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Marpaung DSS, Sinaga AOY, Damayanti D, Taharuddin T. Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation. ANAL SCI 2024; 40:1225-1237. [PMID: 38607600 DOI: 10.1007/s44211-024-00566-y] [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: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
The escalating threat of emerging diseases, often stemming from contaminants and lethal pathogens, has precipitated a heightened demand for sophisticated diagnostic tools. Within this landscape, the functional nucleic acid (FNA) biosensor, harnessing the power of single-stranded DNA (ssDNA), has emerged as a preeminent choice for target analyte detection. However, the dependence on ssDNA has raised difficulties in realizing it in biological samples. Therefore, the production of high-quality ssDNA from biological samples is critical. This review aims to discuss strategies for generating ssDNA from biological samples for integration into biosensors. Several innovative strategies for ssDNA generation have been deployed, encompassing techniques, such as asymmetric PCR, Exonuclease-PCR, isothermal amplification, biotin-streptavidin PCR, transcription-reverse transcription, ssDNA overhang generation, and urea denaturation PAGE. These approaches have been seamlessly integrated with biosensors for biological sample analysis, ushering in a new era of disease detection and monitoring. This amalgamation of ssDNA generation techniques with biosensing applications holds significant promise, not only in improving the speed and accuracy of diagnostic processes but also in fortifying the global response to deadly diseases, thereby underlining the pivotal role of cutting-edge biotechnology in public health and disease prevention.
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Affiliation(s)
- David Septian Sumanto Marpaung
- Department of Biosystems Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia.
| | - Ayu Oshin Yap Sinaga
- Department of Biology, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Damayanti Damayanti
- Department of Chemical Engineering, Institut Teknologi Sumatera, Jl. Terusan Ryacudu, Way Huwi, Kec. Jati Agung, Lampung Selatan, Lampung, 35365, Indonesia
| | - Taharuddin Taharuddin
- Department of Chemical Engineering, University of Lampung, Jl. Prof. Dr. Ir. Sumantri Brojonegoro No.1, Gedong Meneng, Kec. Rajabasa, Kota Bandar Lampung, Lampung, 35141, Indonesia
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Ding S, Chen R, Chen G, Li M, Wang J, Zou J, Du F, Dong J, Cui X, Huang X, Deng Y, Tang Z. One-step colorimetric genotyping of single nucleotide polymorphism using probe-enhanced loop-mediated isothermal amplification (PE-LAMP). Am J Cancer Res 2019; 9:3723-3731. [PMID: 31281509 PMCID: PMC6587344 DOI: 10.7150/thno.33980] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/10/2019] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphism (SNP) is the most abundant molecular marker associated with many physiologic and pathologic phenotypes. An isothermal, accurate and cost-effective SNP detection could make a great difference in point-of-care testing (POCT) or on-site diagnosis. However, there are two challenges, the expensive instrument and labor-intensive process, faced by the development of on-site SNP detection. We reported a novel SNP typing method based on the probe-enhanced loop-mediated isothermal amplification (PE-LAMP), which combines the oligonucleotide probe with a conventional LAMP to realize the SNP discrimination by analyzing the great discrepancy in amplification efficiency. Methods: We firstly constructed the genotyping method by combining the hybridization of the specific probe with the powerful amplification of LAMP. Then we validated the method by genotyping the SNP rs3741219 and we sought to realize one-step visualized typing. Finally, we applied the method to pharmacogenomic testing by genotyping CYP2C19*2 and MDR1 C3435T. Results: The PE-LAMP was successfully constructed to detect SNP and the sensitivity of our method is as low as 1000 copies of target DNA, which is sufficient to routine diagnosis. The high specificity in detecting mutant in the presence of excess wild-type allele could be achieved. It has shown good performance in helping predict the individual response of antiplatelet drug Clopidogrel through typing simply treated saliva samples. Conclusions: The proposed method is one-step, colorimetric, specific and sensitive enough to detect crudely treated samples, showing great potential in the pharmacogenomic study and POCT use.
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Merrick CJ, Jiang RHY, Skillman KM, Samarakoon U, Moore RM, Dzikowski R, Ferdig MT, Duraisingh MT. Functional analysis of sirtuin genes in multiple Plasmodium falciparum strains. PLoS One 2015; 10:e0118865. [PMID: 25780929 PMCID: PMC4364008 DOI: 10.1371/journal.pone.0118865] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 01/07/2015] [Indexed: 12/22/2022] Open
Abstract
Plasmodium falciparum, the causative agent of severe human malaria, employs antigenic variation to avoid host immunity. Antigenic variation is achieved by transcriptional switching amongst polymorphic var genes, enforced by epigenetic modification of chromatin. The histone-modifying 'sirtuin' enzymes PfSir2a and PfSir2b have been implicated in this process. Disparate patterns of var expression have been reported in patient isolates as well as in cultured strains. We examined var expression in three commonly used laboratory strains (3D7, NF54 and FCR-3) in parallel. NF54 parasites express significantly lower levels of var genes compared to 3D7, despite the fact that 3D7 was originally a clone of the NF54 strain. To investigate whether this was linked to the expression of sirtuins, genetic disruption of both sirtuins was attempted in all three strains. No dramatic changes in var gene expression occurred in NF54 or FCR-3 following PfSir2b disruption, contrasting with previous observations in 3D7. In 3D7, complementation of the PfSir2a genetic disruption resulted in a significant decrease in previously-elevated var gene expression levels, but with the continued expression of multiple var genes. Finally, rearranged chromosomes were observed in the 3D7 PfSir2a knockout line. Our results focus on the potential for parasite genetic background to contribute to sirtuin function in regulating virulence gene expression and suggest a potential role for sirtuins in maintaining genome integrity.
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Affiliation(s)
- Catherine J. Merrick
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Rays H. Y. Jiang
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Kristen M. Skillman
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Rachel M. Moore
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Michael T. Ferdig
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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4
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Panova M, Johansson T, Canbäck B, Bentzer J, Rosenblad MA, Johannesson K, Tunlid A, André C. Species and gene divergence in Littorina snails detected by array comparative genomic hybridization. BMC Genomics 2014; 15:687. [PMID: 25135785 PMCID: PMC4148934 DOI: 10.1186/1471-2164-15-687] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background Array comparative genomic hybridization (aCGH) is commonly used to screen different types of genetic variation in humans and model species. Here, we performed aCGH using an oligonucleotide gene-expression array for a non-model species, the intertidal snail Littorina saxatilis. First, we tested what types of genetic variation can be detected by this method using direct re-sequencing and comparison to the Littorina genome draft. Secondly, we performed a genome-wide comparison of four closely related Littorina species: L. fabalis, L. compressa, L. arcana and L. saxatilis and of populations of L. saxatilis found in Spain, Britain and Sweden. Finally, we tested whether we could identify genetic variation underlying “Crab” and “Wave” ecotypes of L. saxatilis. Results We could reliably detect copy number variations, deletions and high sequence divergence (i.e. above 3%), but not single nucleotide polymorphisms. The overall hybridization pattern and number of significantly diverged genes were in close agreement with earlier phylogenetic reconstructions based on single genes. The trichotomy of L. arcana, L. compressa and L. saxatilis could not be resolved and we argue that these divergence events have occurred recently and very close in time. We found evidence for high levels of segmental duplication in the Littorina genome (10% of the transcripts represented on the array and up to 23% of the analyzed genomic fragments); duplicated genes and regions were mostly the same in all analyzed species. Finally, this method discriminated geographically distant populations of L. saxatilis, but we did not detect any significant genome divergence associated with ecotypes of L. saxatilis. Conclusions The present study provides new information on the sensitivity and the potential use of oligonucleotide arrays for genotyping of non-model organisms. Applying this method to Littorina species yields insights into genome evolution following the recent species radiation and supports earlier single-gene based phylogenies. Genetic differentiation of L. saxatilis ecotypes was not detected in this study, despite pronounced innate phenotypic differences. The reason may be that these differences are due to single-nucleotide polymorphisms. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-687) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Panova
- Department of Biological and Environmental Sciences - Tjärnö, Gothenburg University, Gothenburg, Sweden.
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5
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Nair SC, Pattaradilokrat S, Zilversmit MM, Dommer J, Nagarajan V, Stephens MT, Xiao W, Tan JC, Su XZ. Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii. Mol Biochem Parasitol 2014; 194:9-15. [PMID: 24685548 DOI: 10.1016/j.molbiopara.2014.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 03/14/2014] [Accepted: 03/20/2014] [Indexed: 11/18/2022]
Abstract
The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes.
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Affiliation(s)
- Sethu C Nair
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sittiporn Pattaradilokrat
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Martine M Zilversmit
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer Dommer
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vijayaraj Nagarajan
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melissa T Stephens
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Wenming Xiao
- Metabolism Branch, National Cancer Institutes, National Institutes of Health, Bethesda, MD 20892, USA
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Comprehensive analysis of prokaryotes in environmental water using DNA microarray analysis and whole genome amplification. Pathogens 2013; 2:591-605. [PMID: 25437334 PMCID: PMC4235703 DOI: 10.3390/pathogens2040591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022] Open
Abstract
The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.
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Flannery EL, Fidock DA, Winzeler EA. Using genetic methods to define the targets of compounds with antimalarial activity. J Med Chem 2013; 56:7761-71. [PMID: 23927658 DOI: 10.1021/jm400325j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although phenotypic cellular screening has been used to drive antimalarial drug discovery in recent years, in some cases target-based drug discovery remains more attractive. This is especially true when appropriate high-throughput cellular assays are lacking, as is the case for drug discovery efforts that aim to provide a replacement for primaquine (4-N-(6-methoxyquinolin-8-yl)pentane-1,4-diamine), the only drug that can block Plasmodium transmission to Anopheles mosquitoes and eliminate liver-stage hypnozoites. At present, however, there are no known chemically validated parasite protein targets that are important in all Plasmodium parasite developmental stages and that can be used in traditional biochemical compound screens. We propose that a plethora of novel, chemically validated, cross-stage antimalarial targets still remain to be discovered from the ~5,500 proteins encoded by the Plasmodium genomes. Here we discuss how in vitro evolution of drug-resistant strains of Plasmodium falciparum and subsequent whole-genome analysis can be used to find the targets of some of the many compounds discovered in whole-cell phenotypic screens.
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Affiliation(s)
- Erika L Flannery
- Department of Pediatrics, University of California, San Diego, School of Medicine , 9500 Gilman Drive 0741, La Jolla, California 92093, United States
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8
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Guler JL, Freeman DL, Ahyong V, Patrapuvich R, White J, Gujjar R, Phillips MA, DeRisi J, Rathod PK. Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications. PLoS Pathog 2013; 9:e1003375. [PMID: 23717205 PMCID: PMC3662640 DOI: 10.1371/journal.ppat.1003375] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
Malaria drug resistance contributes to up to a million annual deaths. Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites. Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorotate dehydrogenase (DHODH) inhibitor reproducibly selected for resistant parasites. Genome-wide analysis of independently-derived resistant clones revealed a two-step strategy to evolutionary success. Some haploid blood-stage parasites first survive antimalarial pressure through fortuitous DNA duplications that always included the DHODH gene. Independently-selected parasites had different sized amplification units but they were always flanked by distant A/T tracks. Higher level amplification and resistance was attained using a second, more efficient and more accurate, mechanism for head-to-tail expansion of the founder unit. This second homology-based process could faithfully tune DNA copy numbers in either direction, always retaining the unique DNA amplification sequence from the original A/T-mediated duplication for that parasite line. Pseudo-polyploidy at relevant genomic loci sets the stage for gaining additional mutations at the locus of interest. Overall, we reveal a population-based genomic strategy for mutagenesis that operates in human stages of P. falciparum to efficiently yield resistance-causing genetic changes at the correct locus in a successful parasite. Importantly, these founding events arise with precision; no other new amplifications are seen in the resistant haploid blood stage parasite. This minimizes the need for meiotic genetic cleansing that can only occur in sexual stage development of the parasite in mosquitoes. Malaria parasites kill up to a million people around the world every year. Emergence of resistance to drugs remains a key obstacle against elimination of malaria. In the laboratory, parasites can efficiently acquire resistance to experimental antimalarials by changing DNA at the target locus. This happens efficiently even for an antimalarial that the parasite has never encountered in a clinical setting. In this study, we formally demonstrate how parasites achieve this feat: first, individual parasites in a population of millions randomly amplify large regions of DNA between short sequence repeats of adenines (A) or thymines (T) that are peppered throughout the malaria parasite genome. The rare lucky parasite that amplifies DNA coding for the target of the antimalarial, along with dozens of its neighboring genes, gains an evolutionary advantage and survives. In a second step, to withstand increasing drug pressure and to achieve higher levels of resistance, each parasite line makes additional copies of this region. This second expansion does not rely on the random A/T-based DNA rearrangements but, instead, a more precise amplification mechanism that retains the unique signature of co-amplified genes created earlier in each parasite. Generation of multiple copies of the target genes in the parasite genome may be the beginning of other beneficial changes for the parasite, including the future acquisition of mutations.
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Affiliation(s)
- Jennifer L. Guler
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Daniel L. Freeman
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Vida Ahyong
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Rapatbhorn Patrapuvich
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - John White
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Ramesh Gujjar
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
| | - Margaret A. Phillips
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Joseph DeRisi
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Pradipsinh K. Rathod
- Departments of Chemistry and Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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9
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Singh R. Signal oscillation is another reason for variability in microarray-based gene expression quantification. PLoS One 2013; 8:e54753. [PMID: 23349963 PMCID: PMC3549950 DOI: 10.1371/journal.pone.0054753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Microarrays have been widely used for various biological applications, such as, gene expression profiling, determination of SNPs, and disease profiling. However, quantification and analysis of microarray data have been a challenge. Previously, by taking into account translational and rotational diffusion of the target DNA, we have shown that the rate of hybridization depends on its size. Here, by mathematical modeling of surface diffusion of transcript, we show that the dynamics of hybridization on DNA microarray surface is inherently oscillatory and the amplitude of oscillation depends on fluid velocity. We found that high fluid velocity enhances the signal without affecting the background, and reduces the oscillation, thereby reducing likelihood of inter- and intra-experiment variability. We further show that a strong probe reduces dependence of signal-to-noise ratio on probe strength, decreasing inter-microarray variability. On the other hand, weaker probes are required for SNP detection. Therefore, we recommend high fluid velocity and strong probes for all microarray applications except determination of SNPs. For SNP detection, we recommend high fluid velocity with weak probe on the spot. We also recommend a surface with high adsorption and desorption rates of transcripts.
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Affiliation(s)
- Raghvendra Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur, India.
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10
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Cai H, Zhou Z, Gu J, Wang Y. Comparative Genomics and Systems Biology of Malaria Parasites Plasmodium.. Curr Bioinform 2012; 7. [PMID: 24298232 DOI: 10.2174/157489312803900965] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Malaria is a serious infectious disease that causes over one million deaths yearly. It is caused by a group of protozoan parasites in the genus Plasmodium. No effective vaccine is currently available and the elevated levels of resistance to drugs in use underscore the pressing need for novel antimalarial targets. In this review, we survey omics centered developments in Plasmodium biology, which have set the stage for a quantum leap in our understanding of the fundamental processes of the parasite life cycle and mechanisms of drug resistance and immune evasion.
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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11
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Kundu LM, Tsukada H, Matsuoka Y, Kanayama N, Takarada T, Maeda M. Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis. Anal Chem 2012; 84:5204-9. [PMID: 22624952 DOI: 10.1021/ac301025m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Upon applying a voltage, the DNA hairpin migrated slowly compared to a random sequence ssDNA in the presence of the PNA probe. This retardation was induced by strand invasion of the PNA into the DNA hairpin to form a hybridized complex, where the PEG segment received a large amount of hydrodynamic friction during electrophoresis. The binding constant between the PNA probe and the DNA hairpin was easily determined by mobility analysis. This simple method would be potentially beneficial in studying binding behaviors of various artificial nucleotides to natural DNA or RNA.
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Affiliation(s)
- Lal Mohan Kundu
- Bioengineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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12
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Abstract
Malaria is an important human disease and is the target of a global eradication campaign. New technological and informatics advancements in population genomics are being leveraged to identify genetic loci under selection in the malaria parasite and to find variants that are associated with key clinical phenotypes, such as drug resistance. This article provides a timely Review of how population-genetics-based strategies are being applied to Plasmodium falciparum both to identify genetic loci as key targets of interventions and to develop monitoring and surveillance tools that are crucial for the successful elimination and eradication of malaria.
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Application of genomics to field investigations of malaria by the international centers of excellence for malaria research. Acta Trop 2012; 121:324-32. [PMID: 22182668 DOI: 10.1016/j.actatropica.2011.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 11/28/2011] [Accepted: 12/02/2011] [Indexed: 12/15/2022]
Abstract
Success of the global research agenda toward eradication of malaria will depend on development of new tools, including drugs, vaccines, insecticides and diagnostics. Genomic information, now available for the malaria parasites, their mosquito vectors, and human host, can be leveraged to both develop these tools and monitor their effectiveness. Although knowledge of genomic sequences for the malaria parasites, Plasmodium falciparum and Plasmodium vivax, have helped advance our understanding of malaria biology, simply knowing this sequence information has not yielded a plethora of new interventions to reduce the burden of malaria. Here we review and provide specific examples of how genomic information has increased our knowledge of parasite biology, focusing on P. falciparum malaria. We then discuss how population genetics can be applied toward the epidemiological and transmission-related goals outlined by the International Centers of Excellence for Malaria Research groups recently established by the National Institutes of Health. Finally, we propose genomics is a research area that can promote coordination and collaboration between various ICEMR groups, and that working together as a community can significantly advance the value of this information toward reduction of the global malaria burden.
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14
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Nguyen C, Grimes J, Gerasimova YV, Kolpashchikov DM. Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids. Chemistry 2011; 17:13052-8. [PMID: 21956816 PMCID: PMC3221966 DOI: 10.1002/chem.201101987] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Indexed: 01/13/2023]
Abstract
Hybridization probes are often inefficient in the analysis of single-stranded DNA or RNA that are folded in stable secondary structures. A molecular beacon (MB) probe is a short DNA hairpin with a fluorophore and a quencher attached to opposite sides of the oligonucleotide. The probe is widely used in real-time analysis of specific DNA and RNA sequences. This study demonstrates how a conventional MB probe can be used for the analysis of nucleic acids that form very stable (T(m) > 80 °C) hairpin structures. Here we demonstrate that the MB probe is not efficient in direct analysis of secondary structure-folded analytes, whereas a MB-based tricomponent probe is suitable for these purposes. The tricomponent probe takes advantage of two oligonucleotide adaptor strands f and m. Each adaptor strand contains a fragment complementary to the analyte and a fragment complementary to a MB probe. In the presence of a specific analyte, the two adaptor strands hybridize to the analyte and the MB probe, thus forming a quadripartite complex. DNA strand f binds to the analyte with high affinity and unwinds its secondary structure. Strand m forms a stable complex only with the fully complementary analyte. The MB probe fluorescently reports the formation of the quadripartite associate. It was demonstrated that the DNA analytes folded in hairpin structures with stems containing 5, 6, 7, 8, 9, 11, or 13 base pairs can be detected in real time with the limit of detection (LOD) lying in the nanomolar range. The stability of the stem region in the DNA analyte did not affect the LOD. Analytes containing single base substitutions in the stem or in the loop positions were discriminated from the fully complementary DNA at room temperature. The tricomponent probe promises to simplify nucleic acid analysis at ambient temperatures in such applications as in vivo RNA monitoring, detection of pathogens, and single nucleotide polymorphism (SNP) genotyping by DNA microarrays.
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Affiliation(s)
- Camha Nguyen
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Jeffrey Grimes
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Yulia V. Gerasimova
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
| | - Dmitry M. Kolpashchikov
- Camha Nguyen, Jeffrey Grimes, Dr. Y. V. Gerasimova, Dr. D. M. Kolpashchikov Chemistry Department University of Central Florida 4000 Central Florida Blvd., Orlando, FL 32816, USA
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15
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Samarakoon U, Gonzales JM, Patel JJ, Tan A, Checkley L, Ferdig MT. The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross. BMC Genomics 2011; 12:457. [PMID: 21936954 PMCID: PMC3191341 DOI: 10.1186/1471-2164-12-457] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 09/22/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs. RESULTS We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation. CONCLUSIONS CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.
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Affiliation(s)
- Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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16
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Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet 2011; 7:e1001383. [PMID: 21533027 PMCID: PMC3080868 DOI: 10.1371/journal.pgen.1001383] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 03/25/2011] [Indexed: 11/25/2022] Open
Abstract
The Plasmodium falciparum parasite's ability to adapt to
environmental pressures, such as the human immune system and antimalarial drugs,
makes malaria an enduring burden to public health. Understanding the genetic
basis of these adaptations is critical to intervening successfully against
malaria. To that end, we created a high-density genotyping array that assays
over 17,000 single nucleotide polymorphisms (∼1 SNP/kb), and applied it to
57 culture-adapted parasites from three continents. We characterized genome-wide
genetic diversity within and between populations and identified numerous loci
with signals of natural selection, suggesting their role in recent adaptation.
In addition, we performed a genome-wide association study (GWAS), searching for
loci correlated with resistance to thirteen antimalarials; we detected both
known and novel resistance loci, including a new halofantrine resistance locus,
PF10_0355. Through functional testing we demonstrated that
PF10_0355 overexpression decreases sensitivity to
halofantrine, mefloquine, and lumefantrine, but not to structurally unrelated
antimalarials, and that increased gene copy number mediates resistance. Our GWAS
and follow-on functional validation demonstrate the potential of genome-wide
studies to elucidate functionally important loci in the malaria parasite
genome. Malaria infection with the human pathogen Plasmodium falciparum
results in almost a million deaths each year, mostly in African children.
Efforts to eliminate malaria are underway, but the parasite is adept at eluding
both the human immune response and antimalarial treatments. Thus, it is
important to understand how the parasite becomes resistant to drugs and to
develop strategies to overcome resistance mechanisms. Toward this end, we used
population genetic strategies to identify genetic loci that contribute to
parasite adaptation and to identify candidate genes involved in drug resistance.
We examined over 17,000 genetic variants across the parasite genome in over 50
strains in which we also measured responses to many known antimalarial
compounds. We found a number of genetic loci showing signs of recent natural
selection and a number of loci potentially involved in modulating the
parasite's response to drugs. We further demonstrated that one of the novel
candidate genes (PF10_0355) modulates resistance to the
antimalarial compounds halofantrine, mefloquine, and lumefantrine. Overall, this
study confirms that we can use genome-wide approaches to identify clinically
relevant genes and demonstrates through functional testing that at least one of
these candidate genes is indeed involved in antimalarial drug resistance.
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17
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Tan JC, Miller BA, Tan A, Patel JJ, Cheeseman IH, Anderson TJC, Manske M, Maslen G, Kwiatkowski DP, Ferdig MT. An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations. Genome Biol 2011; 12:R35. [PMID: 21477297 PMCID: PMC3218861 DOI: 10.1186/gb-2011-12-4-r35] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/04/2011] [Accepted: 04/08/2011] [Indexed: 11/13/2022] Open
Abstract
We present an optimized probe design for copy number variation (CNV) and SNP genotyping in the Plasmodium falciparum genome. We demonstrate that variable length and isothermal probes are superior to static length probes. We show that sample preparation and hybridization conditions mitigate the effects of host DNA contamination in field samples. The microarray and workflow presented can be used to identify CNVs and SNPs with 95% accuracy in a single hybridization, in field samples containing up to 92% human DNA contamination.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA
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18
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-time SNP analysis in secondary-structure-folded nucleic acids. Angew Chem Int Ed Engl 2011; 49:8950-3. [PMID: 20963740 DOI: 10.1002/anie.201004475] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jeffrey Grimes
- Chemistry Department, University of Central Florida, 4000 Central Blvd, Orlando, FL 32816, USA
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19
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Samarakoon U, Regier A, Tan A, Desany BA, Collins B, Tan JC, Emrich SJ, Ferdig MT. High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum. BMC Genomics 2011; 12:116. [PMID: 21324207 PMCID: PMC3055840 DOI: 10.1186/1471-2164-12-116] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 02/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knowledge of the origins, distribution, and inheritance of variation in the malaria parasite (Plasmodium falciparum) genome is crucial for understanding its evolution; however the 81% (A+T) genome poses challenges to high-throughput sequencing technologies. We explore the viability of the Roche 454 Genome Sequencer FLX (GS FLX) high throughput sequencing technology for both whole genome sequencing and fine-resolution characterization of genetic exchange in malaria parasites. RESULTS We present a scheme to survey recombination in the haploid stage genomes of two sibling parasite clones, using whole genome pyrosequencing that includes a sliding window approach to predict recombination breakpoints. Whole genome shotgun (WGS) sequencing generated approximately 2 million reads, with an average read length of approximately 300 bp. De novo assembly using a combination of WGS and 3 kb paired end libraries resulted in contigs ≤ 34 kb. More than 8,000 of the 24,599 SNP markers identified between parents were genotyped in the progeny, resulting in a marker density of approximately 1 marker/3.3 kb and allowing for the detection of previously unrecognized crossovers (COs) and many non crossover (NCO) gene conversions throughout the genome. CONCLUSIONS By sequencing the 23 Mb genomes of two haploid progeny clones derived from a genetic cross at more than 30× coverage, we captured high resolution information on COs, NCOs and genetic variation within the progeny genomes. This study is the first to resequence progeny clones to examine fine structure of COs and NCOs in malaria parasites.
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Affiliation(s)
- Upeka Samarakoon
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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20
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Anderson T, Nkhoma S, Ecker A, Fidock D. How can we identify parasite genes that underlie antimalarial drug resistance? Pharmacogenomics 2011; 12:59-85. [PMID: 21174623 PMCID: PMC3148835 DOI: 10.2217/pgs.10.165] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This article outlines genome-scale approaches that can be used to identify mutations in malaria (Plasmodium) parasites that underlie drug resistance and contribute to treatment failure. These approaches include genetic mapping by linkage or genome-wide association studies, drug selection and characterization of resistant mutants, and the identification of genome regions under strong recent selection. While these genomic approaches can identify candidate resistance loci, genetic manipulation is needed to demonstrate causality. We therefore also describe the growing arsenal of available transfection approaches for direct incrimination of mutations suspected to play a role in resistance. Our intention is both to review past progress and highlight promising approaches for future investigations.
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Affiliation(s)
- Tim Anderson
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, TX 78245, USA.
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21
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Grimes J, Gerasimova YV, Kolpashchikov DM. Real-Time SNP Analysis in Secondary-Structure-Folded Nucleic Acids. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Dharia NV, Plouffe D, Bopp SER, González-Páez GE, Lucas C, Salas C, Soberon V, Bursulaya B, Kochel TJ, Bacon DJ, Winzeler EA. Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites. Genome Res 2010; 20:1534-44. [PMID: 20829224 DOI: 10.1101/gr.105163.110] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here, we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos region using genome scanning, a microarray-based technique that delineates the majority of single-base changes, indels, and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon bears a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes, indicating mutations arising during self-mating or mitotic replication. The data also reveal that one or two meioses separate different isolates, showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pairwise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species, but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase of clindamycin EC(50) in strains harboring one of these mutations. This evidence of clindamycin-resistant parasites in the Amazon suggests that a shift should be made in health policy away from quinine + clindamycin therapy for malaria in pregnant women and infants, and that the development of new lincosamide antibiotics for malaria should be reconsidered.
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Affiliation(s)
- Neekesh V Dharia
- Department of Cell Biology, ICND 202, The Scripps Research Institute, La Jolla, California 92037, USA
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23
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Tan JC, Tan A, Checkley L, Honsa CM, Ferdig MT. Variable numbers of tandem repeats in Plasmodium falciparum genes. J Mol Evol 2010; 71:268-78. [PMID: 20730584 DOI: 10.1007/s00239-010-9381-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 08/09/2010] [Indexed: 11/29/2022]
Abstract
Genome variation studies in Plasmodium falciparum have focused on SNPs and, more recently, large-scale copy number polymorphisms and ectopic rearrangements. Here, we examine another source of variation: variable number tandem repeats (VNTRs). Interspersed low complexity features, including the well-studied P. falciparum microsatellite sequences, are commonly classified as VNTRs; however, this study is focused on longer coding VNTR polymorphisms, a small class of copy number variations. Selection against frameshift mutation is a main constraint on tandem repeats (TRs) in coding regions, while limited propagation of TRs longer than 975 nt total length is a minor restriction in coding regions. Comparative analysis of three P. falciparum genomes reveals that more than 9% of all P. falciparum ORFs harbor VNTRs, much more than has been reported for any other species. Moreover, genotyping of VNTR loci in a drug-selected line, progeny of a genetic cross, and 334 field isolates demonstrates broad variability in these sequences. Functional enrichment analysis of ORFs harboring VNTRs identifies stress and DNA damage responses along with chromatin modification activities, suggesting an influence on genome mutability and functional variation. Analysis of the repeat units and their flanking regions in both P. falciparum and Plasmodium reichenowi sequences implicates a replication slippage mechanism in the generation of TRs from an initially unrepeated sequence. VNTRs can contribute to rapid adaptation by localized sequence duplication. They also can confound SNP-typing microarrays or mapping short-sequence reads and therefore must be accounted for in such analyses.
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Affiliation(s)
- John C Tan
- The Eck Institute for Global Health, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN, 46556, USA.
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24
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Khmelinskii A, Ventura R, Sanches J. A Novel Metric for Bone Marrow Cells Chromosome Pairing. IEEE Trans Biomed Eng 2010; 57:1420-9. [DOI: 10.1109/tbme.2010.2040279] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Genetic changes during laboratory propagation: copy number At the reticulocyte-binding protein 1 locus of Plasmodium falciparum. Mol Biochem Parasitol 2010; 172:145-8. [PMID: 20363264 DOI: 10.1016/j.molbiopara.2010.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 03/25/2010] [Accepted: 03/28/2010] [Indexed: 01/26/2023]
Abstract
Comparative genomic hybridization studies have revealed elevated copy number (CN) at the reticulocyte-binding protein 1 gene (PfRh1) in fast growing lab-adapted parasites, while genetic manipulation demonstrates a causal link between cell invasion and PfRh1 CN. We therefore examined PfRh1 copy number variation (CNV) in 202 single clone parasite isolates from four countries to quantify the extent of CNV within natural populations. Surprisingly, we found that no natural parasite infections showed elevated CN. In contrast, 4/28 independent laboratory reference strains show elevated CN. One possibility is that amplification of PfRh1 (or neighboring loci) is selected during laboratory culture. In the case of FCR3 group of parasites, clone trees show that PfRh1 amplification arose in laboratory lines following establishment in culture. These data show that CNV at PfRh1 is rare or non-existent in natural populations, but can arise during laboratory propagation. We conclude that PfRh1 CNV is not an important determinant of gene expression, cell invasion or growth rate in natural parasite populations.
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Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes. Proc Natl Acad Sci U S A 2010; 107:1482-7. [PMID: 20080586 DOI: 10.1073/pnas.0913883107] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The use of DNA microarrays to identify nucleotide variation is almost 20 years old. A variety of improvements in probe design and experimental conditions have brought this technology to the point that single-nucleotide differences can be efficiently detected in unmixed samples, although developing reliable methods for detection of mixed sequences (e.g., heterozygotes) remains challenging. Surprisingly, a comprehensive study of the probe design parameters and experimental conditions that optimize discrimination of single-nucleotide polymorphisms (SNPs) has yet to be reported, so the limits of this technology remain uncertain. By targeting 24,549 SNPs that differ between two Saccharomyces cerevisiae strains, we studied the effect of SNPs on hybridization efficiency to DNA microarray probes of different lengths under different hybridization conditions. We found that the critical parameter for optimization of sequence discrimination is the relationship between probe melting temperature (T(m)) and the temperature at which the hybridization reaction is performed. This relationship can be exploited through the design of microarrays containing probes of equal T(m) by varying the length of probes. We demonstrate using such a microarray that we detect >90% homozygous SNPs and >80% heterozygous SNPs using the SNPScanner algorithm. The optimized design and experimental parameters determined in this study should guide DNA microarray designs for applications that require sequence discrimination such as mutation detection, genotyping of unmixed and mixed samples, and allele-specific gene expression. Moreover, designing microarray probes with optimized sensitivity to mismatches should increase the accuracy of standard microarray applications such as copy-number variation detection and gene expression analysis.
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