1
|
Fei H, Cui J, Zhu S, Xia Y, Xing Y, Gao Y, Shi S. Integrative Analyses of Transcriptomics and Metabolomics in Immune Response of Leguminivora glycinivorella Mats to Beauveria bassiana Infection. INSECTS 2024; 15:126. [PMID: 38392545 PMCID: PMC10889468 DOI: 10.3390/insects15020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
This study utilized Beauveria bassiana to infect Leguminivora glycinivorella, analyzed the effects on the transcriptome and metabolome, and further investigated the antibacterial function of L. glycinivorella. We performed transcriptome and metabolome sequencing on the L. glycinivorella infected with B. bassiana and its control groups, and performed a joint analysis of transcriptome and metabolome results. Upon screening, 4560 differentially expressed genes were obtained in the transcriptome and 71 differentially expressed metabolites were obtained in the metabolome. On this basis, further integration of the use of transcriptomics and metabonomics combined an analysis of common enrichments of pathways of which there were three. They were glutathione S-transferase (GSTs) genes, heat shock protein (HSP) genes, and cytochrome P450 (CYP450) genes. These three pathways regulate the transport proteins, such as ppars, and thus affect the digestion and absorption of sugars and fats, thus regulating the development of pests. The above conclusion indicates that B. bassiana can affect the sugar metabolism, lipid metabolism, and amino acid metabolism pathways of L. glycinivorella, and can consume the necessary energy, protein, and lipids of L. glycinivorella. The research on the immune response mechanism of pests against pathogens can provide an important scientific basis and target for the development of immunosuppressants. This study laid an information foundation for the application of entomogenous fungi to control soybean borer at the molecular level.
Collapse
Affiliation(s)
- Hongqiang Fei
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
- Jilin City Academy of Agricultural Sciences, Jilin 132101, China
| | - Juan Cui
- Agriculture Science and Technology College, Jilin 132109, China
| | - Shiyu Zhu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Ye Xia
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yichang Xing
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Yu Gao
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Shusen Shi
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| |
Collapse
|
2
|
Fu Y, Liu Y, Song W, Yang D, Wu W, Lin J, Yang X, Zeng J, Rong L, Xia J, Lei H, Yang R, Zhang M, Liao Y. Early monitoring-to-warning Internet of Things system for emerging infectious diseases via networking of light-triggered point-of-care testing devices. EXPLORATION (BEIJING, CHINA) 2023; 3:20230028. [PMID: 38264687 PMCID: PMC10742204 DOI: 10.1002/exp.20230028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/31/2023] [Indexed: 01/25/2024]
Abstract
Early monitoring and warning arrangements are effective ways to distinguish infectious agents and control the spread of epidemic diseases. Current testing technologies, which cannot achieve rapid detection in the field, have a risk of slowing down the response time to the disease. In addition, there is still no epidemic surveillance system, implementing prevention and control measures is slow and inefficient. Motivated by these clinical needs, a sample-to-answer genetic diagnosis platform based on light-controlled capillary modified with a photocleavable linker is first developed, which could perform nucleic acid separation and release by light irradiation in less than 30 seconds. Then, on site polymerase chain reaction was performed in a handheld closed-loop convective system. Test reports are available within 20 min. Because this method is portable, rapid, and easy to operate, it has great potential for point-of-care testing. Additionally, through multiple device networking, a real-time artificial intelligence monitoring system for pathogens was developed on a cloud server. Through data reception, analysis, and visualization, the system can send early warning signals for disease control and prevention. Thus, anti-epidemic measures can be implemented effectively, and deploying and running this system can improve the capabilities for the prevention and control of infectious diseases.
Collapse
Affiliation(s)
- Yu Fu
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
- Longgang District Central Hospital of ShenzhenShenzhenChina
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yan Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingaporeSingapore
| | - Wenlu Song
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
| | - Delong Yang
- Department of Burn Surgerythe First People's Hospital of FoshanFoshanChina
| | - Wenjie Wu
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Jingyan Lin
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Xiongtiao Yang
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jian Zeng
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Lingzhi Rong
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Jiaojiao Xia
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Hongyi Lei
- Longgang District Central Hospital of ShenzhenShenzhenChina
| | - Ronghua Yang
- Department of Burn and Plastic SurgeryGuangzhou First People's HospitalSouth China University of TechnologyGuangzhouChina
| | - Mingxia Zhang
- National Clinical Research Center for Infectious Diseasethe Second Affiliated Hospital of Southern University of Science and TechnologyShenzhen Third People's HospitalShenzhenChina
| | - Yuhui Liao
- Molecular Diagnosis and Treatment Center for Infectious DiseasesDermatology HospitalSouthern Medical UniversityGuangzhouChina
| |
Collapse
|
3
|
Zhou Y, Lauschke VM. Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy. Handb Exp Pharmacol 2023; 280:237-260. [PMID: 35792943 DOI: 10.1007/164_2022_596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Over the last decade, next-generation sequencing (NGS) methods have become increasingly used in various areas of human genomics. In routine clinical care, their use is already implemented in oncology to profile the mutational landscape of a tumor, as well as in rare disease diagnostics. However, its utilization in pharmacogenomics is largely lacking behind. Recent population-scale genome data has revealed that human pharmacogenes carry a plethora of rare genetic variations that are not interrogated by conventional array-based profiling methods and it is estimated that these variants could explain around 30% of the genetically encoded functional pharmacogenetic variability.To interpret the impact of such variants on drug response a multitude of computational tools have been developed, but, while there have been major advancements, it remains to be shown whether their accuracy is sufficient to improve personalized pharmacogenetic recommendations in robust trials. In addition, conventional short-read sequencing methods face difficulties in the interrogation of complex pharmacogenes and high NGS test costs require stringent evaluations of cost-effectiveness to decide about reimbursement by national healthcare programs. Here, we illustrate current challenges and discuss future directions toward the clinical implementation of NGS to inform genotype-guided decision-making.
Collapse
Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tuebingen, Tuebingen, Germany.
| |
Collapse
|
4
|
Bennet D, Vo‐Dinh T, Zenhausern F. Current and emerging opportunities in biological medium‐based computing and digital data storage. NANO SELECT 2021. [DOI: 10.1002/nano.202100275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Devasier Bennet
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
| | - Tuan Vo‐Dinh
- Department of Biomedical Engineering Department of Chemistry Fitzpatrick Institute for Photonics Duke University Durham North Carolina USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
- Department of Basic Medical Sciences College of Medicine Phoenix The University of Arizona Phoenix Arizona USA
- Department of Biomedical Engineering; and BIO5 Institute College of Engineering The University of Arizona Tucson Arizona USA
- School of Pharmaceutical Sciences University of Geneva Geneva Switzerland
| |
Collapse
|
5
|
Filges S, Mouhanna P, Ståhlberg A. Digital Quantification of Chemical Oligonucleotide Synthesis Errors. Clin Chem 2021; 67:1384-1394. [PMID: 34459892 DOI: 10.1093/clinchem/hvab136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Chemically synthesized oligonucleotides are vital to most nucleic acids-based technologies and several applications are sensitive to oligonucleotide sequence errors. However, it is challenging to identify and quantify the types and amount of errors in synthetic oligonucleotides. METHODS We applied a digital sequencing approach using unique molecular identifiers to quantify errors in chemically synthesized oligonucleotides from multiple manufacturers with different synthesis strategies, purity grades, batches, and sequence context. RESULTS We detected both deletions and substitutions in chemical oligonucleotide synthesis, but deletions were 7 times more common. We found that 97.2% of all analyzed oligonucleotide molecules were intact across all manufacturers and purity grades, although the number of oligonucleotide molecules with deletions ranged between 0.2% and 11.7% for different types. Different batches of otherwise identical oligonucleotide types also varied significantly, and batch effect can impact oligonucleotide quality more than purification. We observed a bias of increased deletion rates in chemically synthesized oligonucleotides toward the 5'-end for 1 out of 2 sequence configurations. We also demonstrated that the performance of sequencing assays depends on oligonucleotide quality. CONCLUSIONS Our data demonstrate that manufacturer, synthesis strategy, purity, batch, and sequence context all contribute to errors in chemically synthesized oligonucleotides and need to be considered when choosing and evaluating oligonucleotides. High-performance oligonucleotides are essential in numerous molecular applications, including clinical diagnostics.
Collapse
Affiliation(s)
- Stefan Filges
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenberg, Sweden
| | - Pia Mouhanna
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenberg, Sweden
| | - Anders Ståhlberg
- Department of Laboratory Medicine, Sahlgrenska Center for Cancer Research, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenberg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
6
|
Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Res 2020; 48:11982-11993. [PMID: 33152081 PMCID: PMC7708046 DOI: 10.1093/nar/gkaa999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
A set of modified 2′-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
Collapse
Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| |
Collapse
|
7
|
Chen HH, Lu CC. Optimized Fluorescence-Based Detection in Single Molecule Synthesis Process. J Comput Biol 2020; 28:195-208. [PMID: 33202153 DOI: 10.1089/cmb.2020.0226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single molecule sequencing is imperative to overall genetic analysis in areas such as genomics, transcriptomics, clinical test, drug development, and cancer screening. In addition, fluorescence-based sequencing is primarily applied in single molecule sequencing besides other methods, precisely in the fields of DNA sequencing. Modern-day fluorescence labeling methods exploit a charge-coupled device camera to capture snapshots of a number of pixels on the single molecule sequencing. The method discussed in this article involves fluorescence labeling detection with a single pixel, outrivals in high accuracy and low resource requirement under low signal-to-noise ratio conditions, as well as benefits from higher throughput comparing with others. Through discussion in this article, we explore the single molecule synthesis process modeling using negative binomial distributions. Furthermore, incorporating the method of maximum likelihood and Viterbi algorithm in this modeling enhances the signal detection accuracy. The fluorescence-based model benefits in simulating actual experiment processes and assisting in understanding relations between the fluorescence emission and the signal receiving events. Last but not least, the model offers potential candidates on fluorescence dye selection that yields more accurate experiment results.
Collapse
Affiliation(s)
- Hsin-Hao Chen
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu City, Taiwan
| | - Chung-Chin Lu
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu City, Taiwan
| |
Collapse
|
8
|
Choi SK, Rho J, Yoon SE, Seok JH, Kim H, Min J, Yoon W, Lee S, Yun H, Kwon OP, Kim JH, Kim W, Kim E. Full Color Tunable Aggregation-Induced Emission Luminogen for Bioimaging Based on an Indolizine Molecular Framework. Bioconjug Chem 2020; 31:2522-2532. [PMID: 32985867 DOI: 10.1021/acs.bioconjchem.0c00467] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
By taking advantage of a unique mechanism of aggregation-induced emission (AIE) phenomena, AIE luminogens (AIEgens) have been provided as a solution to overcome the limitations of conventional fluorophores bearing the feature of aggregation-caused quenching (ACQ) phenomena. Especially, AIEgens paved the way to develop fluorogenic probes ideal for fluorescent imaging in live cell conditions. Despite the high demand for discovery of new AIEgens, it is still challenging to find a versatile molecular platform to generate diverse AIEgens. Herein, we report a new colorful molecular framework, Kaleidolizine (KIz), as a molecular platform for AIEgen generation. The KIz system allows systematic tuning of the emission wavelength from 455 to 564 nm via perturbation of the electron density of substituents on the indolizine core. Increasing the water fraction of the KIz solution in the THF/water mixture induces the fluorescence intensity increase up to 120-fold. Crystal structure analysis, computational calculations, and solvatochromism studies suggest that a synergistic effect between the intramolecular charge transfer and restriction of intramolecular rotation acts as the AIE mechanism in the KIz system. Conjugation of the triphenylphosphonium moiety to KIz allows successful development of triphenylphosphonium (TPP)-KIz for real-time bioimaging of innate mitochondria in live cells, thereby revealing the potential of KIz as a versatile molecular platform to generate fluorogenic probes based on AIE phenomena. We do believe the KIz system could serve as a new, reliable, and generally applicable molecular platform to develop various AIEgens having desired photophysical properties along with an excellent signal-to-noise ratio and with experimental convenience especially for fluorogenic live cell imaging.
Collapse
Affiliation(s)
- Sang-Kee Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Jungi Rho
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Sang Eun Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Jin-Hong Seok
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Hyungi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Junsik Min
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Woojin Yoon
- Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - Sanghee Lee
- Center for Neuro-Medicine, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Hoseop Yun
- Department of Chemistry, Ajou University, Suwon 16499, Korea
| | - O-Pil Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Jong H Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | - Eunha Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| |
Collapse
|
9
|
Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective. AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
10
|
Xing C, Chen Z, Dai J, Zhou J, Wang L, Zhang KL, Yin X, Lu C, Yang H. Light-Controlled, Toehold-Mediated Logic Circuit for Assembly of DNA Tiles. ACS APPLIED MATERIALS & INTERFACES 2020; 12:6336-6342. [PMID: 31918539 DOI: 10.1021/acsami.9b21778] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Inspired by cytoskeletal structures that respond sensitively to environmental changes and chemical inputs, we report a strategy to trigger and finely control the assembly of stimulus-responsive DNA nanostructures with light under isothermal conditions. The strategy is achieved via integrating an upstream light-controlled, toehold-mediated DNA strand displacement circuit with a downstream DNA tile self-assembly process. By rationally designing an upstream DNA strand module, we further transform the upstream DNA strand displacement circuit to an "AND gate" circuit to control the assembly of DNA nanostructures. This example represents the demonstration of the spatial and temporal assembly of DNA nanostructures using a noninvasive chemical input. Such a light-controlled DNA logic circuit not only adds a new element to the tool box of DNA nanotechnology but also inspires us to assemble complex and responsive nanostructures.
Collapse
Affiliation(s)
- Chao Xing
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
- Fujian Provincial Key Laboratory of Functional Marine Sensing Materials, Center for Advanced Marine Materials and Smart Sensors , Minjiang University , Fuzhou 350108 , P. R. China
| | - Ziyi Chen
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Junduan Dai
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Jie Zhou
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Liping Wang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Kai-Long Zhang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Xiaofei Yin
- First Institute of Oceanography, Ministry of Natural Resources , Qingdao 266061 , P. R. China
| | - Chunhua Lu
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| | - Huanghao Yang
- MOE Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry , Fuzhou University , Fuzhou 350116 , P. R. China
| |
Collapse
|
11
|
Giani AM, Gallo GR, Gianfranceschi L, Formenti G. Long walk to genomics: History and current approaches to genome sequencing and assembly. Comput Struct Biotechnol J 2019; 18:9-19. [PMID: 31890139 PMCID: PMC6926122 DOI: 10.1016/j.csbj.2019.11.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/03/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Genomes represent the starting point of genetic studies. Since the discovery of DNA structure, scientists have devoted great efforts to determine their sequence in an exact way. In this review we provide a comprehensive historical background of the improvements in DNA sequencing technologies that have accompanied the major milestones in genome sequencing and assembly, ranging from early sequencing methods to Next-Generation Sequencing platforms. We then focus on the advantages and challenges of the current technologies and approaches, collectively known as Third Generation Sequencing. As these technical advancements have been accompanied by progress in analytical methods, we also review the bioinformatic tools currently employed in de novo genome assembly, as well as some applications of Third Generation Sequencing technologies and high-quality reference genomes.
Collapse
Key Words
- BAC, Bacterial Artificial Chromosome
- Bioinformatics
- Genome assembly
- HGP, Human Genome Project
- HMW, high molecular weight
- HapMap, haplotype map
- NGS, Next Generation Sequencing
- Next-generation
- OLC, Overlap-Layout-Consensus
- QV, Quality Value (QV)
- Reference
- SBS, Sequencing by Synthesis
- SMRT, Single Molecule Real-Time
- SNPs, Single Nucleotide Polymorphisms
- SRA, Short Read Archive
- SV, Structural Variant
- Sequencing
- TGS, Third Generation Sequencing
- Third-generation
- WGS, Whole Genome Sequencing
- ZMW, Zero-Mode Waveguide
- bp, base pair
- dNTPs, deoxynucleoside triphosphates
- ddNTP, 2,3-dideoxynucleoside triphosphate
Collapse
Affiliation(s)
- Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, New York, NY, USA
| | | | | | | |
Collapse
|
12
|
Sun X, Soini TM, Poater J, Hamlin TA, Bickelhaupt FM. PyFrag 2019-Automating the exploration and analysis of reaction mechanisms. J Comput Chem 2019; 40:2227-2233. [PMID: 31165500 PMCID: PMC6771738 DOI: 10.1002/jcc.25871] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 02/06/2023]
Abstract
We present a substantial update to the PyFrag 2008 program, which was originally designed to perform a fragment-based activation strain analysis along a provided potential energy surface. The original PyFrag 2008 workflow facilitated the characterization of reaction mechanisms in terms of the intrinsic properties, such as strain and interaction, of the reactants. The new PyFrag 2019 program has automated and reduced the time-consuming and laborious task of setting up, running, analyzing, and visualizing computational data from reaction mechanism studies to a single job. PyFrag 2019 resolves three main challenges associated with the automated computational exploration of reaction mechanisms: it (1) computes the reaction path by carrying out multiple parallel calculations using initial coordinates provided by the user; (2) monitors the entire workflow process; and (3) tabulates and visualizes the final data in a clear way. The activation strain and canonical energy decomposition results that are generated relate the characteristics of the reaction profile in terms of intrinsic properties (strain, interaction, orbital overlaps, orbital energies, populations) of the reactant species. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Xiaobo Sun
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 1083, 1081 HVAmsterdamNetherlands
| | - Thomas M. Soini
- Software for Chemistry & Materials B.V.De Boelelaan 1083, 1081 HVAmsterdamNetherlands
| | - Jordi Poater
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain and Departament de Química Inorgànica i Orgànica & IQTCUBUniversitat de Barcelona08028BarcelonaCataloniaSpain
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 1083, 1081 HVAmsterdamNetherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale ModelingVrije Universiteit AmsterdamDe Boelelaan 1083, 1081 HVAmsterdamNetherlands
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 135, 6525 AJNijmegenNetherlands
| |
Collapse
|
13
|
A Cu-free clickable surface with controllable surface density. Colloid Polym Sci 2019. [DOI: 10.1007/s00396-019-04515-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
14
|
Hamlin TA, Levandowski BJ, Narsaria AK, Houk KN, Bickelhaupt FM. Structural Distortion of Cycloalkynes Influences Cycloaddition Rates both by Strain and Interaction Energies. Chemistry 2019; 25:6342-6348. [PMID: 30779472 PMCID: PMC6519225 DOI: 10.1002/chem.201900295] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 02/16/2019] [Indexed: 12/27/2022]
Abstract
The reactivities of 2‐butyne, cycloheptyne, cyclooctyne, and cyclononyne in the 1,3‐dipolar cycloaddition reaction with methyl azide were evaluated through DFT calculations at the M06‐2X/6‐311++G(d)//M06‐2X/6‐31+G(d) level of theory. Computed activation free energies for the cycloadditions of cycloalkynes are 16.5–22.0 kcal mol−1 lower in energy than that of the acyclic 2‐butyne. The strained or predistorted nature of cycloalkynes is often solely used to rationalize this significant rate enhancement. Our distortion/interaction–activation strain analysis has been revealed that the degree of geometrical predistortion of the cycloalkyne ground‐state geometries acts to enhance reactivity compared with that of acyclic alkynes through three distinct mechanisms, not only due to (i) a reduced strain or distortion energy, but also to (ii) a smaller HOMO–LUMO gap, and (iii) an enhanced orbital overlap, which both contribute to more stabilizing orbital interactions.
Collapse
Affiliation(s)
- Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Brian J Levandowski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Ayush K Narsaria
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University of Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| |
Collapse
|
15
|
Hamlin TA, Svatunek D, Yu S, Ridder L, Infante I, Visscher L, Bickelhaupt FM. Elucidating the Trends in Reactivity of Aza-1,3-Dipolar Cycloadditions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800572] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Trevor A. Hamlin
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Dennis Svatunek
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute of Applied Synthetic Chemistry; Technische Universität Wien (TU Wien); Getreidemarkt 9 1060 Vienna Austria
| | - Song Yu
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Lars Ridder
- Netherlands eScience Center; Science Park 140 1098 XG Amsterdam The Netherlands
| | - Ivan Infante
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lucas Visscher
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM); Vrije Universiteit Amsterdam; De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials (IMM); Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| |
Collapse
|
16
|
Zhuang B. Introduction. DEVELOPMENT OF A FULLY INTEGRATED “SAMPLE-IN-ANSWER-OUT” SYSTEM FOR AUTOMATIC GENETIC ANALYSIS 2018:1-30. [DOI: 10.1007/978-981-10-4753-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
|
17
|
Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature 2017; 550:345-353. [DOI: 10.1038/nature24286] [Citation(s) in RCA: 552] [Impact Index Per Article: 78.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 12/31/2022]
|
18
|
Tan L, Liu Y, Yang Q, Li X, Wu XY, Gong B, Shen YM, Shao Z. Design and synthesis of fluorescence-labeled nucleotide with a cleavable azo linker for DNA sequencing. Chem Commun (Camb) 2016; 52:954-7. [PMID: 26587573 DOI: 10.1039/c5cc09131d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cleavable azo linker was synthesized and reacted with 5-(6)-carboxytetramethyl rhodamine succinimidyl ester, followed by further reactions with di(N-succinimidyl) carbonate and 5-(3-amino-1-propynyl)-2'-deoxyuridine 5'-triphosphate [dUTP(AP3)] to obtain the terminal product dUTP-azo linker-TAMRA as a potential reversible terminator for DNA sequencing by synthesis with no need for 3'-OH blocking.
Collapse
Affiliation(s)
- Lianjiang Tan
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yazhi Liu
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China. and Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qinglai Yang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Xiaowei Li
- Bio-ID Center, School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Yan Wu
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Bing Gong
- College of Chemistry, Beijing Normal University, Beijing 100875, China and Department of Chemistry, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Yu-Mei Shen
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhifeng Shao
- Bio-ID Center, School of Bio-medical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
19
|
Gade CR, Dixit M, Sharma NK. Dideoxy nucleoside triphosphate (ddNTP) analogues: Synthesis and polymerase substrate activities of pyrrolidinyl nucleoside triphosphates (prNTPs). Bioorg Med Chem 2016; 24:4016-4022. [PMID: 27377861 DOI: 10.1016/j.bmc.2016.06.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 01/05/2023]
Abstract
The dideoxynucleoside triphosphates (ddNTPs) terminate the bio-polymerization of DNA and become essential chemical component of DNA sequencing technology which is now basic tool for molecular biology research. In this method the radiolabeled or fluorescent dye labeled ddNTP analogues are being used for DNA sequencing by detection of the terminated DNA fragment after single labeled ddNTP incorporation into DNA under PCR conditions. This report describes the syntheses of rationally designed novel amino-functionalized ddNTP analogue such as Pyrrolidine nucleoside triphosphates (prNTPs), and their polymerase activities with DNA polymerase by LC-MS and Gel-electrophoretic techniques. The Mass and PAGE analyses strongly support the incorporation of prNTPs into DNA oligonucleotide with Therminator DNA polymerase as like control substrate ddNTP. As resultant the DNA oligonucleotide are functionalized as amine group by prNTP incorporation with polymerase. Hence prNTPs provide opportunities to prepare demandable conjugated DNA with other biomolecules/dyes/fluorescence molecule without modifying nucleobase structure.
Collapse
Affiliation(s)
- Chandrasekhar Reddy Gade
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Jatni 752050, Odisha, India
| | - Manjusha Dixit
- School of Biological Sciences, NISER, Bhubaneswar, Jatni 752050, Odisha, India
| | - Nagendra K Sharma
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Jatni 752050, Odisha, India.
| |
Collapse
|
20
|
Tan L, Liu Y, Li X, Wu XY, Gong B, Shen YM, Shao Z. Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing. Chem Commun (Camb) 2016; 52:2549-52. [PMID: 26744748 DOI: 10.1039/c5cc09578f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.
Collapse
Affiliation(s)
- Lianjiang Tan
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | | | | | | | | | | | | |
Collapse
|
21
|
Flaender M, Costa G, Nonglaton G, Saint-Pierre C, Gasparutto D. A DNA array based on clickable lesion-containing hairpin probes for multiplexed detection of base excision repair activities. Analyst 2016; 141:6208-6216. [DOI: 10.1039/c6an01165a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An electrophoresis-free fluorescent functional assay has been developed to measure DNA repair activities in a miniaturized and parallelized manner.
Collapse
Affiliation(s)
- Mélanie Flaender
- Université Grenoble Alpes
- INAC – SyMMES/CEA
- F-38000 Grenoble
- France
| | - Guillaume Costa
- Université Grenoble Alpes
- LETI/DTBS-SBSC/CEA
- F-38000 Grenoble
- France
| | | | | | | |
Collapse
|
22
|
Karmakar S, Datta A. Metal Free Azide-Alkyne Click Reaction: Role of Substituents and Heavy Atom Tunneling. J Phys Chem B 2015; 119:11540-7. [PMID: 26264958 DOI: 10.1021/acs.jpcb.5b05758] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal free click reactions provide an excellent noninvasive tool to modify and understand the processes in biological systems. Release of ring strain in cyclooctynes on reaction with azides on the formation of triazoles results in small activation energies for various intermolecular Huisgen reactions (1-9). Substitution of difluoro groups at the α, α' position of the cyclooctyne ring enhances the rates of cycloadditions by 10 and 20 times for methyl azide and benzyl azide respectively at room temperature. The computed rate enhancement on difluoro substitution using direct dynamical calculations using the canonical variational transition state theory (CVT/CAG) with small curvature tunneling (SCT) corrections are in excellent agreement with the experimental results. For the intramolecular click reaction (10) notwithstanding its much higher activation energy, quantum mechanical tunneling (QMT) enhances the rate of cycloaddition significantly and increases the N(14)/N(15) primary kinetic isotope effect at 298 K. QMT is shown to be rather efficient in 10 due to a thin barrier of ∼2.4 Å. The present study shows that tunneling effects can be significant for intramolecular click reactions.
Collapse
Affiliation(s)
- Sharmistha Karmakar
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S. C. Mullick Road, Jadavpur - 700032, Kolkata, West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science , 2A and 2B Raja S. C. Mullick Road, Jadavpur - 700032, Kolkata, West Bengal, India
| |
Collapse
|
23
|
Comprehensive transcriptome analysis discovers novel candidate genes related to leaf color in a Lagerstroemia indica yellow leaf mutant. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0317-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
|
24
|
Jiang M, Tang D, Zhao X, Li Q, Zhuang Y, Wei X, Li X, Liu Y, Wu XY, Shao Z, Gong B, Shen YM. Design and synthesis of new acid cleavable linkers for DNA sequencing by synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:774-85. [PMID: 25372993 DOI: 10.1080/15257770.2014.945647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
A new kind of acid sensitive tetrahydrofuranyl (THF) linker was synthesized and then reacted with 5-(6)-carboxytetramethylrhodaminesuccinimidyl ester (5(6)-TAMRA, SE), followed by di(N-succinimidyl) carbonate (DSC) and modified 2'-deoxyuridine triphosphate (dUTP); the final product, as a reversible terminator for DNA sequencing by synthesis (DNA SBS), was given obtained and confirmed by 1H-NMR, 31P-NMR, and HRMS with purity of up to 99%. The synthesized dye-labeled terminator incorporated into DNA strand successfully, and the fluorophore was cleaved completely under acidic conditions. The preliminary results encourage us to explore more acid-sensitive linkers for DNA SBS to increase the cleavage efficiency under weakly acidic conditions.
Collapse
Affiliation(s)
- Min Jiang
- a Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine and Bio-ID Center , Shanghai Jiao Tong University , Shanghai , China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Chen Z, Duan H, Qiao S, Zhou W, Qiu H, Kang L, Xie XS, Huang Y. Fluorogenic sequencing using halogen-fluorescein-labeled nucleotides. Chembiochem 2015; 16:1153-7. [PMID: 25846104 DOI: 10.1002/cbic.201500117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 01/23/2023]
Abstract
Fluorogenic sequencing is a sequencing-by-synthesis technology that combines the advantages of pyrosequencing and fluorescence detection. With native duplex DNA as the major product, we employ polymerase to incorporate the complement- arily matched terminal phosphate-labeled fluorogenic nucleotides into the DNA template and release halogen-fluorescein as the reporter. This red-emitting fluorophore successfully avoids spectral overlap with the autofluorescence background of the flow chip. We fully characterized the enzymatic reaction kinetics of the new substrates, and performed a 35-base sequencing experiment with 60 reaction cycles. Our achievement expands the substrate repertoire for fluorogenic sequencing, and extends the spectral range to obtain better signal-to-background performance.
Collapse
Affiliation(s)
- Zitian Chen
- College of Engineering, Peking University, Beijing 100871 (China) http://www.gene.pku.edu.cn.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Haifeng Duan
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).
| | - Shuo Qiao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Wenxiong Zhou
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Haiwei Qiu
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - Li Kang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China)
| | - X Sunney Xie
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138 (USA)
| | - Yanyi Huang
- College of Engineering, Peking University, Beijing 100871 (China) http://www.gene.pku.edu.cn. .,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871 (China).
| |
Collapse
|
26
|
Abstract
The "$1000 Genome" project has been drawing increasing attention since its launch a decade ago. Nanopore sequencing, the third-generation, is believed to be one of the most promising sequencing technologies to reach four gold standards set for the "$1000 Genome" while the second-generation sequencing technologies are bringing about a revolution in life sciences, particularly in genome sequencing-based personalized medicine. Both of protein and solid-state nanopores have been extensively investigated for a series of issues, from detection of ionic current blockage to field-effect-transistor (FET) sensors. A newly released protein nanopore sequencer has shown encouraging potential that nanopore sequencing will ultimately fulfill the gold standards. In this review, we address advances, challenges, and possible solutions of nanopore sequencing according to these standards.
Collapse
Affiliation(s)
- Yue Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Qiuping Yang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| | - Zhimin Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University Shanghai, China
| |
Collapse
|
27
|
Alapati A, Goetz K, Suk J, Navani M, Al-Tarouti A, Jayasundera T, Tumminia SJ, Lee P, Ayyagari R. Molecular diagnostic testing by eyeGENE: analysis of patients with hereditary retinal dystrophy phenotypes involving central vision loss. Invest Ophthalmol Vis Sci 2014; 55:5510-21. [PMID: 25082885 DOI: 10.1167/iovs.14-14359] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To analyze the genetic test results of probands referred to eyeGENE with a diagnosis of hereditary maculopathy. METHODS Patients with Best macular dystrophy (BMD), Doyne honeycomb retinal dystrophy (DHRD), Sorsby fundus dystrophy (SFD), or late-onset retinal degeneration (LORD) were screened for mutations in BEST1, EFEMP1, TIMP3, and CTRP5, respectively. Patients with pattern dystrophy (PD) were screened for mutations in PRPH2, BEST1, ELOVL4, CTRP5, and ABCA4; patients with cone-rod dystrophy (CRD) were screened for mutations in CRX, ABCA4, PRPH2, ELOVL4, and the c.2513G>A p.Arg838His variant in GUCY2D. Mutation analysis was performed by dideoxy sequencing. Impact of novel variants was evaluated using the computational tool PolyPhen. RESULTS Among the 213 unrelated patients, 38 had BMD, 26 DHRD, 74 PD, 8 SFD, 6 LORD, and 54 CRD; six had both PD and BMD, and one had no specific clinical diagnosis. BEST1 variants were identified in 25 BMD patients, five with novel variants of unknown significance (VUS). Among the five patients with VUS, one was diagnosed with both BMD and PD. A novel EFEMP1 variant was identified in one DHRD patient. TIMP3 novel variants were found in two SFD patients, PRPH2 variants in 14 PD patients, ABCA4 variants in four PD patients, and p.Arg838His GUCY2D mutation in six patients diagnosed with dominant CRD; one patient additionally had a CRX VUS. ABCA4 mutations were identified in 15 patients with recessive CRD. CONCLUSIONS Of the 213 samples, 55 patients (26%) had known causative mutations, and 13 (6%) patients had a VUS that was possibly pathogenic. Overall, selective screening for mutations in BEST1, PRPH2, and ABCA4 would likely yield the highest success rate in identifying the genetic basis for macular dystrophy phenotypes. Because of the overlap in phenotypes between BMD and PD, it would be beneficial to screen genes associated with both diseases.
Collapse
Affiliation(s)
- Akhila Alapati
- Shiley Eye Center, University of California-San Diego, La Jolla, California, United States
| | - Kerry Goetz
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - John Suk
- Shiley Eye Center, University of California-San Diego, La Jolla, California, United States
| | - Mili Navani
- Shiley Eye Center, University of California-San Diego, La Jolla, California, United States
| | - Amani Al-Tarouti
- W. K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Thiran Jayasundera
- W. K. Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States
| | - Santa J Tumminia
- Office of the Director, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Pauline Lee
- Shiley Eye Center, University of California-San Diego, La Jolla, California, United States
| | - Radha Ayyagari
- Shiley Eye Center, University of California-San Diego, La Jolla, California, United States
| |
Collapse
|
28
|
Abstract
The immobilization of DNA molecules onto a solid support is a crucial step in biochip research and related applications. In this work, we report a DNA photolithography method based on photocleavage of 2-nitrobenzyl linker-modified DNA strands. These strands were subjected to ultraviolet light irradiation to generate multiple short DNA strands in a programmable manner. Coupling the toehold-mediated DNA strand-displacement reaction with DNA photolithography enabled the fabrication of a DNA chip surface with multifunctional DNA patterns having complex geometrical structures at the microscale level. The erasable DNA photolithography strategy was developed to allow different paintings on the same chip. Furthermore, the asymmetrical modification of colloidal particles was carried out by using this photolithography strategy. This strategy has broad applications in biosensors, nanodevices, and DNA-nanostructure fabrication.
Collapse
Affiliation(s)
- Fujian Huang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Huaguo Xu
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan 410082, China
- Address correspondence to ,
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Address correspondence to ,
| |
Collapse
|
29
|
Abstract
High-throughput DNA sequencing development for mutation screening and identification is essential to realize the goal of pharmacogenomics and personalized medicine, which will lead to a new era in clinical medicine and healthcare. Molecular engineering approaches to modify the building blocks of DNA by introducing functional groups for purification and detection has led to the development of high-throughput genetic analysis technologies. This review is focused on the following two DNA sequencing approaches. The first approach is based on the use of molecular affinity and mass spectrometry to perform quick and highly accurate mutation screening, heterozygote identification and insertion/deletion detection. The second approach is based on a sequencing-by-synthesis platform that has the potential for generating DNA sequencing data in a massive, parallel manner. The basic principles, fundamental challenges and methods of implementation of these exciting new technologies will be discussed.
Collapse
Affiliation(s)
- Xiaopeng Bai
- Columbia University, Department of Chemical Engineering, NY 10027, USA.
| | | | | |
Collapse
|
30
|
Wu J, Wang J, Tang X. Synthesis of photolabile dUTP analogues and their enzymatic incorporation for DNA labeling. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5034-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
31
|
Tang X, Zhang J, Sun J, Wang Y, Wu J, Zhang L. Caged nucleotides/nucleosides and their photochemical biology. Org Biomol Chem 2013; 11:7814-24. [PMID: 24132515 DOI: 10.1039/c3ob41735b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides and nucleosides are not only key units of DNA/RNA that store genetic information, but are also the regulators of many biological events of our lives. By caging the key functional groups or key residues of nucleotides with photosensitive moieties, it will be possible to trigger biological events of target nucleotides with spatiotemporal resolution and amplitude upon light activation or photomodulate polymerase reactions with the caged nucleotide analogues for next-generation sequencing (NGS) and bioorthogonal labeling. This review highlights three different caging strategies for nucleotides and demonstrates the photochemical biology of these caged nucleotides.
Collapse
Affiliation(s)
- Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing 100191, China.
| | | | | | | | | | | |
Collapse
|
32
|
Bergen K, Betz K, Welte W, Diederichs K, Marx A. Structures of KOD and 9°N DNA polymerases complexed with primer template duplex. Chembiochem 2013; 14:1058-62. [PMID: 23733496 DOI: 10.1002/cbic.201300175] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Indexed: 12/29/2022]
Abstract
Replicate it: Structures of KOD and 9°N DNA polymerases, two enzymes that are widely used to replicate DNA with highly modified nucleotides, were solved at high resolution in complex with primer/template duplex. The data elucidate substrate interaction of the two enzymes and pave the way for further optimisation of the enzymes and substrates.
Collapse
Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | | | | | | | | |
Collapse
|
33
|
Huang F, You M, Han D, Xiong X, Liang H, Tan W. DNA branch migration reactions through photocontrollable toehold formation. J Am Chem Soc 2013; 135:7967-73. [PMID: 23642046 PMCID: PMC3742003 DOI: 10.1021/ja4018495] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Strand displacement cascades are commonly used to make dynamically assembled structures. Particularly, the concept of "toehold-mediated DNA branch migration reactions" has attracted considerable attention in relation to dynamic DNA nanostructures. However, it is a challenge to obtain and control the formation of pure 1:1 ratio DNA duplexes with toehold structures. Here, for the first time, we report a photocontrolled toehold formation method, which is based on the photocleavage of 2-nitrobenzyl linker-embedded DNA hairpin precursor structures. UV light irradiation (λ ≈ 365 nm) of solutions containing these DNA hairpin structures causes the complete cleavage of the nitrobenzyl linker, and pure 1:1 DNA duplexes with toehold structures are easily formed. Our experimental results indicate that the amount of toehold can be controlled by simply changing the dose of UV irradiation and that the resulting toehold structures can be used for subsequent toehold-mediated DNA branch migration reactions, e.g., DNA hybridization chain reactions. This newly established method will find broad application in the construction of light-powered, controllable, and dynamic DNA nanostructures or large-scale DNA circuits.
Collapse
Affiliation(s)
- Fujian Huang
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovative Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Mingxu You
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Da Han
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
| | - Xiangling Xiong
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovative Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Shands Cancer Center and Center for Research at the Interface of Bio/Nano, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, United States
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology and College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University, Changsha, 410082, China
| |
Collapse
|
34
|
Synthesis and enzymatic incorporation of photolabile dUTP analogues into DNA and their applications for DNA labeling. Bioorg Med Chem 2013; 21:6205-11. [PMID: 23719284 DOI: 10.1016/j.bmc.2013.04.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 04/26/2013] [Accepted: 04/30/2013] [Indexed: 11/22/2022]
Abstract
Two novel photolabile nucleotide triphosphate (NTP) analogues were synthesized through Sonogashira coupling and their enzymatic incorporation into DNA was evaluated with three different DNA polymerases (Taq, Vent exo- and T4) by polymerase chain reaction. Both nucleotide triphosphate analogues were recognized by these DNA polymerases as substrates for primer extension. Light irradiation of PCR products removed the photolabile group and released the amino and carboxyl moieties. Further site-specific dual-labeling for oligodeoxynucleotides (ODNs) and random labeling for a long DNA construct with fluorophores were successfully achieved with incorporation of the photolabile amine modified deoxyuridine triphosphate (dUnTP).
Collapse
|
35
|
Obeid S, Busskamp H, Welte W, Diederichs K, Marx A. Interactions of non-polar and "Click-able" nucleotides in the confines of a DNA polymerase active site. Chem Commun (Camb) 2012; 48:8320-2. [PMID: 22766607 DOI: 10.1039/c2cc34181f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modified nucleotides play a paramount role in many cutting-edge biomolecular techniques. The present structural study highlights the plasticity and flexibility of the active site of a DNA polymerase while incorporating non-polar "Click-able" nucleotide analogs and emphasizes new insights into rational design guidelines for modified nucleotides.
Collapse
Affiliation(s)
- Samra Obeid
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | | | | | | | | |
Collapse
|
36
|
Bergen K, Steck AL, Strütt S, Baccaro A, Welte W, Diederichs K, Marx A. Structures of KlenTaq DNA polymerase caught while incorporating C5-modified pyrimidine and C7-modified 7-deazapurine nucleoside triphosphates. J Am Chem Soc 2012; 134:11840-3. [PMID: 22475415 DOI: 10.1021/ja3017889] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.
Collapse
Affiliation(s)
- Konrad Bergen
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 10, 78457 Konstanz, Germany
| | | | | | | | | | | | | |
Collapse
|
37
|
Holzberger B, Strohmeier J, Siegmund V, Diederichsen U, Marx A. Enzymatic synthesis of 8-vinyl- and 8-styryl-2'-deoxyguanosine modified DNA--novel fluorescent molecular probes. Bioorg Med Chem Lett 2012; 22:3136-9. [PMID: 22483394 DOI: 10.1016/j.bmcl.2012.03.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 12/19/2022]
Abstract
Fluorescent analogs of the natural nucleobases are widely used as molecular probes for investigating DNA hybridization and topology. In this study the guanosine analogs 8-vinyl- and 8-styryl-2'-deoxyguanosine were synthesized and converted into the corresponding 5'-triphosphates. These C8 modified nucleotides were processed by various DNA polymerases to create fluorescent DNA. Whereas the 8-styryl modified nucleotide somewhat hampers DNA synthesis 8-vinyl-2'-deoxyguanosine is processed by DNA polymerases emphasizing the broad applicability as a molecular probe for fluorescence spectroscopy.
Collapse
Affiliation(s)
- Bastian Holzberger
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | | | | | | | | |
Collapse
|
38
|
|
39
|
Baccaro A, Steck AL, Marx A. Barcoded nucleotides. Angew Chem Int Ed Engl 2011; 51:254-7. [PMID: 22083884 DOI: 10.1002/anie.201105717] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/15/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Baccaro
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | | | | |
Collapse
|
40
|
Optical waveguides for the evanescent wave-induced cleavage of photolabile linker compounds. Anal Bioanal Chem 2011; 401:777-82. [PMID: 21611735 DOI: 10.1007/s00216-011-5086-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 05/03/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
Abstract
Functional surfaces and especially the control of surface properties depending on external parameters such as light illumination have gained increasing importance in the last few years. We present the characterization of polymers from the cycloolefin (co)polymer class (COC/COP) functionalized with an aminosilane as a basis for the further immobilization of compounds. In a first step, an assay using AlexaFluor®647 fluorescent dye was used to assess surface homogeneity and reproducibility. A coefficient of variation of less than 15% for dot-to-dot and less than 25% for chip-to-chip could be achieved. The same amino-functionalized surfaces were then used to immobilize a biotinylated photolabile linker compound, binding AlexaFluor®647-labeled streptavidin. The linker was photocleaved with high efficiency at λ = 365 nm and P = 0.15 mW/cm(2). Fluorescence measurements show that polymers of the COC/COP class can be used as versatile surfaces for the photoinduced release of compounds immobilized via photolabile linkers.
Collapse
|
41
|
Zhang S, Prud'homme RK, Link AJ. Block copolymer nanoparticles as nanobeads for the polymerase chain reaction. NANO LETTERS 2011; 11:1723-1726. [PMID: 21417430 DOI: 10.1021/nl200271d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
New sequencing technologies based on massively parallel signature sequencing (MPSS) have been developed to reduce the cost of genome sequencing. In some current MPSS platforms, DNA-modified micrometer-scale beads are used to template the polymerase chain reaction (PCR). Reducing the size of the beads to nanoscale can lead to significant improvements in sequencing throughput. To this end, we have assembled polymeric nanobeads that efficiently template PCR, resulting in DNA-decorated "nanobeads" with a high extent of functionalization.
Collapse
Affiliation(s)
- Siyan Zhang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | | | | |
Collapse
|
42
|
Roy NC, Altermann E, Park ZA, McNabb WC. A comparison of analog and Next-Generation transcriptomic tools for mammalian studies. Brief Funct Genomics 2011; 10:135-50. [DOI: 10.1093/bfgp/elr005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
43
|
Litosh VA, Wu W, Stupi BP, Wang J, Morris SE, Hersh MN, Metzker ML. Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates. Nucleic Acids Res 2011; 39:e39. [PMID: 21227920 PMCID: PMC3064798 DOI: 10.1093/nar/gkq1293] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We describe a novel 3′-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2′-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous bacteriophages and lower eukaryotes. A series of 5-(2-nitrobenzyloxy)methyl-dUTP analogs (dU.I–dU.V) were synthesized based on our previous work with photochemically cleavable terminators. These 2-nitrobenzyl alkylated HOMedUTP analogs were characterized with respect to incorporation, single-base termination, nucleotide selectivity and photochemical cleavage properties. Substitution at the α-methylene carbon of 2-nitrobenzyl with alkyl groups of increasing size was discovered as a key structural feature that provided for the molecular tuning of enzymatic properties such as single-base termination and improved nucleotide selectivity over that of natural nucleotides. 5-[(S)-α-tert-Butyl-2-nitrobenzyloxy]methyl-dUTP (dU.V) was identified as an efficient reversible terminator, whereby, sequencing feasibility was demonstrated in a cyclic reversible termination (CRT) experiment using a homopolymer repeat of ten complementary template bases without detectable UV damage during photochemical cleavage steps. These results validate our overall strategy of creating 3′-OH unblocked reversible terminator reagents that, upon photochemical cleavage, transform back into a natural state. Modified nucleotides based on 5-hydroxymethyl-pyrimidines and 7-deaza-7-hydroxymethyl-purines lay the foundation for development of a complete set of four reversible terminators for application in NGS technologies.
Collapse
|
44
|
Structural basis for the synthesis of nucleobase modified DNA by Thermus aquaticus DNA polymerase. Proc Natl Acad Sci U S A 2010; 107:21327-31. [PMID: 21123743 DOI: 10.1073/pnas.1013804107] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Numerous 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with spacious modifications such as dyes and affinity tags like biotin are substrates for DNA polymerases. They are widely employed in many cutting-edge technologies like advanced DNA sequencing approaches, microarrays, and single molecule techniques. Modifications attached to the nucleobase are accepted by many DNA polymerases, and thus, dNTPs bearing nucleobase modifications are predominantly employed. When pyrimidines are used the modifications are almost exclusively at the C5 position to avoid disturbing of Watson-Crick base pairing ability. However, the detailed molecular mechanism by which C5 modifications are processed by a DNA polymerase is poorly understood. Here, we present the first crystal structures of a DNA polymerase from Thermus aquaticus processing two C5 modified substrates that are accepted by the enzyme with different efficiencies. The structures were obtained as ternary complex of the enzyme bound to primer/template duplex with the respective modified dNTP in position poised for catalysis leading to incorporation. Thus, the study provides insights into the incorporation mechanism of the modified nucleotides elucidating how bulky modifications are accepted by the enzyme. The structures show a varied degree of perturbation of the enzyme substrate complexes depending on the nature of the modifications suggesting design principles for future developments of modified substrates for DNA polymerases.
Collapse
|
45
|
|
46
|
Ustinov AV, Stepanova IA, Dubnyakova VV, Zatsepin TS, Nozhevnikova EV, Korshun VA. Modification of nucleic acids using [3 + 2]-dipolar cycloaddition of azides and alkynes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:437-81. [DOI: 10.1134/s1068162010040011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
47
|
Vidal Pinheiro A, Conde J, Parola A, Lima J, Baptista P. Use of cyclodextrins as scavengers of inhibitory photo-products in light controlled in vitro synthesis of RNA. J Photochem Photobiol A Chem 2010. [DOI: 10.1016/j.jphotochem.2010.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
48
|
Guo J, Yu L, Turro NJ, Ju J. An integrated system for DNA sequencing by synthesis using novel nucleotide analogues. Acc Chem Res 2010; 43:551-63. [PMID: 20121268 DOI: 10.1021/ar900255c] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The Human Genome Project has concluded, but its successful completion has increased, rather than decreased, the need for high-throughput DNA sequencing technologies. The possibility of clinically screening a full genome for an individual's mutations offers tremendous benefits, both for pursuing personalized medicine and for uncovering the genomic contributions to diseases. The Sanger sequencing method, although enormously productive for more than 30 years, requires an electrophoretic separation step that, unfortunately, remains a key technical obstacle for achieving economically acceptable full-genome results. Alternative sequencing approaches thus focus on innovations that can reduce costs. The DNA sequencing by synthesis (SBS) approach has shown great promise as a new sequencing platform, with particular progress reported recently. The general fluorescent SBS approach involves (i) incorporation of nucleotide analogs bearing fluorescent reporters, (ii) identification of the incorporated nucleotide by its fluorescent emissions, and (iii) cleavage of the fluorophore, along with the reinitiation of the polymerase reaction for continuing sequence determination. In this Account, we review the construction of a DNA-immobilized chip and the development of novel nucleotide reporters for the SBS sequencing platform. Click chemistry, with its high selectivity and coupling efficiency, was explored for surface immobilization of DNA. The first generation (G-1) modified nucleotides for SBS feature a small chemical moiety capping the 3'-OH and a fluorophore tethered to the base through a chemically cleavable linker; the design ensures that the nucleotide reporters are good substrates for the polymerase. The 3'-capping moiety and the fluorophore on the DNA extension products, generated by the incorporation of the G-1 modified nucleotides, are cleaved simultaneously to reinitiate the polymerase reaction. The sequence of a DNA template immobilized on a surface via click chemistry is unambiguously identified with this chip-SBS system. The second generation (G-2) SBS system was developed based on the concept that the closer the structures of the added nucleotide and the primer are to their natural counterparts, the more faithfully the polymerase would incorporate the nucleotide. In this approach, the polymerase reaction is performed with the combination of 3'-capped nucleotide reversible terminators (NRTs) and cleavable fluorescent dideoxynucleotides (ddNTPs). By sacrifice of a small amount of the primers permanently terminated by ddNTPs, the majority of the primers extended by the reversible terminators are reverted to the natural ones after each sequencing cycle. We have also developed the 3'-capped nucleotide reversible terminators to solve the problem of deciphering the homopolymeric regions of the template in conventional pyrosequencing. The 3'-capping moiety on the DNA extension product temporarily terminates the polymerase reaction, which allows only one nucleotide to be incorporated during each sequencing cycle. Thus, the number of nucleotides in the homopolymeric regions are unambiguously determined using the 3'-capped NRTs. It has been established that millions of DNA templates can be immobilized on a chip surface through a variety of approaches. Therefore, the integration of these high-density DNA chips with the molecular-level SBS approaches described in this Account is expected to generate a high-throughput and accurate DNA sequencing system with wide applications in biological research and health care.
Collapse
Affiliation(s)
- Jia Guo
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, New York 10032
- Department of Chemical Engineering
- Department of Chemistry
| | - Lin Yu
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, New York 10032
- Department of Chemical Engineering
| | | | - Jingyue Ju
- Columbia Genome Center, Columbia University College of Physicians and Surgeons, New York, New York 10032
- Department of Chemical Engineering
| |
Collapse
|
49
|
DING KJ, ZHANG HY, HU HG, ZHAO HM, Guan WJ, Ma YH. Progress of Research on Nanopore-macromolecule Detection. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60022-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
50
|
Haensch C, Hoeppener S, Schubert US. Chemical modification of self-assembled silane based monolayers by surface reactions. Chem Soc Rev 2010; 39:2323-34. [DOI: 10.1039/b920491a] [Citation(s) in RCA: 311] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|