Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics

Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.

[1]  B. Vogelstein,et al.  Preparative and analytical purification of DNA from agarose. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R Higuchi,et al.  Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. , 2013, BioTechniques.

[3]  K. Esser,et al.  maxXbond: first regeneration system for DNA binding silica matrices , 2006 .

[4]  J. Coffin,et al.  Interactions of Murine APOBEC3 and Human APOBEC3G with Murine Leukemia Viruses , 2008, Journal of Virology.

[5]  Y. Auffray,et al.  Comparison of the bile salts and sodium dodecyl sulfate stress responses in Enterococcus faecalis , 1996, Applied and environmental microbiology.

[6]  Fei Li,et al.  Advances in paper-based point-of-care diagnostics. , 2014, Biosensors & bioelectronics.

[7]  A. Lesk Why does DNA contain thymine and RNA uracil? , 1969, Journal of theoretical biology.

[8]  W. Rutter,et al.  Rat insulin genes: construction of plasmids containing the coding sequences. , 1977, Science.

[9]  Helen H. Lee,et al.  Sample preparation: a challenge in the development of point-of-care nucleic acid-based assays for resource-limited settings. , 2007, The Analyst.

[10]  J. Fritsche,et al.  Recent Developments and Applications of Solid Phase Microextraction (SPME) in Food and Environmental Analysis—A Review , 2015 .

[11]  R. Scott,et al.  Buccal DNA Collection: Comparison of Buccal Swabs with FTA Cards , 2006, Cancer Epidemiology Biomarkers & Prevention.

[12]  Christoph Syldatk,et al.  Mechanical disruption of Arthrobacter sp. DSM 3747 in stirred ball mills for the release of hydantoin-cleaving enzymes , 1992 .

[13]  R. Komel,et al.  Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells , 2010, Microbial cell factories.

[14]  I. Maudlin,et al.  A novel procedure for total nucleic acid extraction from small numbers of Eimeria species oocysts. , 2007, Turkiye parazitolojii dergisi.

[15]  L. Welch,et al.  A comparison of methods for forensic DNA extraction: Chelex-100® and the QIAGEN DNA Investigator Kit (manual and automated). , 2012, Forensic science international. Genetics.

[16]  A. Siegbahn,et al.  Genetic variation of CYP2C19 affects both pharmacokinetic and pharmacodynamic responses to clopidogrel but not prasugrel in aspirin-treated patients with coronary artery disease , 2009, European heart journal.

[17]  Ralph Rapley,et al.  The Nucleic Acid Protocols Handbook , 2000, Humana Press.

[18]  G Ronald Jenkins,et al.  Influence of DNA extraction methods, PCR inhibitors and quantification methods on real-time PCR assay of biotechnology-derived traits , 2010, Analytical and bioanalytical chemistry.

[19]  M. Klimek-Ochab,et al.  Comparative study of fungal cell disruption—scope and limitations of the methods , 2011, Folia Microbiologica.

[20]  L. Feldman,et al.  A rapid TRIzol‐based two‐step method for DNA‐free RNA extraction from Arabidopsis siliques and dry seeds , 2010, Biotechnology journal.

[21]  J. Pawliszyn,et al.  Solid phase microextraction with thermal desorption using fused silica optical fibers , 1990 .

[22]  Xianting Ding,et al.  A Review on Microfluidic Paper-Based Analytical Devices for Glucose Detection , 2016, Sensors.

[23]  Daniel C Leslie,et al.  Nucleic acid extraction techniques and application to the microchip. , 2009, Lab on a chip.

[24]  C. J. Di Como,et al.  Effects of ethidium bromide and SYBR Green I on different polymerase chain reaction systems. , 2000, Journal of biochemical and biophysical methods.

[25]  Lm Smith,et al.  Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper , 2004, BMC Ecology.

[26]  Manabu Tokeshi,et al.  Advances in Microfluidic Paper-Based Analytical Devices for Food and Water Analysis , 2016, Micromachines.

[27]  J. Kiel,et al.  Use of magnetic beads in selection and detection of biotoxin aptamers by electrochemiluminescence and enzymatic methods. , 2002, BioTechniques.

[28]  Somenath Mitra,et al.  Sample preparation techniques in analytical chemistry , 2003 .

[29]  Sang Kwang Lee,et al.  Rapid DNA Extraction from Dried Blood Spots on Filter Paper: Potential Applications in Biobanking , 2014, Osong public health and research perspectives.

[30]  H. Swaisgood,et al.  Isolation of RNA and DNA fragments using diatomaceous earth , 1998 .

[31]  Eduardo Gotuzzo,et al.  Rapid molecular detection of tuberculosis and rifampin resistance. , 2010, The New England journal of medicine.

[32]  L. Robeson,et al.  Environmental stress cracking: A review , 2013 .

[33]  H. Birnboim,et al.  A rapid alkaline extraction procedure for screening recombinant plasmid DNA. , 1979, Nucleic acids research.

[34]  P. Chomczyński,et al.  Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. , 1987, Analytical biochemistry.

[35]  C. Hankins,et al.  Diagnosis of vertical HIV-1 transmission using the polymerase chain reaction and dried blood spot specimens. , 1992, Journal of acquired immune deficiency syndromes.

[36]  D. DeVoe,et al.  Microfluidic device fabrication by thermoplastic hot-embossing. , 2013, Methods in molecular biology.

[37]  R. Gifford,et al.  The Extraordinary Evolutionary History of the Reticuloendotheliosis Viruses , 2013, PLoS biology.

[38]  Gavin Nixon,et al.  A magnetic bead-based DNA extraction and purification microfluidic device , 2011 .

[39]  M. Jit,et al.  Systematic review, meta-analysis and economic modelling of molecular diagnostic tests for antibiotic resistance in tuberculosis. , 2015, Health technology assessment.

[40]  S. Ogino,et al.  LINE‐1 hypomethylation is inversely associated with microsatellite instability and CpG island methylator phenotype in colorectal cancer , 2008, International journal of cancer.

[41]  D. Low,et al.  Prevalence and Characterization of the Mechanisms of Macrolide, Lincosamide, and Streptogramin Resistance in Isolates ofStreptococcus pneumoniae , 1998, Antimicrobial Agents and Chemotherapy.

[42]  L. Griffiths,et al.  Methods for extracting genomic DNA from whole blood samples: current perspectives , 2014 .

[43]  J. Tester,et al.  Ultrasonic cavitation for disruption of microalgae. , 2015, Bioresource technology.

[44]  S. Goldberg Mechanical/physical methods of cell distribution and tissue homogenization. , 2015, Methods in molecular biology.

[45]  Chi-Hwa Wang,et al.  Fabrication and characterization of PLGA/HAp composite scaffolds for delivery of BMP-2 plasmid DNA. , 2007, Journal of controlled release : official journal of the Controlled Release Society.

[46]  M. Biziuk,et al.  Solid phase extraction technique-trends, opportunities and applications , 2006 .

[47]  C. Brandl,et al.  RNA isolation from yeast using silica matrices. , 2005, Journal of biomolecular techniques : JBT.

[48]  C. Lim,et al.  Malaria detection using inertial microfluidics. , 2015, Lab on a chip.

[49]  S. Jonsson,et al.  Trace determination of volatile sulfur compounds by solid-phase microextraction and GC-MS. , 2002, The Analyst.

[50]  Daniel Citterio,et al.  Toward practical application of paper-based microfluidics for medical diagnostics: state-of-the-art and challenges. , 2017, Lab on a chip.

[51]  T. Ried,et al.  Isolation and solubilization of proteins after TRIzol extraction of RNA and DNA from patient material following prolonged storage. , 2007, BioTechniques.

[52]  Jungkyu Kim,et al.  Microfluidic sample preparation: cell lysis and nucleic acid purification. , 2009, Integrative biology : quantitative biosciences from nano to macro.

[53]  J. Henion,et al.  A 384-well solid-phase extraction for LC/MS/MS determination of methotrexate and its 7-hydroxy metabolite in human urine and plasma. , 2001, Analytical chemistry.

[54]  G. Whitesides,et al.  Diagnostics for the developing world: microfluidic paper-based analytical devices. , 2010, Analytical chemistry.

[55]  H. Parkes,et al.  Detection of genetically modified crops and their derivatives: critical steps in sample preparation and extraction. , 2002, Journal of AOAC International.

[56]  S. Esposito,et al.  Comparison of Manual Methods of Extracting Genomic DNA from Dried Blood Spots Collected on Different Cards: Implications for Clinical Practice , 2013, International journal of immunopathology and pharmacology.

[57]  Alexander R. Martin,et al.  A Single Promoter Inversion Switches Photorhabdus Between Pathogenic and Mutualistic States , 2012, Science.

[58]  Utkan Demirci,et al.  Advances in addressing technical challenges of point-of-care diagnostics in resource-limited settings , 2016, Expert review of molecular diagnostics.

[59]  P. Prabakaran,et al.  A comparative study on effective cell disruption methods for lipid extraction from microalgae , 2011, Letters in applied microbiology.

[60]  R. Shankar Sample Preparation Techniques In Analytical Chemistry , 2013 .

[61]  M. Salimans,et al.  Rapid and simple method for purification of nucleic acids , 1990, Journal of clinical microbiology.

[62]  S. Thatcher,et al.  DNA/RNA preparation for molecular detection. , 2015, Clinical chemistry.

[63]  D. Wright,et al.  Comparison of three magnetic bead surface functionalities for RNA extraction and detection. , 2015, ACS applied materials & interfaces.

[64]  N. Ban,et al.  Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 , 2011, Science.

[65]  David Huckle,et al.  The impact of new trends in POCTs for companion diagnostics, non-invasive testing and molecular diagnostics , 2015, Expert review of molecular diagnostics.

[66]  Chao Huang,et al.  A Microfluidic Platform for Precision Small-volume Sample Processing and Its Use to Size Separate Biological Particles with an Acoustic Microdevice , 2015, Journal of visualized experiments : JoVE.

[67]  M. Mascini,et al.  Strategies for electrochemical detection in immunochemistry. , 2009, Bioanalysis.

[68]  S. Tan,et al.  DNA, RNA, and Protein Extraction: The Past and The Present , 2009, Journal of biomedicine & biotechnology.

[69]  W. Rutter,et al.  Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. , 1979, Biochemistry.

[70]  A. Villaverde,et al.  Isolation of cell-free bacterial inclusion bodies , 2010, Microbial cell factories.

[71]  H. Yamagata,et al.  Ethidium bromide and SYBR Green I enhance the genotoxicity of UV-irradiation and chemical mutagens in E. coli. , 2001, Mutation research.

[72]  M. Zaman,et al.  Low-cost tools for diagnosing and monitoring HIV infection in low-resource settings. , 2012, Bulletin of the World Health Organization.

[73]  S. Berensmeier Magnetic particles for the separation and purification of nucleic acids , 2006, Applied Microbiology and Biotechnology.

[74]  G. Whitesides,et al.  Applications of microfluidics in chemical biology. , 2006, Current opinion in chemical biology.

[75]  S. A. Whalen,et al.  Laboratory automation: trajectory, technology, and tactics. , 2000, Clinical chemistry.

[76]  C. Schrader,et al.  PCR inhibitors – occurrence, properties and removal , 2012, Journal of applied microbiology.

[77]  SOLD MEDUMAND METHOD FOR DNA STORAGE , 2017 .

[78]  David A Stenger,et al.  Magnetic bead-based solid phase for selective extraction of genomic DNA. , 2006, Analytical biochemistry.

[79]  William A. Mcmillan,et al.  Rapid, automated nucleic acid probe assays using silicon microstructures for nucleic acid concentration. , 1999, Journal of biomechanical engineering.

[80]  N. Lapointe,et al.  Dried blood spots collected on filter paper: an international resource for the diagnosis and genetic characterization of human immunodeficiency virus type-1. , 1996, Memorias do Instituto Oswaldo Cruz.

[81]  R. Kambour,et al.  The Role of Organic Agents in the Stress Crazing and Cracking of Poly(2,6-dimethyl-1,4-phenylene oixde) , 1968 .

[82]  J. Asenjo,et al.  Enzymatic lysis of microbial cells , 2007, Biotechnology Letters.

[83]  Maïwenn Kersaudy-Kerhoas,et al.  Opportunities and challenges for the application of microfluidic technologies in point-of-care veterinary diagnostics. , 2016, Molecular and cellular probes.

[84]  Gina A. Keppel,et al.  Exploring the barriers and facilitators to use of point of care tests in family medicine clinics in the United States , 2016, BMC Family Practice.

[85]  Anubhav Tripathi,et al.  Microfluidic Sample Preparation for Medical Diagnostics. , 2015, Annual review of biomedical engineering.

[86]  S. Carr,et al.  Rapid isolation of animal mitochondrial DNA in a small fixed-angle rotor at ultrahigh speed , 1987, Biochemical Genetics.

[87]  David W. Burden,et al.  Guide to the Disruption of Biological Samples – 2012 Version 1 . 1 , 2012 .

[88]  R. Karalus,et al.  Electricity-free, sequential nucleic acid and protein isolation. , 2012, Journal of visualized experiments : JoVE.

[89]  D. Howells,et al.  Stem Cell Transplantation in Traumatic Spinal Cord Injury: A Systematic Review and Meta-Analysis of Animal Studies , 2013, PLoS biology.

[90]  Dapeng Sun,et al.  Disruption and protein release by ultrasonication of yeast cells , 2013 .

[91]  Matthias Franzreb,et al.  Protein purification using magnetic adsorbent particles , 2006, Applied Microbiology and Biotechnology.

[92]  Haim H Bau,et al.  Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection. , 2015, Methods in molecular biology.

[93]  Dennis Jenke,et al.  Evaluation of the chemical compatibility of plastic contact materials and pharmaceutical products; safety considerations related to extractables and leachables. , 2007, Journal of pharmaceutical sciences.

[94]  C. Suttle,et al.  A Virophage at the Origin of Large DNA Transposons , 2011, Science.

[95]  P. Chomczyński,et al.  The single-step method of RNA isolation by acid guanidinium thiocyanate–phenol–chloroform extraction: twenty-something years on , 2006, Nature Protocols.

[96]  S. Tam,et al.  Isolation and characterization of RNA from snap-frozen tissues and cultured cells , 1992 .