Recent developments in nucleic acid identification using solid-phase enzymatic assays

AbstractThis review (containing 101 refs.) covers recent achievements in the development of new approaches for enzymatically assisted detection of nucleic acids on microarrays. We discuss molecular techniques including the polymerase chain reaction, reverse transcription, allele specific primer extension and a range of isothermal techniques for the amplification and discrimination of nucleic acids. This also includes their implementation into microfluidic systems. These techniques all show great promise for use in the life sciences by allowing for high throughput, cost effective and highly sensitive and specific analysis of nucleic acids. Importantly, they can be potentially integrated into personalized and point-of-care medicine. FigureThis review highlights recent developments in molecular techniques including polymerase chain reaction, reverse transcription, allele specific primer extension and isothermal amplification on microarrays for the amplification and discrimination of nucleic acids. Their use in microfluidic platforms is also discussed.

[1]  Sheng-Ce Tao,et al.  A universal multiplex PCR strategy for 100-plex amplification using a hydrophobically patterned microarray. , 2011, Lab on a chip.

[2]  Benjamin Meder,et al.  Next-generation sequencing entering the clinical arena. , 2011, Molecular and cellular probes.

[3]  C. Fan,et al.  Nano rolling-circle amplification for enhanced SERS hot spots in protein microarray analysis. , 2012, Analytical chemistry.

[4]  Martin Dufva,et al.  An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes. , 2008, BioTechniques.

[5]  D. Xing,et al.  An electrochemiluminescent assay for high sensitive detection of mercury (II) based on isothermal rolling circular amplification. , 2012, Analytica chimica acta.

[6]  Harald Noedl,et al.  Novel Nested Direct PCR Technique for Malaria Diagnosis Using Filter Paper Samples , 2011, Journal of Clinical Microbiology.

[7]  Alexandra S. Whale,et al.  Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation , 2012, Nucleic acids research.

[8]  Andrew D Griffiths,et al.  Amplification of complex gene libraries by emulsion PCR , 2006, Nature Methods.

[9]  E. Schopf,et al.  Attomole DNA detection assay via rolling circle amplification and single molecule detection. , 2010, Analytical biochemistry.

[10]  Yang Liu,et al.  tuberculosis detection via rolling circle amplification. , 2011, Analytical methods : advancing methods and applications.

[11]  Kenji Kinoshita,et al.  Detection and Identification of Species with Bacterial Cells Using a Plastic DNA Array , 2008 .

[12]  Taihua Li,et al.  Investigation of the signaling mechanism and verification of the performance of an electrochemical real-time PCR system based on the interaction of methylene blue with DNA. , 2011, The Analyst.

[13]  E. Southern.  Detection of specific sequences among DNA fragments separated by gel electrophoresis. , 1975, Journal of molecular biology.

[14]  A. Mirzabekov,et al.  DNA analysis and diagnostics on oligonucleotide microchips. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Farre,et al.  A four-ferrocene modified stem-loop structure as a probe for sensitive detection and single-base mismatch discrimination of DNA , 2012 .

[16]  D. Park,et al.  Enhanced solid phase PCR: mechanisms to increase priming by solid support primers. , 2008, Analytical biochemistry.

[17]  He Zhang,et al.  Microfluidic bead-based enzymatic primer extension for single-nucleotide discrimination using quantum dots as labels. , 2012, Analytical biochemistry.

[18]  R. Zahorchak,et al.  Dendron-modified surfaces provide an ideal environment for stem-loop DNA probes. , 2012, Analytical biochemistry.

[19]  Gwo-Bin Lee,et al.  A magnetic bead-based assay for the rapid detection of methicillin-resistant Staphylococcus aureus by using a microfluidic system with integrated loop-mediated isothermal amplification. , 2011, Lab on a chip.

[20]  Hai-Qing Gong,et al.  Rapid distribution of a liquid column into a matrix of nanoliter wells for parallel real-time quantitative PCR , 2009 .

[21]  Hai-Qing Gong,et al.  A microfluidic liquid phase nucleic acid purification chip to selectively isolate DNA or RNA from low copy/single bacterial cells in minute sample volume followed by direct on-chip quantitative PCR assay. , 2013, Analytical chemistry.

[22]  N. Zakharova,et al.  Simultaneous qualitative and quantitative identification of multiple targets by polymerase chain reaction on microarray , 2008, 0811.1263.

[23]  Chaoyong James Yang,et al.  Massively parallel single-molecule and single-cell emulsion reverse transcription polymerase chain reaction using agarose droplet microfluidics. , 2012, Analytical chemistry.

[24]  Mats Nilsson,et al.  A dual-tag microarray platform for high-performance nucleic acid and protein analyses , 2008, Nucleic acids research.

[25]  G. Turcatti,et al.  Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms. , 2000, Nucleic acids research.

[26]  Masao Kamahori,et al.  A gel‐free SNP genotyping method: bioluminometric assay coupled with modified primer extension reactions (BAMPER) directly from double‐stranded PCR products , 2004, Human mutation.

[27]  Olaf Piepenburg,et al.  DNA Detection Using Recombination Proteins , 2006, PLoS biology.

[28]  Pengfeng Xiao,et al.  A gel-based solid-phase amplification and its application for SNP typing and sequencing on-chip. , 2009, The Analyst.

[29]  Rui Zhang,et al.  A high-throughput microfluidic biochip to quantify bacterial adhesion to single host cells by real-time PCR assay , 2013, Analytical and Bioanalytical Chemistry.

[30]  Lei Wang,et al.  Sensitive detection of proteins using assembled cascade fluorescent DNA nanotags based on rolling circle amplification. , 2012, Bioconjugate chemistry.

[31]  Lingwen Zeng,et al.  Spectrophotometric and ultrasensitive DNA bioassay by circular-strand displacement polymerization reaction. , 2013, The Analyst.

[32]  Weiling Fu,et al.  Isothermal detection of multiple point mutations by a surface plasmon resonance biosensor with Au nanoparticles enhanced surface-anchored rolling circle amplification. , 2013, Biosensors & bioelectronics.

[33]  Single-tube genotyping using a solid-phase method that combines alpha-phosphorothioate-mediated primer extension and ExoIII: proof of concept with the F508del cystic fibrosis diagnosis. , 2008, Molecular and cellular probes.

[34]  F. Bier,et al.  Reverse transcription-polymerase chain reaction on a microarray: the integrating concept of “active arrays” , 2008, Analytical and bioanalytical chemistry.

[35]  K. Fujiwara,et al.  Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer , 2006, Nucleic acids research.

[36]  Y. Yun,et al.  Dramatic increase in signal by integration of polymerase chain reaction and hybridization on surface of DNA microarray. , 2010, Analytical biochemistry.

[37]  A. Steel,et al.  Immobilization of nucleic acids at solid surfaces: effect of oligonucleotide length on layer assembly. , 2000, Biophysical journal.

[38]  Shusheng Zhang,et al.  A chemiluminescence imaging array for the detection of cancer cells by dual-aptamer recognition and bio-bar-code nanoprobe-based rolling circle amplification. , 2013, Chemical communications.

[39]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[40]  Yong Shin,et al.  Real-time, label-free isothermal solid-phase amplification/detection (ISAD) device for rapid detection of genetic alteration in cancers. , 2013, Lab on a chip.

[41]  N. Zakharova,et al.  An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV. , 2008, BioTechniques.

[42]  Joonhyung Lee,et al.  Diffractometric detection of proteins using microbead-based rolling circle amplification. , 2010, Analytical chemistry.

[43]  Zuhong Lu,et al.  PCR‐product microarray based on polyacrylic acid‐modified surface for SNP genotyping , 2009, Electrophoresis.

[44]  A. Tretyn,et al.  Sequencing technologies and genome sequencing , 2011, Journal of Applied Genetics.

[45]  Haiping Wu,et al.  Digital analysis of the expression levels of multiple colorectal cancer-related genes by multiplexed digital-PCR coupled with hydrogel bead-array. , 2011, The Analyst.

[46]  Bong Jin Hong,et al.  Effects of lateral spacing on enzymatic on-chip DNA polymerization. , 2011, Biosensors & bioelectronics.

[47]  Yi Sun,et al.  A lab-on-a-chip device for rapid identification of avian influenza viral RNA by solid-phase PCR. , 2011, Lab on a Chip.

[48]  M. Chmielewski,et al.  Application of click chemistry to the production of DNA microarrays. , 2012, Lab on a chip.

[49]  Zuhong Lu,et al.  An Emulsion System Based on a Chip Polymerase Chain Reaction , 2008, Molecules.

[50]  Takehiko Kitamori,et al.  Microbead-based rolling circle amplification in a microchip for sensitive DNA detection. , 2010, Lab on a chip.

[51]  Jeroen Lammertyn,et al.  Real-time monitoring of solid-phase PCR using fiber-optic SPR. , 2011, Small.

[52]  S. Hernández,et al.  In situ DNA amplification with magnetic primers for the electrochemical detection of food pathogens. , 2007, Biosensors & bioelectronics.

[53]  Guoming Xie,et al.  Ultrasensitive electrochemical immunosensor for HE4 based on rolling circle amplification. , 2012, Biosensors & bioelectronics.

[54]  G. Whitesides,et al.  Enzyme immobilization by condensation copolymerization into crosslinked polyacrylamide gels , 1980 .

[55]  Jian-hui Jiang,et al.  Ultrasensitive electrochemical DNA detection based on dual amplification of circular strand-displacement polymerase reaction and hybridization chain reaction. , 2013, Biosensors & bioelectronics.

[56]  M. W. Mueller,et al.  Microarray-Based Identification of Bacteria in Clinical Samples by Solid-Phase PCR Amplification of 23S Ribosomal DNA Sequences , 2004, Journal of Clinical Microbiology.

[57]  C. Smith,et al.  Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection. , 1999, Genetic analysis : biomolecular engineering.

[58]  C. O’Sullivan,et al.  Electrochemical detection of Francisella tularensis genomic DNA using solid-phase recombinase polymerase amplification. , 2014, Biosensors & bioelectronics.

[59]  O. V. Moiseeva,et al.  Comparison of surface and hydrogel-based protein microchips. , 2007, Analytical biochemistry.

[60]  Takaaki Kojima,et al.  PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets , 2005, Nucleic acids research.

[61]  Strategies for Attaching Oligonucleotides to Solid Supports , 2005 .

[62]  Rustem F Ismagilov,et al.  Nanoliter multiplex PCR arrays on a SlipChip. , 2010, Analytical chemistry.

[63]  Kae Sato,et al.  Bead-based padlock rolling circle amplification for single DNA molecule counting. , 2013, Analytical biochemistry.

[64]  Roland Zengerle,et al.  Microfluidic lab-on-a-foil for nucleic acid analysis based on isothermal recombinase polymerase amplification (RPA). , 2010, Lab on a chip.

[65]  I-Ming Hsing,et al.  Electrochemistry-based real-time PCR on a microchip. , 2008, Analytical chemistry.

[66]  H. John Crabtree,et al.  A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs. , 2012, Lab on a chip.

[67]  A. Lee,et al.  1-Million droplet array with wide-field fluorescence imaging for digital PCR. , 2011, Lab on a chip.

[68]  D. Meldrum,et al.  Real-time PCR of single bacterial cells on an array of adhering droplets. , 2011, Lab on a chip.

[69]  N. Ramalingam,et al.  Real-time PCR array chip with capillary-driven sample loading and reactor sealing for point-of-care applications , 2009, Biomedical microdevices.

[70]  Jianlong Zhao,et al.  A colorimetric method for H1N1 DNA detection using rolling circle amplification. , 2013, The Analyst.

[71]  Rustem F Ismagilov,et al.  Microfluidics using spatially defined arrays of droplets in one, two, and three dimensions. , 2011, Annual review of analytical chemistry.

[72]  Roland Zengerle,et al.  Universal protocol for grafting PCR primers onto various lab-on-a-chip substrates for solid-phase PCR , 2012 .

[73]  Nongyue He,et al.  Multiplex single nucleotide polymorphisms genotyping using solid-phase single base extension on magnetic nanoparticles. , 2009, Analytical biochemistry.

[74]  L. Pilarski,et al.  An enclosed in-gel PCR amplification cassette with multi-target, multi-sample detection for platform molecular diagnostics. , 2013, Lab on a chip.

[75]  Frank F Bier,et al.  Helicase dependent OnChip-amplification and its use in multiplex pathogen detection. , 2009, Clinica chimica acta; international journal of clinical chemistry.

[76]  Frank F Bier,et al.  Functional peptide microarrays for specific and sensitive antibody diagnostics , 2006, Proteomics.

[77]  H. Ju,et al.  Sensitive fluorescence detection of DNA using isothermal exponential amplification coupled quantum dots coated silica nanospheres as label , 2013 .

[78]  Luke P. Lee,et al.  Digital LAMP in a sample self-digitization (SD) chip. , 2012, Lab on a chip.

[79]  H. Koga,et al.  A novel SNP detection technique utilizing a multiple primer extension (MPEX) on a phospholipid polymer-coated surface. , 2007, Molecular bioSystems.

[80]  S. Franceschi,et al.  Development of a Sensitive and Specific Multiplex PCR Method Combined with DNA Microarray Primer Extension To Detect Betapapillomavirus Types , 2007, Journal of Clinical Microbiology.

[81]  Qiao Lin,et al.  A MEMS-Based Approach to Single Nucleotide Polymorphism Genotyping. , 2013, Sensors and actuators. A, Physical.

[82]  J. Ilonen,et al.  Solid-phase PCR with hybridization and time-resolved fluorometry for detection of HLA-B27. , 2001, Clinical chemistry.

[83]  B. Ye,et al.  Multiplexed bead-based mesofluidic system for gene diagnosis and genotyping. , 2010, Analytical chemistry.

[84]  M. Shapero,et al.  SNP genotyping by multiplexed solid-phase amplification and fluorescent minisequencing. , 2001, Genome research.

[85]  James P Landers,et al.  Dynamic solid phase DNA extraction and PCR amplification in polyester-toner based microchip. , 2011, Analytical chemistry.

[86]  Robert M. Corn,et al.  Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging. , 2011, Journal of the American Chemical Society.

[87]  A. Mirzabekov,et al.  Manual manufacturing of oligonucleotide, DNA, and protein microchips. , 1997, Analytical biochemistry.

[88]  Zhengping Li,et al.  Chemiluminescent detection of DNA hybridization and single-nucleotide polymorphisms on a solid surface using target-primed rolling circle amplification. , 2008, The Analyst.

[89]  N. Zakharova,et al.  The role of DNA diffusion in solid phase polymerase chain reaction with gel-immobilized primers in planar and capillary microarray format. , 2009, Biomicrofluidics.

[90]  Wenqiang Lai,et al.  Hybridization-induced isothermal cycling signal amplification for sensitive electronic detection of nucleic acid. , 2013, Biosensors & bioelectronics.

[91]  Haiping Wu,et al.  Digital detection of multiple minority mutants in stool DNA for noninvasive colorectal cancer diagnosis. , 2012, Analytical chemistry.

[92]  J. Odeberg,et al.  SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays. , 2002, Nucleic acids research.

[93]  Lida K. Gifford,et al.  Attomole detection of mesophilic DNA polymerase products by nanoparticle-enhanced surface plasmon resonance imaging on glassified gold surfaces. , 2010, Journal of the American Chemical Society.

[94]  A. Wolff,et al.  DNA microarray-based solid-phase RT-PCR for rapid detection and identification of influenza virus type A and subtypes H5 and H7. , 2011, Diagnostic microbiology and infectious disease.

[95]  Yan Deng,et al.  A Novel SNPs Detection Method Based on Gold Magnetic Nanoparticles Array and Single Base Extension , 2012, Theranostics.

[96]  Erik L. McCarthy,et al.  Nucleic acid sensing by regenerable surface-associated isothermal rolling circle amplification. , 2007, Biosensors & bioelectronics.

[97]  Rustem F Ismagilov,et al.  Digital isothermal quantification of nucleic acids via simultaneous chemical initiation of recombinase polymerase amplification reactions on SlipChip. , 2011, Analytical chemistry.

[98]  Roland Zengerle,et al.  Solid-phase PCR in a picowell array for immobilizing and arraying 100,000 PCR products to a microscope slide. , 2012, Lab on a chip.

[99]  P. Singh,et al.  A novel method for whole blood PCR without pretreatment. , 2012, Gene.