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Khan A, Singh A, Singh P, Kumar R, Ojha KK, Singh VK, Srivastava A. LCN2-Fungal siderophore-iron binding and uptake leads to oxidative stress and cell death in hepatocellular carcinoma cell line HepG2. J Biomol Struct Dyn 2023; 41:12714-12733. [PMID: 36762696 DOI: 10.1080/07391102.2023.2175380] [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] [Received: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
Microorganisms produce non-ribosomal peptides called siderophores for the purpose of iron acquisition. Mammalian immune system is well-known for producing small secretory proteins called lipocalins upon bacterial infection. These proteins sequester siderophores produced by invading bacterial pathogens rendering them unable to acquire iron from the host. However, this is not their sole function. In addition to transferrin and lactoferrin, lipocalins are also known to transport siderophore-bound iron to the host cells. While binding of bacterial siderophores with human lipocalin is well studied, binding of the fungal counterpart is still not confirmed and fully understood. Apart from pathogen-affected cells, developing cancerous cells also show varying expression level of different proteins including those involved in iron transport. The possibility of exogenous fungal siderophore-mediated iron transport via lipocalin and its receptor in mammalian cells has not yet been explored much. In present investigation we have checked differential expression of human lipocalin, LCN2 in hepatocellular carcinoma cell lines HepG2 as well as its normal counterpart WRL-68 and computationally determined the feasibility of LCN2 binding with fungal siderophore. Further in case of a stable complex being formed, whether this complex has the ability to transport iron through its specific receptor was assessed. Also, we have tried to explore possible mechanism of fungal-siderophore mediated oxidative stress leading to significant cell death in cancerous cells. This study will thus be useful towards finding a new way of treating hepatocellular carcinoma via inducing siderophore-mediated cell death in cancerous cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Azmi Khan
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Ashutosh Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Pratika Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Rakesh Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Krishna Kumar Ojha
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Vijay Kumar Singh
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
| | - Amrita Srivastava
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar
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2
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Chen Q, Wu G, Chen H, Li H, Li S, Zhang C, Pang X, Wang L, Zhao L, Shen J. Quantification of Human Oral and Fecal Streptococcus parasanguinis by Use of Quantitative Real-Time PCR Targeting the groEL Gene. Front Microbiol 2020; 10:2910. [PMID: 31921079 PMCID: PMC6933288 DOI: 10.3389/fmicb.2019.02910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/03/2019] [Indexed: 11/13/2022] Open
Abstract
Two pairs of species-specific PCR primers targeting the housekeeping groEL gene, Spa146f-Spa525r and Spa93f-Spa525r, were designed to quantify human oral and fecal Streptococcus parasanguinis. Blast analysis against reference sequences of NCBI nucleotide collection database and the Chaperonin Sequence Database showed the forward primers Spa146f and Spa93f 100% matched only with S. parasanguinis, and the in silico Simulated PCR algorithm showed both primer pairs hit only S. parasanguinis groEL gene in Chaperonin Sequence Database. The two primer pairs were respectively used to perform PCR with saliva DNA of each of 6 human subjects, and the amplicons of individual PCR reactions were cloned. The phylogenetic analysis showed cloned sequences were all affiliated to S. parasanguinis, which further validates the specificity of two primer pairs, and that individual subjects harbored multiple genotypes of S. parasanguinis in saliva. By spiking S. parasanguinis into human fecal samples, we found the quantification limit of quantitative real-time PCR (qPCR) assays for both primer pairs was 5-6 log10 groEL copies/g feces. Human fecal S. parasanguinis amounts quantified with qPCR using each of the two primer pairs correlated well with those determined with metagenomic sequencing. qPCR with either primer pair showed periodontitis patients had significantly lower level of saliva S. parasanguinis than healthy people. In both feces and saliva, the S. parasanguinis abundances quantified with two primer pairs exhibited strong and significant correlation. Our results show that the two S. parasanguinis-specific primer pairs can be used to quantify and profile human saliva and fecal S. parasanguinis.
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Affiliation(s)
- Qiurong Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guojun Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hui Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuo Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyan Pang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linghua Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Liping Zhao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Shen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
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3
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Sarzi DS, Justolin B, Silva CDA, Lemos RPM, Stefenon VM. Discovery and characterization of SSR markers in Eugenia uniflora L. (Myrtaceae) using low coverage genome sequencing. AN ACAD BRAS CIENC 2019; 91:e20180420. [PMID: 30994767 DOI: 10.1590/0001-3765201920180420] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/03/2018] [Indexed: 01/11/2023] Open
Abstract
Eugenia uniflora L. (Myrtaceae) is a tree species widely distributed in South America suffering the effects of the exploitation of natural populations. In this study, we employed low coverage sequencing of the E. uniflora genome for mining of SSR markers. The de novo assembly generated 2,601 contigs with an average length of 1139 bp and spans 3.15 Mb. A total of 76 dimer, 33 trimer and two compound SSR loci were identified. Twelve selected SSR loci were employed to genotype 30 individuals from two natural populations. A total of 73 alleles were detected (mean A= 6.1) were observed, the mean effective number of alleles was Ae = 3.91, mean Ho was 0.23 and mean HE was 0.70). The mean Wright's within population fixation index was FIS = 0.66 and significant deviation of HWE was observed in all loci, except one. The FST between populations equaled 0.27. The levels of genetic diversity and structure estimated with these 12 SSR markers are in accordance with data from genetics studies performed on other tree species of the Pampa biome, presenting moderate to high polymorphism and may be employed in studies of species conservation measures and breeding programs.
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Affiliation(s)
- Deise S Sarzi
- Universidade Federal do Pampa, Núcleo de Ecologia Molecular e Micropropagação de Plantas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil.,Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 07, s/n, Zona Rural, 23890-000 Seropédica, RJ, Brazil
| | - Beatriz Justolin
- Universidade Federal do Pampa, Núcleo de Ecologia Molecular e Micropropagação de Plantas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil
| | - Clariane DA Silva
- Universidade Federal do Pampa, Núcleo de Ecologia Molecular e Micropropagação de Plantas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil
| | - Rafael P M Lemos
- Universidade Federal do Pampa, Núcleo de Ecologia Molecular e Micropropagação de Plantas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil.,Universidade Federal do Pampa Programa de Pós-graduação em Ciências Biológicas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil
| | - Valdir Marcos Stefenon
- Universidade Federal do Pampa, Núcleo de Ecologia Molecular e Micropropagação de Plantas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil.,Universidade Federal do Pampa Programa de Pós-graduação em Ciências Biológicas, Rodovia BR 290, Campus Universitário, 97300-000 São Gabriel, RS, Brazil
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4
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Lemos RPM, Matielo CBD, Beise DC, da Rosa VG, Sarzi DS, Roesch LFW, Stefenon VM. Characterization of Plastidial and Nuclear SSR Markers for Understanding Invasion Histories and Genetic Diversity of Schinus molle L. BIOLOGY 2018; 7:biology7030043. [PMID: 30103413 PMCID: PMC6163545 DOI: 10.3390/biology7030043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 11/16/2022]
Abstract
Invasive plant species are expected to display high dispersal capacity but low levels of genetic diversity due to the founder effect occurring at each invasion episode. Understanding the history of invasions and the levels of genetic diversity of such species is an important task for planning management and monitoring strategy for these events. Peruvian Peppertree (Schinus molle L.) is a pioneer tree species native from South America which was introduced in North America, Europe and Africa, becoming a threat to these non-native habitats. In this study, we report the discovery and characterization of 17 plastidial (ptSSR) and seven nuclear (nSSR) markers for S. molle based on low-coverage whole-genome sequencing data acquired through next-generation sequencing. The markers were tested in 56 individuals from two natural populations sampled in the Brazilian Caatinga and Pampa biomes. All loci are moderately to highly polymorphic and revealed to be suitable for genetic monitoring of new invasions, for understanding the history of old invasions, as well as for genetic studies of native populations in their natural occurrence range and of orchards established with commercial purposes.
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Affiliation(s)
- Rafael Plá Matielo Lemos
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa, São Gabriel ZIP 97307-020, Brazil.
| | | | - Dalvan Carlos Beise
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa, São Gabriel ZIP 97307-020, Brazil.
| | - Vanessa Gonçalves da Rosa
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa, São Gabriel ZIP 97307-020, Brazil.
| | - Deise Schröder Sarzi
- Instituto de Bioquímica Médica Leopoldo de Meis-CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil.
| | - Luiz Fernando Würdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia-CIP-Biotec, Campus São Gabriel, Universidade Federal do Pampa, São Gabriel ZIP 97307-020, Brazil.
| | - Valdir Marcos Stefenon
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa, São Gabriel ZIP 97307-020, Brazil.
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Rodrigues-Luiz GF, Cardoso MS, Valdivia HO, Ayala EV, Gontijo CMF, Rodrigues TDS, Fujiwara RT, Lopes RS, Bartholomeu DC. TipMT: Identification of PCR-based taxon-specific markers. BMC Bioinformatics 2017; 18:104. [PMID: 28187714 PMCID: PMC5303226 DOI: 10.1186/s12859-017-1485-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 01/11/2017] [Indexed: 12/02/2022] Open
Abstract
Background Molecular genetic markers are one of the most informative and widely used genome features in clinical and environmental diagnostic studies. A polymerase chain reaction (PCR)-based molecular marker is very attractive because it is suitable to high throughput automation and confers high specificity. However, the design of taxon-specific primers may be difficult and time consuming due to the need to identify appropriate genomic regions for annealing primers and to evaluate primer specificity. Results Here, we report the development of a Tool for Identification of Primers for Multiple Taxa (TipMT), which is a web application to search and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using Multiplex PCR. This pipeline was applied to the genomes of four species of Leishmania (L. amazonensis, L. braziliensis, L. infantum and L. major) and validated by PCR using artificial genomic DNA mixtures of the Leishmania species as templates. This experimental validation demonstrates the reliability of TipMT because amplification profiles showed discrimination of genomic DNA samples from Leishmania species. Conclusions The TipMT web tool allows for large-scale identification and design of taxon-specific primers and is freely available to the scientific community at http://200.131.37.155/tipMT/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1485-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriela F Rodrigues-Luiz
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana S Cardoso
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Hugo O Valdivia
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edward V Ayala
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Thiago de S Rodrigues
- Departamento de Computação, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ricardo T Fujiwara
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Robson S Lopes
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Computação, Universidade Federal do Mato Grosso, Barra do Garças, Mato Grosso, Brazil
| | - Daniella C Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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6
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Srivastava D, Shanker A. Identification of Simple Sequence Repeats in Chloroplast Genomes of Magnoliids Through Bioinformatics Approach. Interdiscip Sci 2015; 8:327-336. [PMID: 26471998 DOI: 10.1007/s12539-015-0129-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 06/11/2015] [Accepted: 09/30/2015] [Indexed: 10/22/2022]
Abstract
Basal angiosperms or Magnoliids is an important clade of commercially important plants which mainly include spices and edible fruits. In this study, 17 chloroplast genome sequences belonging to clade Magnoliids were screened for the identification of chloroplast simple sequence repeats (cpSSRs). Simple sequence repeats or microsatellites are short stretches of DNA up to 1-6 base pair in length. These repeats are ubiquitous and play important role in the development of molecular markers and to study the mapping of traits of economic, medical or ecological interest. A total of 479 SSRs were detected, showing average density of 1 SSR/6.91 kb. Depending on the repeat units, the length of SSRs ranged from 12 to 24 bp for mono-, 12 to 18 bp for di-, 12 to 26 bp for tri-, 12 to 24 bp for tetra-, 15 bp for penta- and 18 bp for hexanucleotide repeats. Mononucleotide repeats were the most frequent (207, 43.21 %) followed by tetranucleotide repeats (130, 27.13 %). Penta- and hexanucleotide repeats were least frequent or absent in these chloroplast genomes.
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Affiliation(s)
- Deepika Srivastava
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304022, India
| | - Asheesh Shanker
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Banasthali, Rajasthan, 304022, India.
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7
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Abstract
This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a program to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, and linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with CG or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyzes sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and online version at http://primerdigital.com/tools/pcr.html .
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8
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Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 2011; 98:137-44. [PMID: 21569836 DOI: 10.1016/j.ygeno.2011.04.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 04/22/2011] [Accepted: 04/25/2011] [Indexed: 11/23/2022]
Abstract
The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.
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9
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Victoria FC, da Maia LC, de Oliveira AC. In silico comparative analysis of SSR markers in plants. BMC PLANT BIOLOGY 2011; 11:15. [PMID: 21247422 PMCID: PMC3037304 DOI: 10.1186/1471-2229-11-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
BACKGROUND The adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes. RESULTS In this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools. CONCLUSIONS The comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.
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Affiliation(s)
- Filipe C Victoria
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
- Graduate Program in Biotechnology, Universidade Federal de Pelotas, RS, Brasil
| | - Luciano C da Maia
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil
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10
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Gans JD, Wolinsky M. Improved assay-dependent searching of nucleic acid sequence databases. Nucleic Acids Res 2008; 36:e74. [PMID: 18515842 PMCID: PMC2475610 DOI: 10.1093/nar/gkn301] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMan™ probe (i.e. in silico or ‘virtual’ PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature.
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Affiliation(s)
- Jason D Gans
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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11
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Arányi T, Váradi A, Simon I, Tusnády GE. The BiSearch web server. BMC Bioinformatics 2006; 7:431. [PMID: 17022803 PMCID: PMC1609187 DOI: 10.1186/1471-2105-7-431] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 10/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large number of PCR primer-design softwares are available online. However, only very few of them can be used for the design of primers to amplify bisulfite-treated DNA templates, necessary to determine genomic DNA methylation profiles. Indeed, the number of studies on bisulfite-treated templates exponentially increases as determining DNA methylation becomes more important in the diagnosis of cancers. Bisulfite-treated DNA is difficult to amplify since undesired PCR products are often amplified due to the increased sequence redundancy after the chemical conversion. In order to increase the efficiency of PCR primer-design, we have developed BiSearch web server, an online primer-design tool for both bisulfite-treated and native DNA templates. RESULTS The web tool is composed of a primer-design and an electronic PCR (ePCR) algorithm. The completely reformulated ePCR module detects potential mispriming sites as well as undesired PCR products on both cDNA and native or bisulfite-treated genomic DNA libraries. Due to the new algorithm of the current version, the ePCR module became approximately hundred times faster than the previous one and gave the best performance when compared to other web based tools. This high-speed ePCR analysis made possible the development of the new option of high-throughput primer screening. BiSearch web server can be used for academic researchers at the http://bisearch.enzim.hu site. CONCLUSION BiSearch web server is a useful tool for primer-design for any DNA template and especially for bisulfite-treated genomes. The ePCR tool for fast detection of mispriming sites and alternative PCR products in cDNA libraries and native or bisulfite-treated genomes are the unique features of the new version of BiSearch software.
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Affiliation(s)
- Tamás Arányi
- lnstitute of Enzymology, BRC, HAS, H-1113 Karolina út 29, Budapest, Hungary
| | - András Váradi
- lnstitute of Enzymology, BRC, HAS, H-1113 Karolina út 29, Budapest, Hungary
| | - István Simon
- lnstitute of Enzymology, BRC, HAS, H-1113 Karolina út 29, Budapest, Hungary
| | - Gábor E Tusnády
- lnstitute of Enzymology, BRC, HAS, H-1113 Karolina út 29, Budapest, Hungary
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12
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Andreson R, Reppo E, Kaplinski L, Remm M. GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics 2006; 7:172. [PMID: 16566824 PMCID: PMC1450303 DOI: 10.1186/1471-2105-7-172] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 03/27/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments. RESULTS In order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences. CONCLUSION The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10,000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.
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Affiliation(s)
- Reidar Andreson
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
| | | | - Lauris Kaplinski
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - Maido Remm
- Department of Bioinformatics, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
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