y, Wu Y, Wang Y, Li K, Chang Y, Wei L. Point-of-care testing of rpoB in Mycobacterium tuberculosis using multiply-primed-RCA coupled with CRISPR/Cas12a. Heliyon 2024; 10:e37640. [PMID: 39309806 PMCID: PMC11416492 DOI: 10.1016/j.heliyon.2024.e37640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 08/06/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Purpose Due to the serious threat of tuberculosis to global health and limitations of existing diagnostic methods, this study combined the CRISPR/Cas12a system with Multiply-primed-RCA (MRCA) technology for Mycobacterium tuberculosis Point-of-care Testing (POCT). Method We utilized T4 and Taq DNA ligases, compared the effects of specific primers and random 6NS primers on the method, and integrated MRCA and the CRISPR-Cas12a system in one tube. By optimizing conditions such as the concentration of DNA ligase, the concentration of padlock probes, and the number of cycles, we finally established T4-MRCA-Cas12a and Taq-MRCA-Cas12a methods for both stepwise and one-step. Results The limits of detection of the one-step T4/Taq-MRCA-Cas12a were 104aM and 103aM. With no cross-reactivity with DNA from other bacterial strains. The accuracy and specificity were 88 % and 100 % for T4-MRCA-Cas12a, and 96 % and 100 % for Taq-MRCA-Cas12a, respectively. Conclusion We developed a POCT method that can directly identify MTB through the naked eye.
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Affiliation(s)
- Yingying Sun
- School of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000, PR China
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Yaozhou Wu
- First School of Clinical Medicine, Lanzhou University, Lanzhou, 730000, PR China
| | - Yulin Wang
- First School of Clinical Medicine, Ningxia Medical University, Yinchuan, 750000, PR China
| | - Keke Li
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Yanbin Chang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
| | - Lianhua Wei
- School of Public Health, Gansu University of Chinese Medicine, Lanzhou, 730000, PR China
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, 730000, PR China
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2
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Sun W, Hu K, Liu M, Luo J, An R, Liang X. Facile Splint-Free Circularization of ssDNA with T4 DNA Ligase by Redesigning the Linear Substrate to Form an Intramolecular Dynamic Nick. Biomolecules 2024; 14:1027. [PMID: 39199414 PMCID: PMC11352879 DOI: 10.3390/biom14081027] [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: 07/30/2024] [Revised: 08/11/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings' numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template. After the simulation of the secondary structure for desired circular ssDNA, the linear ssDNA substrate is designed to have its ends on the duplex part (≥5 bp). By using this permuted substrate with 5'-phosphate, the splint-free circularization is simply carried out by T4 DNA ligase. Very interestingly, formation of only several base pairs (2-4) flanking the nick is enough for ligation, although they form only instantaneously under ligation conditions. More significantly, the 5-bp intramolecular duplex part commonly exists in genomes or functional DNA, demonstrating the high generality of our approach. Our findings are also helpful for understanding the mechanism of enzymatic DNA ligation from the viewpoint of substrate binding.
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Affiliation(s)
- Wenhua Sun
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
| | - Kunling Hu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
| | - Mengqin Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
| | - Jian Luo
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
| | - Ran An
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, No. 1 Wenhai Road, Qingdao 266237, China
| | - Xingguo Liang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, No. 1299 Sansha Road, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, No. 1 Wenhai Road, Qingdao 266237, China
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3
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Prosdocimi F, de Farias ST. Major evolutionary transitions before cells: A journey from molecules to organisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 191:11-24. [PMID: 38971326 DOI: 10.1016/j.pbiomolbio.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/25/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK
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4
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Wu Y, Guo J, Li W, Xiu X, Thirunavukarasu D, Wang Y, Wang K, Chen W, Yu Zhang D, Yang X, Fan C, Song P. Enhanced Detection of Novel Low-Frequency Gene Fusions via High-Yield Ligation and Multiplexed Enrichment Sequencing. Angew Chem Int Ed Engl 2024; 63:e202316484. [PMID: 38494435 DOI: 10.1002/anie.202316484] [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: 10/31/2023] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Panel-based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double-stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7-fold enrichment of novel gene fusions. Leveraging the pre-enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra-fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies.
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Affiliation(s)
- Yi Wu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinxiao Guo
- Shanghai Sixth People's Hospital Affiliated to, Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Wenjun Li
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xuehao Xiu
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | | | - Yudong Wang
- Department of Gynecologic Oncology, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Kai Wang
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - Weiyu Chen
- Department of Respiratory and Critical Care Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 322000, China
| | - David Yu Zhang
- NuProbe USA, Inc., 2575 West Bellfort Avenue, Ste. 200 Houston, TX 77054, USA
| | - Xiurong Yang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ping Song
- School of Biomedical Engineering, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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5
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Cheng JC, Swarup N, Wong DTW, Chia D. A review on the impact of single-stranded library preparation on plasma cell-free diversity for cancer detection. Front Oncol 2024; 14:1332004. [PMID: 38511142 PMCID: PMC10951391 DOI: 10.3389/fonc.2024.1332004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/07/2024] [Indexed: 03/22/2024] Open
Abstract
In clinical oncology, cell-free DNA (cfDNA) has shown immense potential in its ability to noninvasively detect cancer at various stages and monitor the progression of therapy. Despite the rapid improvements in cfDNA liquid biopsy approaches, achieving the required sensitivity to detect rare tumor-derived cfDNA still remains a challenge. For next-generation sequencing, the perceived presentation of cfDNA is strongly linked to the extraction and library preparation protocols. Conventional double-stranded DNA library preparation (dsDNA-LP) focuses on assessing ~167bp double-stranded mononucleosomal (mncfDNA) and its other oligonucleosomal cell-free DNA counterparts in plasma. However, dsDNA-LP methods fail to include short, single-stranded, or nicked DNA in the final library preparation, biasing the representation of the actual cfDNA populations in plasma. The emergence of single-stranded library preparation (ssDNA-LP) strategies over the past decade has now allowed these other populations of cfDNA to be studied from plasma. With the use of ssDNA-LP, single-stranded, nicked, and ultrashort cfDNA can be comprehensively assessed for its molecular characteristics and clinical potential. In this review, we overview the current literature on applications of ssDNA-LP on plasma cfDNA from a potential cancer liquid biopsy perspective. To this end, we discuss the molecular principles of single-stranded DNA adapter ligation, how library preparation contributes to the understanding of native cfDNA characteristics, and the potential for ssDNA-LP to improve the sensitivity of circulating tumor DNA detection. Additionally, we review the current literature on the newly reported species of plasma ultrashort single-stranded cell-free DNA plasma, which appear biologically distinct from mncfDNA. We conclude with a discussion of future perspectives of ssDNA-LP for liquid biopsy endeavors.
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Affiliation(s)
- Jordan C. Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
- Stanford Cancer Institute, Stanford University, Stanford, CA, United States
| | - Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David T. W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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6
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Qian L, Xiao J, Li K, Zhou Y. Multiplex Detection of RNA Viruses Based on Ligation Reaction and Universal PCR Amplification. Curr Microbiol 2024; 81:75. [PMID: 38261072 DOI: 10.1007/s00284-023-03582-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/02/2023] [Indexed: 01/24/2024]
Abstract
To detect several RNA viruses simultaneously, a method based on multiplex ligation reaction combined with multiplex qPCR or multiplex PCR+capillary electrophoresis was established to detect four RNA viruses: human immunodeficiency virus (HIV), hepatitis C (HCV), influenza A virus (IAV) H1N1 and H5N1. The experimental conditions including ligation probe concentration, annealing procedure, ligation temperature and ligase dosage were optimized intensively. We found that the specificity of the ligation reaction was affected by the probe concentration predominantly, high-probe concentration (100 nM) resulted in splint-independent ligation with efficiency comparable to that with RNA splint. The sensitivity of the ligation reaction was affected by the annealing mode apparently as the sensitivity of the step-down annealing mode was 100 times higher than that of the isothermal annealing at 37 °C. Under the optimized condition, this assay could detect virus RNA as low as 16 viral copies per reaction in doubleplex and triplex real-time quantitative PCR detection with satisfactory specificity and precision. By multiplex PCR+capillary electrophoresis, four RNA viruses could be detected in one tube with the sensitivity of 10 copies per reaction.
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Affiliation(s)
- Lijun Qian
- College of Biological Science and Medical Engineering, Donghua University, #2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Junhua Xiao
- College of Biological Science and Medical Engineering, Donghua University, #2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Kai Li
- College of Biological Science and Medical Engineering, Donghua University, #2999 North Renmin Road, Songjiang District, Shanghai, 201620, China
| | - Yuxun Zhou
- College of Biological Science and Medical Engineering, Donghua University, #2999 North Renmin Road, Songjiang District, Shanghai, 201620, China.
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7
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Abstract
Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.
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Affiliation(s)
- Paul C Kirchberger
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA;
| | - Howard Ochman
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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8
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Zuo S, Li X, Yang Y, Zhou J, He Q. A Quick Method to Synthesize Extrachromosomal Circular DNA In Vitro. Molecules 2023; 28:molecules28104236. [PMID: 37241975 DOI: 10.3390/molecules28104236] [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] [Received: 03/12/2023] [Revised: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a special class of circular DNA in eukaryotes. Recent studies have suggested that eccDNA is the product of genomic instability and has important biological functions to regulate many downstream biological processes. While NGS (Next-Generation Sequencing)-based eccDNA sequencing has led to the identification of many eccDNAs in both healthy and diseased tissues, the specific biological functions of individual eccDNAs have yet to be clearly elucidated. Synthesizing eccDNAs longer than 1 kb with specific sequences remains a major challenge in the field, which has hindered our ability to fully understand their functions. Current methods for synthesizing eccDNAs primarily rely on chemical oligo synthesis, ligation, or the use of a specific gene editing and recombination systems. Therefore, these methods are often limited by the length of eccDNAs and are complex, expensive, as well as time-consuming. In this study, we introduce a novel method named QuickLAMA (Ligase-Assisted Minicircle Accumulation) for rapidly synthesizing eccDNAs up to 2.6 kb using a simple PCR and ligation approach. To validate the efficacy of our method, we synthesized three eccDNAs of varying lengths from cancer tissue and PC3 cells and confirmed successful circularization through sequencing and restriction enzyme digestion. Additional analyses have demonstrated that this method is highly efficient, cost-effective, and time-efficient, with good reproducibility. Using the method, a well-trained molecular biologist can synthesize and purify multiple eccDNAs within a single day, and it can be easily standardized and processed in a high-throughput manner, indicating the potential of the method to produce a wide range of desired eccDNAs and promote the translation of eccDNA research into clinical applications.
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Affiliation(s)
- Shanru Zuo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
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9
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Bhuiyan A, Asakawa S. Synthesis and cloning of long repeat sequences using single-stranded circular DNA. Front Bioeng Biotechnol 2023; 11:1115159. [PMID: 36970617 PMCID: PMC10033958 DOI: 10.3389/fbioe.2023.1115159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Non-coding repeat expansion causes several neurodegenerative diseases, such as fragile X syndrome, amyotrophic lateral sclerosis/frontotemporal dementia, and spinocerebellar ataxia (SCA31). Such repetitive sequences must be investigated to understand disease mechanisms and prevent them, using novel approaches. However, synthesizing repeat sequences from synthetic oligonucleotides is challenging as they are unstable, lack unique sequences, and exhibit propensity to make secondary structures. Synthesizing long repeat sequence using polymerase chain reaction is often difficult due to lack of unique sequence. Here, we employed a rolling circle amplification technique to obtain seamless long repeat sequences using tiny synthetic single-stranded circular DNA as template. We obtained 2.5–3 kbp uninterrupted TGGAA repeats, which is observed in SCA31, and confirmed it using restriction digestion, Sanger and Nanopore sequencing. This cell-free, in vitro cloning method may be applicable for other repeat expansion diseases and be used to produce animal and cell culture models to study repeat expansion diseases in vivo and in vitro.
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10
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Petersen KV, Tesauro C, Hede MS, Pages C, Marcussen LB, Keller JG, Bugge M, Holm K, Bjergbæk L, Stougaard M, Wejse C, Knudsen BR. Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts. SENSORS (BASEL, SWITZERLAND) 2022; 22:7763. [PMID: 36298113 PMCID: PMC9608553 DOI: 10.3390/s22207763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The method is based on rolling circle amplification of circular DNA products that can only be formed upon restriction digestion of specially designed DNA substrates. By combining the activity of the target restriction endonuclease with the highly specific Cre recombinase to generate DNA circles, we demonstrate specific detection of selected restriction endonuclease activities even in crude cell extracts. This is, to our knowledge, the first example of a sensor system that allows activity measurements of restriction endonucleases in crude samples. The presented sensor system may prove valuable for future characterization of bacteria species or strains based on their expression of restriction endonucleases as well as for quantification of restriction endonuclease activities directly in extracts from recombinant cells.
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Affiliation(s)
- Kamilla Vandsø Petersen
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
| | | | | | - Camilla Pages
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Lærke Bay Marcussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Josephine Geertsen Keller
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Bugge
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Kasper Holm
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Lotte Bjergbæk
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Magnus Stougaard
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, 8000 Aarhus, Denmark
| | - Christian Wejse
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Public Health, Aarhus University, 8000 Aarhus, Denmark
| | - Birgitta R. Knudsen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
- VPCIR Biosciences Aps, 8000 Aarhus, Denmark
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Luo J, Chen H, An R, Liang X. Efficient preparation of AppDNA/AppRNA by T4 DNA ligase aided by a DNA involving mismatched mini-hairpin structure at its 3′ side. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jian Luo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
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12
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Target-Responsive Template Structure Switching-Mediated Exponential Rolling Circle Amplification for the Direct and Sensitive Detection of MicroRNA. BIOCHIP JOURNAL 2022. [DOI: 10.1007/s13206-022-00071-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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13
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Hameed SS, Al-Ogaili AS, Noori N. Single-stranded DNA aptamer-based rolling circle amplification as anti-chicken Salmonella bacteriostatic. Vet World 2022; 15:1171-1176. [PMID: 35765498 PMCID: PMC9210839 DOI: 10.14202/vetworld.2022.1171-1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 03/21/2022] [Indexed: 11/27/2022] Open
Abstract
Background and Aim: Salmonella is a major foodborne pathogen in the poultry industry, wherein the control measures may include sanitation and antibacterial and vaccines. However, there have been severe global restrictions on using anti-Salmonella antibacterial agents in livestock. This situation, along with rapidly increasing drug-resistant bacterial species, has led to the exploration of unconventional methods to control Salmonella infection in poultry. In recent years, selection techniques of promising DNA aptamers have begun to permeate several medical branches, resulting in the development of numerous anti-Salmonella DNA aptamers, most of which are used as sensing molecules for diagnostic purposes. These DNA aptamers have been demonstrated to interfere with bacterial growth, multiplication, and viability. Aptamers formed in rolling circle amplification products (RCA-p) could improve the potential action of aptamer interference with bacteria. This study aimed to test the use of single-stranded DNA aptamers in the form of RCA-p as a bacteriostatic to Salmonellain vitro. Materials and Methods: Salmonella Typhimurium and Salmonella Enteritidis isolates were subjected to the action of anti-ST and anti-SE DNA aptamers in the form of RCA-p. Each isolate was grown on MacConkey and Luria-Bertani agar media separately in different concentrations in the presence or absence of the cognate RCA-p. Results: The anti-Salmonella species DNA aptamer-based RCA-p were capable of reducing bacterial growth to significant levels in vitro. Conclusion: We describe a potential solution for the rapidly developing drug resistance of several bacterial species. Our findings suggested that the use of non-toxic, non-immunogenic, and low-cost DNA aptamers targeting Salmonella in the form of RCA-p could inhibit the bacterial growth rate. Unlike polymerase chain reaction, RCA yields tandem repeats of single-stranded DNA at isothermal conditions, which would increase the probability of receptor-ligand clustering and increase affinity. Furthermore, as our RCA template was bivalent with two DNA aptamer sequences, we could target multiple sites or antigens on a bacterial cell.
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Affiliation(s)
- Samer Sadeq Hameed
- Department of Pathology and Diseases of Poultry, College of Veterinary Medicine, University of Baghdad, Baghdad, Iraq
| | - Adil Sabr Al-Ogaili
- Department of Medical Laboratory Techniques, Kut-Technical Institute, Middle Technical University, Baghdad, Iraq
| | - Noor Noori
- Department of Medical Laboratory Techniques, Kut-Technical Institute, Middle Technical University, Baghdad, Iraq
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14
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Rosenbohm JM, Klapperich CM, Cabodi M. Tunable Duplex Semiquantitative Detection of Nucleic Acids with a Visual Lateral Flow Immunoassay Readout. Anal Chem 2022; 94:3956-3962. [PMID: 35199994 PMCID: PMC10017168 DOI: 10.1021/acs.analchem.1c05039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Quantitative nucleic acid amplification testing (NAAT) is a key enabling technology for infectious disease management, especially in instances where viral load informs therapeutic decisions. Inadequate access to quantitative NAATs remains a challenge to the successful deployment of antiretroviral therapy (ART) regimens for patients with chronic hepatitis B virus (CHB) in low resourced settings (LRS). Current field-deployable NAATs are generally qualitative (yes/no) rather than quantitative in nature, making them ill-suited for viral load monitoring programs for CHB patients. Here, we report the development of a proof-of-concept molecular diagnostic test, the semiquantitative ligation and amplification (SQLA) assay, which achieves semiquantitative detection of input target DNA at two independently tunable detection thresholds with a simple visual readout. The SQLA assay utilizes a duplex competitive thermophilic helicase-dependent amplification (tHDA) chemistry and can be performed in under 1 h.
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Affiliation(s)
- Justin M Rosenbohm
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Catherine M Klapperich
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Mario Cabodi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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15
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Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets. Int J Mol Sci 2021; 22:ijms222413526. [PMID: 34948321 PMCID: PMC8707343 DOI: 10.3390/ijms222413526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.
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16
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Identification of the insertion site of transgenic DNA based on cyclization of the target gene with the flanking sequence and nested inverse PCR. TALANTA OPEN 2021. [DOI: 10.1016/j.talo.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Zhang XL, Liu YH, Du SM, Yin Y, Kong LQ, Chang YY, Chai YQ, Li ZH, Yuan R. Engineering a Rolling-Circle Strand Displacement Amplification Mediated Label-Free Ultrasensitive Electrochemical Biosensing Platform. Anal Chem 2021; 93:9568-9574. [PMID: 34210120 DOI: 10.1021/acs.analchem.1c01677] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, an original rolling-circle strand displacement amplification (RC-SDA) was developed by introducing a circle DNA with two recognition domains as a template instead of the limited liner DNA template in traditional strand displacement amplification (SDA), which displayed much shorter reaction time down to 30 min and quite higher conversion efficiency of more than 1.77 × 108 compared with those of traditional strand displacement amplification (SDA) and could be applied to construct a label-free biosensor for ultrasensitive detection of an HIV DNA fragment. Once the target HIV DNA fragment interacts with the template circle DNA, the RC-SDA could be activated to dramatically output amounts of mimic target DNA with the assistance of the Phi29 DNA polymerase and Nb.BbvCI enzyme. In application, while the output products were captured by the DNA tetrahedral nanoprobe (DTNP) modified electrode, the electrochemical tag silver nanoclusters (AgNCs) on DTNP would be released from the electrode surface, accompanied with an obviously decreased electrochemical signal. This way, the developed signal-off biosensor was successfully applied to realize the rapid and ultrasensitive detection of target HIV DNA fragment with a detection limit down to 0.21 fM, which exploits the new generation of a universal strategy beyond the traditional ones for applications in biosensing assay, clinic diagnosis, and DNA nanobiotechnology.
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Affiliation(s)
- Xiao-Long Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu-Han Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Shu-Min Du
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yang Yin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ling-Qi Kong
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yuan-Yuan Chang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ya-Qin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Zhao-Hui Li
- Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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18
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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19
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Sui Z, An R, Komiyama M, Liang X. Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments. Chembiochem 2020; 22:1005-1011. [PMID: 33124728 DOI: 10.1002/cbic.202000738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 12/24/2022]
Abstract
Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.
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Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
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20
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Williamson A, Leiros HKS. Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds. Nucleic Acids Res 2020; 48:8225-8242. [PMID: 32365176 PMCID: PMC7470946 DOI: 10.1093/nar/gkaa307] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
DNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
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Affiliation(s)
- Adele Williamson
- School of Science, University of Waikato, Hamilton 3240, New Zealand.,Department of Chemistry, UiT The Arctic University of Norway, Tromsø N-9037, Norway
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21
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Guo Y, Yang H, Ren W, Gu H, Xu G, Xu H. A noise-free, ultrasensitive and accurate miRNAs detection using streptavidin coated magnetic microsphere based stem-loop ligation PCR. Talanta 2020; 213:120845. [DOI: 10.1016/j.talanta.2020.120845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/09/2020] [Accepted: 02/13/2020] [Indexed: 02/08/2023]
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22
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Wang J, Zhu J, Wang C, Zhou G, Yu X, Fan H, An R, Komiyama M, Liang X. Thermus thermophilus DNA Ligase Connects Two Fragments Having Exceptionally Short Complementary Termini at High Temperatures. Biochemistry 2020; 59:400-406. [PMID: 31887028 DOI: 10.1021/acs.biochem.9b00866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermus thermophilus DNA ligase (Tth DNA ligase) is widely employed for cloning, enzymatic synthesis, and molecular diagnostics at high temperatures (e.g., 65 °C). It has been long believed that the complementary ends must be very long (e.g., >30 bp) to place two DNA fragments nearby for the ligation. In the current study, the length of the complementary portion was systematically varied, and the ligation efficiency was evaluated using the high resolution melting (HRM) method. Unexpectedly, very short oligonucleotides (7-10 nt) were successfully ligated on the complementary overhang attached to a dsDNA at 70 °C. Furthermore, sticky ends with the overhang of only 4 nt long, available after scission with many restriction enzymes, were also efficiently ligated at 45-70 °C. The ligation yield for the 6-nt-long sticky ends was as high as 80%. It was concluded that Tth DNA ligase can be used as a unique tool for DNA manipulation that cannot be otherwise easily accomplished.
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Affiliation(s)
- Jing Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,CAS Key laboratory of Marine Ecology and Environmental Sciences , Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 , China
| | - Jianming Zhu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Chenru Wang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Guangqing Zhou
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xin Yu
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Huijun Fan
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ran An
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
| | - Makoto Komiyama
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China.,Laboratory for Marine Drugs and Bioproducts , Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003 , China
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23
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Kollaschinski M, Sobotta J, Schalk A, Frischmuth T, Graf B, Serdjukow S. Efficient DNA Click Reaction Replaces Enzymatic Ligation. Bioconjug Chem 2020; 31:507-512. [PMID: 31874033 DOI: 10.1021/acs.bioconjchem.9b00805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We report a chemical DNA-DNA ligation method based on copper-catalyzed azide-alkyne cycloaddition (CuAAC). We demonstrate that ion addition dramatically influences the efficiency of the so-called click reaction. Even without any further additions, such as typically splint oligonucleotides for preorganization, the "click ligation" yields up to ∼83% product without any byproducts. Additionally, purification of the desired product is straightforward. In comparison to enzymatic ligation methods used to introduce adapters into, e.g., mRNA library preparation, this targeted chemical ligation method exhibits several advantages: increased ligated product and no adapter or cDNA oligomers byproducts. The advantages of the click ligation method were demonstrated by incorporation of azide modified nucleotides by several enzymes as well as broad polymerase acceptance of the obtained triazole linkage in PCR.
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Affiliation(s)
| | | | | | | | - Birgit Graf
- Baseclick GmbH, Floriansbogen 2-4, 82061 Neuried, Germany
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24
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Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C, Morgan JM, Shapiro B, Green RE. A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics 2019; 20:1023. [PMID: 31881841 PMCID: PMC6935139 DOI: 10.1186/s12864-019-6355-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 11/29/2019] [Indexed: 12/16/2022] Open
Abstract
Background Cell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming. Results Here we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding. Conclusions SRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
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Affiliation(s)
| | - Joshua Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Varsha Rao
- Claret Bioscience LLC, Santa Cruz, CA, 95060, USA
| | | | - Charles Cole
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | | | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
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25
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Li X, Zhang H, Zhao Y, Lian L, Wang X, Gao W, Zhu B, Lou D. Design and Synthesis of Ag Nanocluster Molecular Beacon for Adenosine Triphosphate Detection. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2019; 2019:2786156. [PMID: 31737403 PMCID: PMC6815610 DOI: 10.1155/2019/2786156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
This study presents a fluorescence method for detecting adenosine triphosphate (ATP) based on a label-free Ag nanocluster molecular beacon (MB) with high sensitivity. The sensor contains a hairpin-shaped MB, two short single-stranded DNA strands, and T4 DNA ligase. The MB consists of three parts, which are the template DNA sequence for synthesizing Ag nanoclusters at the 5' end, the middle DNA with a hairpin-shaped structure, and the guanine base-rich DNA sequence at the 3' end. The sensor exhibits high fluorescence intensity in the absence of ATP. However, when the probe is used for ATP detection, the two short DNA sequences in the sensor would form a long sequence by enzymatic ligation reaction; this long sequence opens the hairpin-shaped structure of the MB and decreases the fluorescence of the system. Under optimal analytical conditions, a clear linear relationship is observed between ATP concentration and fluorescence intensity in the range of 0.1-10 μM. The interference presented by other small molecules during ATP detection is evaluated, and results confirm the good selectivity of the proposed sensor. Compared with traditional methods, the sensor is label free, easy to operate, inexpensive, and highly sensitive.
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Affiliation(s)
- Xiaoshuang Li
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Hao Zhang
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Ying Zhao
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Lili Lian
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Xiyue Wang
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Wenxiu Gao
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Bo Zhu
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
| | - Dawei Lou
- Department of Analytical Chemistry, Jilin Institute of Chemical Technology, 45 Chengde Street, Jilin 132022, China
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26
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Huber MC, Schreiber A, Schiller SM. Minimalist Protocell Design: A Molecular System Based Solely on Proteins that Form Dynamic Vesicular Membranes Embedding Enzymatic Functions. Chembiochem 2019; 20:2618-2632. [PMID: 31183952 DOI: 10.1002/cbic.201900283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/24/2022]
Abstract
Life in its molecular context is characterized by the challenge of orchestrating structure, energy and information processes through compartmentalization and chemical transformations amenable to mimicry of protocell models. Here we present an alternative protocell model incorporating dynamic membranes based on amphiphilic elastin-like proteins (ELPs) rather than phospholipids. For the first time we demonstrate the feasibility of combining vesicular membrane formation and biocatalytic activity with molecular entities of a single class: proteins. The presented self-assembled protein-membrane-based compartments (PMBCs) accommodate either an anabolic reaction, based on free DNA ligase as an example of information transformation processes, or a catabolic process. We present a catabolic process based on a single molecular entity combining an amphiphilic protein with tobacco etch virus (TEV) protease as part of the enclosure of a reaction space and facilitating selective catalytic transformations. Combining compartmentalization and biocatalytic activity by utilizing an amphiphilic molecular building block with and without enzyme functionalization enables new strategies in bottom-up synthetic biology, regenerative medicine, pharmaceutical science and biotechnology.
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Affiliation(s)
- Matthias C Huber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Andreas Schreiber
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
| | - Stefan M Schiller
- Zentrum für Biosystemanalyse (ZBSA), Albert-Ludwigs-Universität Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79085, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
- Cluster of Excellence livMatS @ FIT, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110, Freiburg, Germany
- IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110, Freiburg, Germany
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27
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Wang L, Xi Y, Zhang W, Wang W, Shen H, Wang X, Zhao X, Alexeev A, Peters BA, Albert A, Xu X, Ren H, Wang O, Kirkconnell K, Perazich H, Clark S, Hurowitz E, Chen A, Xu X, Drmanac R, Jiang Y. 3' Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3'OH ends in DNA or RNA. DNA Res 2019; 26:45-53. [PMID: 30428014 PMCID: PMC6379041 DOI: 10.1093/dnares/dsy037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various genomic tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to insert 5' phosphorylated blunt-end double-stranded DNA to DNA breaks at 3'-recessive ends, gaps, or nicks to form a Y-shaped 3'-branch structure. Therefore, this base pairing-independent ligation is termed 3'-branch ligation (3'BL). In an extensive study of optimal ligation conditions, the presence of 10% PEG-8000 in the ligation buffer significantly increased ligation efficiency to more than 80%. Ligation efficiency was slightly varied between different donor and acceptor sequences. More interestingly, we discovered that T4 DNA ligase efficiently ligated DNA to the 3'-recessed end of RNA, not to that of DNA, in a DNA/RNA hybrid, suggesting a ternary complex formation preference of T4 DNA ligase. These novel properties of T4 DNA ligase can be utilized as a broad molecular technique in many important genomic applications, such as 3'-end labelling by adding a universal sequence; directional tagmentation for NGS library construction that achieve theoretical 100% template usage; and targeted RNA NGS libraries with mitigated structure-based bias and adapter dimer problems.
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Affiliation(s)
- Lin Wang
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Yang Xi
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wenwei Zhang
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Weimao Wang
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Hanjie Shen
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaojue Wang
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xia Zhao
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Andrei Alexeev
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Brock A Peters
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Alayna Albert
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Xu Xu
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Han Ren
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ou Wang
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Killeen Kirkconnell
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Helena Perazich
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Sonya Clark
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Evan Hurowitz
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
| | - Ao Chen
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xun Xu
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Radoje Drmanac
- Institute of Biochemistry, BGI-Shenzhen, Shenzhen, China.,Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Department of R&D, MGI, BGI-Shenzhen, Shenzhen, China
| | - Yuan Jiang
- Advanced Genomics Technology Lab, Complete Genomics Inc., 2904 Orchard Pkwy, San Jose, California, USA
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Zhang C, Chen G, Wang Y, Sun R, Nie X, Zhou J. MHBMDAA: Membrane-based DNA array with high resolution and sensitivity for toxic microalgae monitoring. HARMFUL ALGAE 2018; 80:107-116. [PMID: 30502803 DOI: 10.1016/j.hal.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 06/09/2023]
Abstract
Harmful algal blooms (HAB) involving toxic microalgae have posed a serious threat to the marine industry and environment in the past several decades. Efficient techniques are required to monitor the marine environment to provide an effective warning of imminent HAB. Sequenced the partial large subunit rDNA (D1-D2) sequences of eight toxic harmful algae that are commonly distributed along the Chinese coast were cloned. Specific padlock probes (PLP) that contain linker regions composed of universal primer binding sites and Zip sequences were designed from the obtained target DNA. Taxonomic probes complementary to the Zip sequences were tailed and spotted onto a nylon membrane to prepare a DNA array. An optimized multiplex hyperbranched rolling circle amplification (MHRCA) was used to produce biotin-labeled amplified products. Heat-denatured MHRCA products were used to hybridize with DNA array, followed by dot coloration. An MHRCA-based membrane DNA array assay (MHBMDAA) for detecting toxic microalgae was developed. The specificity of the MHBMDAA was confirmed by double cross-reactivity tests of PLP and taxonomic probes. The MHBMDAA was competent for detecting the simulated samples with 103 to 10-1 cells mL-1, which is 10-fold more sensitive than a multiplex PCR-based membrane DNA array. The effectiveness of the MHBMDAA was also validated by testing with natural samples from the East China Sea. Results indicated that the MHBMDAA provides a valuable tool for the sensitive and reliable detection of toxic microalgae for early warning and research purposes.
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Affiliation(s)
- Chunyun Zhang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China; School of Marine Sciences, Ningbo University, Ningbo, 315211, PR China
| | - Guofu Chen
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Yuanyuan Wang
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Rui Sun
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Xiaoli Nie
- College of Oceanology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Jin Zhou
- Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
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29
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Roushan M, Azad Z, Movahed S, Ray PD, Livshits GI, Lim SF, Weninger KR, Riehn R. Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement. Sci Rep 2018; 8:10036. [PMID: 29968756 PMCID: PMC6030079 DOI: 10.1038/s41598-018-28278-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/20/2018] [Indexed: 01/23/2023] Open
Abstract
We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD+).
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Zubair Azad
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Saeid Movahed
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Paul D Ray
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Gideon I Livshits
- Department of Physics, North Carolina State University, Raleigh, NC, USA.,Department of Chemistry, Osaka University, Osaka, 560-0043, Japan
| | - Shuang Fang Lim
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Keith R Weninger
- Department of Physics, North Carolina State University, Raleigh, NC, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, NC, USA.
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30
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Deng X, Qin S, Chen Y, Liu HY, Yuan E, Deng H, Liu SM. B-RCA revealed circulating miR-33a/b associates with serum cholesterol in type 2 diabetes patients at high risk of ASCVD. Diabetes Res Clin Pract 2018; 140:191-199. [PMID: 29601916 DOI: 10.1016/j.diabres.2018.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 02/23/2018] [Accepted: 03/09/2018] [Indexed: 10/17/2022]
Abstract
AIMS Type 2 diabetes (T2D) is a complex metabolic disease with high incidence throughout the world. Dyslipidemia is the leading cause of atherosclerotic cardiovascular diseases (ASCVD) in T2D patients. hsa-miR-33 (miR-33) serves as a regulator in lipid metabolism. We hypothesized that blood miR-33 associates with serum lipids in T2D patients at high risk of ASCVD events. METHODS We developed a branched rolling circle amplification (B-RCA) method and assessed its sensitivity and specificity with miR-33a/b standards by traditional TaqMan assay. Circulating miR-33a/b level was then determined with B-RCA in 30 T2D patients at high risk for developing ASCVD and 33 healthy controls. Pearson correlation coefficient was used to evaluate the correlation between circulating miR-33a/b and serum cholesterol. RESULTS Compared with TaqMan assay, B-RCA method showed a similar specificity and a 100-fold higher sensitivity for miR-33a detection. Circulating miR-33a/b level is positively correlated with serum total cholesterol (TC) (r = 0.364, p = 0.048) and low-density lipoprotein cholesterol (LDL-C) (r = 0.383, p = 0.037) in T2D patients at high risk for developing ASCVD. CONCLUSIONS Our B-RCA method provided an alternative strategy with specificity and high sensitivity for circulating miRNAs detection, and the results demonstrated that miR-33a/b might play an important role in cholesterol regulation.
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Affiliation(s)
- Xujing Deng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China.
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei, China.
| | - Huan-Yu Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China; Department of Clinical Medicine, Hubei University of Medicine, Hubei 442000, China.
| | - Erfeng Yuan
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Haohua Deng
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
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31
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Gansauge MT, Gerber T, Glocke I, Korlevic P, Lippik L, Nagel S, Riehl LM, Schmidt A, Meyer M. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res 2017; 45:e79. [PMID: 28119419 PMCID: PMC5449542 DOI: 10.1093/nar/gkx033] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/13/2017] [Indexed: 01/21/2023] Open
Abstract
DNA library preparation for high-throughput sequencing of genomic DNA usually involves ligation of adapters to double-stranded DNA fragments. However, for highly degraded DNA, especially ancient DNA, library preparation has been found to be more efficient if each of the two DNA strands are converted into library molecules separately. We present a new method for single-stranded library preparation, ssDNA2.0, which is based on single-stranded DNA ligation with T4 DNA ligase utilizing a splinter oligonucleotide with a stretch of random bases hybridized to a 3΄ biotinylated donor oligonucleotide. A thorough evaluation of this ligation scheme shows that single-stranded DNA can be ligated to adapter oligonucleotides in higher concentration than with CircLigase (an RNA ligase that was previously chosen for end-to-end ligation in single-stranded library preparation) and that biases in ligation can be minimized when choosing splinters with 7 or 8 random nucleotides. We show that ssDNA2.0 tolerates higher quantities of input DNA than CircLigase-based library preparation, is less costly and better compatible with automation. We also provide an in-depth comparison of library preparation methods on degraded DNA from various sources. Most strikingly, we find that single-stranded library preparation increases library yields from tissues stored in formalin for many years by several orders of magnitude.
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Affiliation(s)
- Marie-Theres Gansauge
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tobias Gerber
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Isabelle Glocke
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlevic
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurin Lippik
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Lara Maria Riehl
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, 89075 Ulm, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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32
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High-Frequency Illegitimate Strand Transfers of Nascent DNA Fragments During Reverse Transcription Result in Defective Retrovirus Genomes. J Acquir Immune Defic Syndr 2017; 72:353-62. [PMID: 26885810 DOI: 10.1097/qai.0000000000000952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Two strand transfers of nascent DNA fragments during reverse transcription are required for retrovirus replication. However, whether strand transfers occur at illegitimate sites and how this may affect retrovirus replication are not well understood. METHODS The reverse transcription was carried out with reverse transcriptases (RTs) from HIV-1, HIV-2, and murine leukemia virus. The nascent complementary DNA fragments were directly cloned without polymerase chain reaction amplification. The sequences were compared with the template sequence to determine if new sequences contained mismatched sequences caused by illegitimate strand transfers. RESULTS Among 1067 nascent reverse transcript sequences, most of them (72%) matched to the template sequences, although they randomly stopped across the RNA templates. The other 28% of them contained mismatched 3'-end sequences because of illegitimate strand transfers. Most of the illegitimate strand transfers (81%) were disassociated from RNA templates and realigned onto opposite complementary DNA strands. Up to 3 strand transfers were detected in a single sequence, whereas most of them (93%) contained 1 strand transfer. Because most of the illegitimate strand-transfer fragments were generated from templates at 2 opposite orientations, they resulted in defective viral genomes and could not be detected by previous methods. Further analysis showed that mutations at pause/disassociation sites resulted in significantly higher strand-transfer rates. Moreover, illegitimate strand-transfer rates were significantly higher for HIV-2 RT (38.2%) and murine leukemia virus RT (44.6%) than for HIV-1 RT (5.1%). CONCLUSIONS Illegitimate strand transfers frequently occur during reverse transcription and can result in a large portion of defective retrovirus genomes.
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33
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Koo KM, Wee EJ, Trau M. High-speed biosensing strategy for non-invasive profiling of multiple cancer fusion genes in urine. Biosens Bioelectron 2017; 89:715-720. [DOI: 10.1016/j.bios.2016.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022]
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34
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Lin S, Kang TS, Lu L, Wang W, Ma DL, Leung CH. A G-quadruplex-selective luminescent probe with an anchor tail for the switch-on detection of thymine DNA glycosylase activity. Biosens Bioelectron 2016; 86:849-857. [DOI: 10.1016/j.bios.2016.07.082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/23/2016] [Accepted: 07/23/2016] [Indexed: 11/25/2022]
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35
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Hollenstein M, Damha MJ. Rolling Circle Amplification with Chemically Modified Nucleoside Triphosphates. ACTA ACUST UNITED AC 2016; 67:7.26.1-7.26.15. [PMID: 27911492 DOI: 10.1002/cpnc.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Modified nucleoside triphosphates (dN*TPs) represent facile and versatile precursors for the introduction of chemical diversity into nucleic acids. While dN*TPs have been utilized in a plethora of practical applications, very little attention has been devoted to the assessment of their compatibility with isothermal amplification strategies. In this context, rolling circle amplification (RCA) is a wide-spread enzymatic replication method in which small single-stranded DNA (ssDNA) circles serve as templates in primer extension reactions yielding very long, ssDNA products. RCA is a pivotal tool for the generation of biosensor and diagnostic devices and is currently evaluated for its usefulness to create novel drug delivery systems. This unit describes the experimental procedures for the synthesis of modified RCA products using dN*TPs bearing chemical alterations at any possible location of the nucleosidic scaffold. Two ligation methods are presented for the generation of the DNA nanocircles that serve as templates for RCA, followed by a description of the RCA method itself and an assessment of the nuclease resistance of the ensuing products. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marcel Hollenstein
- Department of Structural Biology and Chemistry, Pasteur Institute, Paris, France
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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36
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Zhang L, Tripathi A. Archaeal RNA ligase from thermoccocus kodakarensis for template dependent ligation. RNA Biol 2016; 14:36-44. [PMID: 27715457 DOI: 10.1080/15476286.2016.1239688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Nicking-sealing RNA ligases play a significant biological role in host defense and cellular repair, and have become an important molecular tool in biomedical engineering. Due to the propensity for RNA to form secondary structures, RNA modifying enzymes with elevated optimum temperatures are highly desired. Current characterized double stranded RNA ligases, such as the bacteriophage T4 RNA ligase 2, while possessing good template dependency, are not active at elevated temperatures. The few characterized RNA ligases from thermophiles exhibit high template independency. We synthesize and characterize here, KOD RNA ligase (KOD1Rnl), a thermostable and template dependent RNA ligase from the archaeon, Thermoccocus Kodakarensis. We disclose that a 13 time reduction in template independent ligation can be achieved with the addition of a single stranded DNase, such as RecJ. We also elucidate the effects of the presence of blood proteins on the activity of KOD1Rnl. Template dependent and thermostable RNA ligases, such as KOD RNA ligase, can be utilized in RNA detection, modification and sequencing.
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Affiliation(s)
- Lei Zhang
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
| | - Anubhav Tripathi
- a Center for Biomedical Engineering, School of Engineering, Brown University , Providence , RI , USA
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38
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Rapid Synthesis of a Long Double-Stranded Oligonucleotide from a Single-Stranded Nucleotide Using Magnetic Beads and an Oligo Library. PLoS One 2016; 11:e0149774. [PMID: 26930667 PMCID: PMC4773231 DOI: 10.1371/journal.pone.0149774] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/22/2016] [Indexed: 11/19/2022] Open
Abstract
Chemical synthesis of oligonucleotides is a widely used tool in the field of biochemistry. Several methods for gene synthesis have been introduced in the growing area of genomics. In this paper, a novel method of constructing dsDNA is proposed. Short (28-mer) oligo fragments from a library were assembled through successive annealing and ligation processes, followed by PCR. First, two oligo fragments annealed to form a dsDNA molecule. The double-stranded oligo was immobilized onto magnetic beads (solid support) via streptavidin-biotin binding. Next, single-stranded oligo fragments were added successively through ligation to form the complete DNA molecule. The synthesized DNA was amplified through PCR and gel electrophoresis was used to characterize the product. Sanger sequencing showed that more than 97% of the nucleotides matched the expected sequence. Extending the length of the DNA molecule by adding single-stranded oligonucleotides from a basis set (library) via ligation enables a more convenient and rapid mechanism for the design and synthesis of oligonucleotides on the go. Coupled with an automated dispensing system and libraries of short oligo fragments, this novel DNA synthesis method would offer an efficient and cost-effective method for producing dsDNA.
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39
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Shen Y, Tian F, Chen Z, Li R, Ge Q, Lu Z. Amplification-based method for microRNA detection. Biosens Bioelectron 2015; 71:322-331. [PMID: 25930002 DOI: 10.1016/j.bios.2015.04.057] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 04/18/2015] [Indexed: 12/20/2022]
Abstract
Over the last two decades, the study of miRNAs has attracted tremendous attention since they regulate gene expression post-transcriptionally and have been demonstrated to be dysregulated in many diseases. Detection methods with higher sensitivity, specificity and selectivity between precursors and mature microRNAs are urgently needed and widely studied. This review gave an overview of the amplification-based technologies including traditional methods, current modified methods and the cross-platforms of them combined with other techniques. Many progresses were found in the modified amplification-based microRNA detection methods, while traditional platforms could not be replaced until now. Several sample-specific normalizers had been validated, suggesting that the different normalizers should be established for different sample types and the combination of several normalizers might be more appropriate than a single universal normalizer. This systematic overview would be useful to provide comprehensive information for subsequent related studies and could reduce the un-necessary repetition in the future.
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Affiliation(s)
- Yanting Shen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Fei Tian
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zhenzhu Chen
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Rui Li
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Qinyu Ge
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
| | - Zuhong Lu
- Research Center for Learning Science, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China; State Key Laboratory of Bioelectronics, Southeast University, Sipailou road no. 2, Nanjing, Jiangsu Province 2100096, PR China.
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40
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Roy CK, Olson S, Graveley BR, Zamore PD, Moore MJ. Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation. eLife 2015; 4. [PMID: 25866926 PMCID: PMC4442144 DOI: 10.7554/elife.03700] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 04/12/2015] [Indexed: 02/04/2023] Open
Abstract
Many RNAs, including pre-mRNAs and long non-coding RNAs, can be thousands of nucleotides long and undergo complex post-transcriptional processing. Multiple sites of alternative splicing within a single gene exponentially increase the number of possible spliced isoforms, with most human genes currently estimated to express at least ten. To understand the mechanisms underlying these complex isoform expression patterns, methods are needed that faithfully maintain long-range exon connectivity information in individual RNA molecules. In this study, we describe SeqZip, a methodology that uses RNA-templated DNA–DNA ligation to retain and compress connectivity between distant sequences within single RNA molecules. Using this assay, we test proposed coordination between distant sites of alternative exon utilization in mouse Fn1, and we characterize the extraordinary exon diversity of Drosophila melanogaster Dscam1. DOI:http://dx.doi.org/10.7554/eLife.03700.001 A flow chart can show how an outcome can be achieved from a particular start point by breaking down an activity into a list of possible steps. Often, a flow chart contains several alternative steps, not all of which are taken every time the flow chart is used. The same can be said of genes, which are biological instructions that often contain many options within their DNA sequences. Proteins—which perform many roles in cells—are built following the instructions contained in genes. First, the DNA sequence of the gene is copied. This produces a molecule of ribonucleic acid (RNA), which is able to move around the cell to find the machinery that can use the genetic information to make a protein. Genes and their RNA copies contain instructions with more steps—called exons—than are necessary to make a working protein, so extra exons are removed (‘spliced’) from the RNA copies. Different combinations of exons can be removed, so splicing can make different versions of the RNA called isoforms. These allow a single gene to build many different proteins. In fruit flies, for example, the different exons of the gene Dscam1 can be spliced into one of 38,016 unique RNA isoforms. Current technology only allows researchers to deduce the sequence of RNA molecules by combining sequences recorded from short fragments of the molecule. However, before splicing, RNA molecules tend to be much longer than this, so this restricts our understanding of the RNA isoforms found in cells. Here, Roy et al. devised and tested a new method called SeqZip to solve this problem. SeqZip uses short fragments of DNA called ligamers that can only stick to the sections of RNA that will remain after the molecule has been spliced. After splicing, the ligamers can be stuck together to make a DNA replica of the spliced RNA. The end product is at least 49 times shorter than the original RNA, so it is easier to sequence. In addition, the combinations of the ligamers in the DNA replica show which exons of a specific gene are kept and which ones are spliced out. To test the method, Roy et al. studied a mouse gene that has six RNA isoforms. SeqZip reduced the length of the RNA by five times and made it possible to measure how frequently the different isoforms naturally arise. Roy et al. also used SeqZip to work out which isoforms of the Dscam1 gene are used at different stages in the life of fruit fly larvae. SeqZip can provide insights into how complex organisms like flies, mice, and humans have evolved with relatively few—a little over 20,000—genes in their genomes. DOI:http://dx.doi.org/10.7554/eLife.03700.002
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Affiliation(s)
- Christian K Roy
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Sara Olson
- Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Brenton R Graveley
- Institute for Systems Genomics, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
| | - Melissa J Moore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States
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Zhao B, Song J, Guan Y. Discriminative identification of miRNA let-7 family members with high specificity and sensitivity using rolling circle amplification. Acta Biochim Biophys Sin (Shanghai) 2015; 47:130-6. [PMID: 25534778 DOI: 10.1093/abbs/gmu121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rolling circle amplification (RCA) is a new method based on virus DNA reproduction, which has been widely used in the field of miRNA detection. However, discrimination of highly homologous miRNAs is a bottleneck in the research of miRNA. In this study, the RCA process was creatively used to conduct the discrimination of miRNAs. Results showed that T4 RNA ligase 2 could reach the highest circularization efficiency during the RCA process with higher specificity. By using RCA technology, a member of highly homologous miRNAs, let-7, could be discriminated at the amount of 2.5 fmol. This sensitivity could not be achieved by using traditional reverse transcription quantitative polymerase chain reaction (RT-qPCR) method. In addition, detection of miRNAs by using RCA could reach the amount limit of fmol with a good linearity. Optimal RCA technology used in this study is better than RT-qPCR in discriminating highly homologous family miRNAs. Results from this study can promote the applications of RCA in clinical diagnosis, environment protection, health care, disease inspection and prevention, and national security.
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Affiliation(s)
- Bin Zhao
- Key Laboratory of National Sport Bureau, Department of Human Movement Sciences, Shenyang Sport University, Shenyang 110102, China
| | - Jirui Song
- Key Laboratory of National Sport Bureau, Department of Human Movement Sciences, Shenyang Sport University, Shenyang 110102, China
| | - Yifu Guan
- Key Laboratory of Medical Cell Biology (Ministry of Education), Department of Biochemistry and Molecular Biology, China Medical University, Shenyang 110001, China
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42
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Nelissen FHT, Goossens EPM, Tessari M, Heus HA. Enzymatic preparation of multimilligram amounts of pure single-stranded DNA samples for material and analytical sciences. Anal Biochem 2015; 475:68-73. [PMID: 25637680 DOI: 10.1016/j.ab.2015.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/15/2022]
Abstract
We present a method for high-yield production of multimilligram amounts of pure single-stranded DNA employing rolling circle amplification (RCA) and processing by restriction enzymes. Pure and homogeneous samples are produced with minimal handling time, reagents, and waste products. The RCA method is more than twice as efficient in dNTP incorporation than conventional polymerase chain reaction in producing end product. The validity and utility of the method are demonstrated in the production of a uniformly (13)C/(15)N-labeled 38-nt cocaine aptamer DNA used in nanosensing devices.
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Affiliation(s)
- Frank H T Nelissen
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Elles P M Goossens
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Marco Tessari
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands
| | - Hans A Heus
- Department of Biophysical Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands.
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Kleiner M, Hooper LV, Duerkop BA. Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 2015; 16:7. [PMID: 25608871 PMCID: PMC4308010 DOI: 10.1186/s12864-014-1207-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 12/24/2014] [Indexed: 01/21/2023] Open
Abstract
Background Viruses are a significant component of the intestinal microbiota in mammals. In recent years, advances in sequencing technologies and data analysis techniques have enabled detailed metagenomic studies investigating intestinal viromes (collections of bacteriophage and eukaryotic viral nucleic acids) and their potential contributions to the ecology of the microbiota. An important component of virome studies is the isolation and purification of virus-like particles (VLPs) from intestinal contents or feces. Several methods have been applied to isolate VLPs from intestinal samples, yet to our knowledge, the efficiency and reproducibility between methods have not been explored. A rigorous evaluation of methods for VLP purification is critical as many studies begin to move from descriptive analyses of virus diversity to studies striving to quantitatively compare viral abundances across many samples. Therefore, reproducible VLP purification methods which allow for high sample throughput are needed. Here we compared and evaluated four methods for VLP purification using artificial intestinal microbiota samples of known bacterial and viral composition. Results We compared the following four methods of VLP purification from fecal samples: (i) filtration + DNase, (ii) dithiothreitol treatment + filtration + DNase, (iii) filtration + DNase + PEG precipitation and (iv) filtration + DNase + CsCl density gradient centrifugation. Three of the four tested methods worked well for VLP purification. We observed several differences between methods related to the removal efficiency of bacterial and host DNAs and biases against specific phages. In particular the CsCl density gradient centrifugation method, which is frequently used for VLP purification, was most efficient in removing host derived DNA, but also showed strong discrimination against specific phages and showed a lower reproducibility of quantitative results. Conclusions Based on our data we recommend the use of methods (i) or (ii) for large scale studies when quantitative comparison of viral abundances across samples is required. The CsCl density gradient centrifugation method, while being excellently suited to achieve highly purified samples, in our opinion, should be used with caution when performing quantitative studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1207-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manuel Kleiner
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Current address: Department of Geoscience, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
| | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,The Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Breck A Duerkop
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Lin C, Chen Y, Cai Z, Zhu Z, Jiang Y, Yang CJ, Chen X. A label-free fluorescence strategy for sensitive detection of ATP based on the ligation-triggered super-sandwich. Biosens Bioelectron 2014; 63:562-565. [PMID: 25168764 DOI: 10.1016/j.bios.2014.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/24/2014] [Accepted: 08/06/2014] [Indexed: 01/01/2023]
Abstract
In this study, a label-free fluorescence strategy for sensitive detection of ATP based on the ligation-triggered super-sandwich is reported. We designed a double-stranded DNA (ds-DNA) probe as the substrate of ATP-dependent ligation. SYBR Green I (SG I), a double-duplex DNA specific dye, was employed as the readout signal. In the absence of ATP, the ligation would not occur and the ds-DNA remained intact. Further, a weak fluorescence could be observed due to the intercalation of SG I into the grooves of the ds-DNA probe. In the presence of ATP, T4 DNA ligase would catalyse the ligation between 3'-OH and 5'-PO4 ends between ds-DNA probes. As a result, more binding sites of the SG I were generated and a fluorescence enhancement was obtained. This method showed a good sensitivity with a detection limit of 200 pM and could perfectly discriminate ATP from its analogs.
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Affiliation(s)
- Chunshui Lin
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yiying Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhixiong Cai
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhi Zhu
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yaqi Jiang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong James Yang
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; State Key Laboratory of Physical Chemistry of Solid Surfaces, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen 361005, China
| | - Xi Chen
- Department of Chemistry and the MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China.
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Roushan M, Kaur P, Karpusenko A, Countryman PJ, Ortiz CP, Fang Lim S, Wang H, Riehn R. Probing transient protein-mediated DNA linkages using nanoconfinement. BIOMICROFLUIDICS 2014; 8:034113. [PMID: 25379073 PMCID: PMC4162420 DOI: 10.1063/1.4882775] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 05/30/2014] [Indexed: 05/16/2023]
Abstract
We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.
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Affiliation(s)
- Maedeh Roushan
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Parminder Kaur
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Alena Karpusenko
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | | | - Carlos P Ortiz
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Shuang Fang Lim
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Hong Wang
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
| | - Robert Riehn
- Department of Physics, NC State University , Raleigh, North Carolina 27695, USA
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Sosic A, Pasqualin M, Pasut G, Gatto B. Enzymatic formation of PEGylated oligonucleotides. Bioconjug Chem 2014; 25:433-41. [PMID: 24450424 DOI: 10.1021/bc400569z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Gene therapy, siRNA, and therapeutic aptamers attract great interest owing to their versatility to treat a wide range of diseases and their potential high selectivity. Unfortunately, oligonucleotide-based therapeutics suffer rapid degradation by nucleases, scarce cell internalization, and fast kidney clearance. To address these limitations, the covalent attachment by mild chemical reactions of an activated polyethylene glycol (PEG) is widely used to obtain PEGylated nucleic acids showing a more favorable pharmacokinetic profile. We describe here a method for the enzymatic formation of PEGylated nucleic acids employing T4 DNA ligase: the ligation protocol was set up and optimized allowing the complete achievement of PEGylated oligonucleotides amenable to further enzymatic reactions. The feasibility of this approach for bioconjugation was demonstrated employing a set of PEG-donors and oligonucleotide acceptors, differing in the chemical link between PEG and the oligonucleotide donor, and in the length, sequence, and structure of the oligonucleotides employed. The ligase reaction allowed us to obtain double-stranded as well as single-stranded oligonucleotides, thus demonstrating the applicability of the method to a variety of substrates suitable for diagnostic and therapeutic applications.
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Affiliation(s)
- Alice Sosic
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , Via F. Marzolo 5, 35131 Padua, Italy
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47
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Mills JD, Kawahara Y, Janitz M. Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling. Curr Genomics 2013; 14:173-81. [PMID: 24179440 PMCID: PMC3664467 DOI: 10.2174/1389202911314030003] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 01/31/2013] [Accepted: 02/25/2013] [Indexed: 01/11/2023] Open
Abstract
RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for unique insights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternative splicing events and the presence of non-coding RNAs. It has been realised non-coding RNAs are more then just artefacts of erroneous transcription and play vital regulatory roles at the genomic, transcriptional and translational level. Transcription of the DNA sense strand produces antisense transcripts. This is known as antisense transcription and often results in the production of non-coding RNAs that are complementary to their associated sense transcripts. Antisense tran-scription has been identified in bacteria, fungi, protozoa, plants, invertebrates and mammals. It seems that antisense tran-scriptional ‘hot spots’ are located around nucleosome-free regions such as those associated with promoters, indicating that it is likely that antisense transcripts carry out important regulatory functions. This underlines the importance of identifying the presence and understanding the function of these antisense non-coding RNAs. The information concerning strand ori-gin is often lost during conventional RNA-Seq; capturing this information would substantially increase the worth of any RNA-Seq experiment. By manipulating the input cDNA during the template preparation stage it is possible to retain this vital information. This forms the basis of strand-specific RNA-Seq. With an ability to unlock immense portions of new in-formation surrounding the transcriptome, this cutting edge technology may hold the key to developing a greater under-standing of the transcriptome.
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Affiliation(s)
- James Dominic Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Lin C, Zhang Y, Zhou X, Yao B, Fang Q. Naked-eye detection of nucleic acids through rolling circle amplification and magnetic particle mediated aggregation. Biosens Bioelectron 2013; 47:515-9. [DOI: 10.1016/j.bios.2013.03.056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 02/28/2013] [Accepted: 03/17/2013] [Indexed: 12/30/2022]
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49
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Xue Q, Wang L, Jiang W. A novel label-free cascade amplification strategy based on dumbbell probe-mediated rolling circle amplification-responsive G-quadruplex formation for highly sensitive and selective detection of NAD+ or ATP. Chem Commun (Camb) 2013; 49:2640-2. [PMID: 23431564 DOI: 10.1039/c3cc39064k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel label-free fluorescent sensing scheme for sensitive and selective detection of NAD(+) and ATP has been developed based on dumbbell probe-mediated rolling circle amplification (D-RCA)-responsive G-quadruplex formation. This approach can detect 0.5 pM for ATP and 100 fM for NAD(+), much lower than those of previously reported biosensors, and exhibits high discrimination ability.
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Affiliation(s)
- Qingwang Xue
- Key Laboratory for Colloid and Interface Chemistry of Education Ministry, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, PR China
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50
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Kwok CK, Ding Y, Sherlock ME, Assmann SM, Bevilacqua PC. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Anal Biochem 2013; 435:181-6. [PMID: 23399535 DOI: 10.1016/j.ab.2013.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/09/2013] [Accepted: 01/12/2013] [Indexed: 01/11/2023]
Abstract
Single-stranded DNA (ssDNA) ligation is a crucial step in many biochemical assays. Efficient ways of carrying out this reaction, however, are lacking. We show here that existing ssDNA ligation methods suffer from slow kinetics, poor yield, and severe nucleotide preference. To resolve these issues, we introduce a hybridization-based strategy that provides efficient and low-bias ligation of ssDNA. Our method uses a hairpin DNA to hybridize to any incoming acceptor ssDNA with low bias, with ligation of these strands mediated by T4 DNA ligase. This technique potentially can be applied in protocols that require ligation of ssDNA, including ligation-mediated polymerase chain reaction (LMPCR) and complementary DNA (cDNA) library construction.
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Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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