Abstract
Paper is a versatile platform for several biological assays. One of the most popular assays performed on paper substrates is the nucleic acid amplification test (NAAT). Compared to other diagnostic techniques, NAATs are specific, sensitive and fast. While the polymerase chain reaction (PCR) is still the most widely-used technique for amplifying nucleic acids, isothermal DNA amplification techniques have emerged as viable alternatives to PCR on paper. Many innovative detection techniques have also been employed to detect the amplified DNA on paper. There are three main aspects of nucleic acid analysis on paper, namely (a) sample preparation to extract the nucleic acids from cells, (b) amplification of DNA, and (c) detection of the amplified DNA. In this chapter, we will review various amplification techniques in detail. We will also briefly cover the mechanisms to detect the amplified nucleic acids on paper. Finally, we will discuss the potential of these technologies to be translated to the point of care.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ali MM et al (2009) Detection of DNA using bioactive paper strips. Chem Commun 43:6640–6642. https://doi.org/10.1039/b911559e
Ali N et al (2017) Current nucleic acid extraction methods and their implications to point-of-care diagnostics. https://doi.org/10.1155/2017/9306564
An L et al (2005) Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification. J Biol Chem 280(32):28952–28958. https://doi.org/10.1074/jbc.M503096200
Bezrukavnikov S et al (2014) Trehalose facilitates DNA melting: a. R Soc Chem, 7269–7277. https://doi.org/10.1039/c4sm01532k
Chao S et al (2014) Two structural scenarios for protein stabilization by PEG. https://doi.org/10.1021/jp502234s
Choi J et al (2015) Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics. Biosens Bioelectron 74:427–439. https://doi.org/10.1016/j.bios.2015.06.065
Choi JR, Hu J, Gong Y et al (2016a) An integrated lateral flow assay for effective DNA amplification and detection at the point of care. Anal R Soc Chem 141(10):2930–2939. https://doi.org/10.1039/c5an02532j
Choi JR, Hu J, Tang R et al (2016b) An integrated paper-based sample-to-answer biosensor for nucleic acid testing at the point of care. Lab Chip R Soc Chem 16(3):611–621. https://doi.org/10.1039/c5lc01388g
Chua AL et al (2019) Development of a dry reagent-based triplex PCR for the detection of toxigenic and non-toxigenic Vibrio cholerae, 481–485. https://doi.org/10.1099/jmm.0.027433-0
Connelly JT, Rolland JP, Whitesides GM (2015) “Paper machine” for molecular diagnostics. Anal Chem 87(15):7595–7601. https://doi.org/10.1021/acs.analchem.5b00411
Cordray MS, Richards-Kortum RR (2015) A paper and plastic device for the combined isothermal amplification and lateral flow detection of plasmodium DNA. Malaria J BioMed Central 14(1):1. https://doi.org/10.1186/s12936-015-0995-6
Crowe LM, Reid DS, Crowe JH (1996) Is trehalose special for preserving dry biomaterials? Biophy J 71:2087–2093
Das S, Mohapatra SC, Hsu JT (1999) Studies on primer-dimer formation in polymerase chain reaction (PCR), 643–646
Dou M et al (2014) A versatile PDMS/paper hybrid microfluidic platform for sensitive infectious disease diagnosis. Anal Chem 86(15):7978–7986. https://doi.org/10.1021/ac5021694
Dou M et al (2017) Multiplexed instrument-free meningitis diagnosis on a polymer/paper hybrid microfluidic biochip. Biosens Bioelectron 87(September 2016):865–873. https://doi.org/10.1016/j.bios.2016.09.033
Fire A, Xu S (1995) Rolling replication of short DNA circles. Proc Natl Acad Sci 92:4641–4645
Free AH et al (1956) Simple specific test for urine glucose, pp 163–168
Fridley GE et al (2012) Lab on a chip controlled release of dry reagents in porous media for tunable temporal and spatial distribution upon rehydration, 4321–4327. https://doi.org/10.1039/c2lc40785j
Gan W et al (2014) A filter paper-based microdevice for low-cost, rapid, and automated DNA extraction and amplification from diverse sample types. Lab Chip R Soc Chem 14(19):3719–3728. https://doi.org/10.1039/c4lc00686k
Hayashida K et al (2017) Direct detection of falciparum and non-falciparum malaria DNA from a drop of blood with high sensitivity by the dried- LAMP system. Parasites Vectors, 1–9. https://doi.org/10.1186/s13071-016-1949-8
Hepburn SP (1976) Imperial chemical industries Ltd. Fibrous materials. U.S. Patent 3996145
Horst AL et al (2018) A paperfluidic platform to detect Neisseria gonorrhoeae in clinical samples. Biomed Microdev 20(2):1–7. https://doi.org/10.1007/s10544-018-0280-x
Kim J, Gale BK (2008) Quantitative and qualitative analysis of a microfluidic DNA extraction system using a nanoporous AlOx membrane, 1516–1523. https://doi.org/10.1039/b804624g
Kumar S, Bhushan P, Krishna V, Bhattacharya S (2018) Tapered lateral flow immunoassay based point-of-care diagnostic device for ultrasensitive colorimetric detection of dengue NS1. Biomicrofluidics 12(3):034104
Lafleur LK et al (2016) A rapid, instrument-free, sample-to-result nucleic acid amplification test. Lab Chip R Soc Chem 16(19):3777–3787. https://doi.org/10.1039/c6lc00677a
Leuvering JHW et al (2006) Sol particle immunoassay (SPIA) 1522. https://doi.org/10.1080/01971528008055777
Linnes JC et al (2014) Paper-based molecular diagnostic for Chlamydia trachomatis. RSC Adv R Soc Chem 4(80):42245–42251. https://doi.org/10.1039/c4ra07911f
Linnes JC et al (2016) Polyethersulfone improves isothermal nucleic acid amplification compared to current paper-based diagnostics. Biomed Microdevice. https://doi.org/10.1007/s10544-016-0057-z
Liu C et al (2011) An isothermal amplification reactor with an integrated isolation membrane for point-of-care detection of infectious diseases, 2069–2076. https://doi.org/10.1039/c1an00007a
Liu D et al (1996) Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases, 1587–1594. https://doi.org/10.1021/ja952786k
Liu M et al (2016) Target-induced and equipment-free DNA amplification with a simple paper device. Angew Chem Int Ed 55(8):2709–2713. https://doi.org/10.1002/anie.201509389
Lutz B et al (2013) Lab on a chip step assays in instrument-free paper diagnostics 3:2840–2847. https://doi.org/10.1039/c3lc50178g
Magro L et al (2017) Paper-based RNA detection and multiplexed analysis for Ebola virus diagnostics. Sci Rep 7(1):1–9. https://doi.org/10.1038/s41598-017-00758-9
Martinez AW et al (2010) Patterned paper as a platform for inexpensive, low-volume, portable, 1318–1320. https://doi.org/10.1002/anie.200603817
Milne E et al (2006) Short communication buccal DNA collection: comparison of Buccal Swabs with FTA Cards, 15:5–10. https://doi.org/10.1158/1055-9965.epi-05-0753
Mori Y, Notomi T (2009) Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J Infect Chemother 15(2):62–69
Mullis KB (1990) The unusual origin of the polymerase chain reaction. Sci Am 262(4):56–65
Mullis KB, Faloona FA (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. In: Methods in enzymology, vol. 155. Academic Press, pp 335–350
Naik P et al (2019) Sensors and actuators B: chemical an integrated one-step assay combining thermal lysis and loop-mediated isothermal DNA amplification (LAMP) in 30 min from E. coli and M. smegmatis cells on a paper substrate
Niemz A, Ferguson TM, Boyle DS (2011) Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol 29(5):240–250. https://doi.org/10.1016/j.tibtech.2011.01.007
Notomi T et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12):E63. https://doi.org/10.1093/nar/28.12.e63
Ota R, Yamada K, Suzuki K, Citterio D (2018) Quantitative evaluation of analyte transport on microfluidic paper-based analytical devices (μPADs). Analyst 143(3):643–653
Oxaal U et al (1987) Viscous fingering on percolation clusters 49(1982), pp 32–37
Paulsson M, Simonson R (2002) Acetylation of lignin and photostabilization of lignin-rich mechanical wood pulp and paper. In: Hu TQ (ed) Chemical modification, properties, and usage of lignin. Springer, Boston, pp 221–245. https://doi.org/10.1007/978-1-4615-0643-0_12
Pelton R (2009) Bioactive paper provides a low-cost platform for diagnostics. Trends Anal Chem 28(8):925–942. https://doi.org/10.1016/j.trac.2009.05.005
0 EA et al (2019) Microfluidic rapid and autonomous analytical device (microRAAD) to detect HIV from whole blood samples. https://doi.org/10.1101/582999
Piepenburg O et al (2006) DNA detection using recombination proteins. PLoS Biol 4(7):1115–1121. https://doi.org/10.1371/journal.pbio.0040204
Ramachandran S et al (2014) System for ELISA in point-of-care devices †, 1456–1462. https://doi.org/10.1039/c3an02296j
Rawat S et al (2015) Molecular mechanism of poly(vinyl alcohol) mediated prevention of aggregation and stabilization of insulin in nanoparticles. https://doi.org/10.1021/mp5003653
Rodriguez NM et al. (2015) Paper-based RNA extraction, in situ isothermal amplification, and lateral flow detection for low-cost, rapid diagnosis of Influenza A (H1N1) from clinical specimens. https://doi.org/10.1021/acs.analchem.5b01594
Rodriguez NM et al (2016) A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples. Lab Chip R Soc Chem 16(4):753–763. https://doi.org/10.1039/c5lc01392e
Rodriguez NM et al (2016b) Paper-based RNA extraction, in situ isothermal amplification, and lateral flow detection for low-cost, rapid diagnosis of Influenza A (H1N1) from clinical specimens Natalia 87(15):7872–7879. https://doi.org/10.1021/acs.analchem.5b01594.the
Rohrman BA, Richards-Kortum RR (2012) A paper and plastic device for performing recombinase polymerase amplification of HIV DNA. Lab Chip 12(17):3082–3088. https://doi.org/10.1039/c2lc40423k
Roy S et al (2017) Colorimetric nucleic acid detection on paper microchip using loop mediated isothermal amplification and crystal violet dye. ACS Sens 2(11):1713–1720. https://doi.org/10.1021/acssensors.7b00671
Schrader C et al (2012) PCR inhibitors—occurrence, properties and removal. J Appl Microbiol 113(5):1014–1026. https://doi.org/10.1111/j.1365-2672.2012.05384.x
Seok Y et al (2017) A paper-based device for performing loop-mediated isothermal amplification with real-time simultaneous detection of multiple DNA targets. Theranostics 7(8):2220–2230. https://doi.org/10.7150/thno.18675
Sharma N et al (2014) Internal controls for the quality assessment of polymerase chain reaction methods for the diagnosis of infectious & autoimmune diseases 2:485–488
Shetty P et al (2016) Rapid amplification of Mycobacterium tuberculosis DNA on a paper substrate. RSC Adv R Soc Chem 6(61):56205–56212. https://doi.org/10.1039/c6ra07529k
Shi R, Panthee DR (2017) ‘A novel plant DNA extraction method using filter paper-based 96-well spin plate. Planta 246(3):579–584. https://doi.org/10.1007/s00425-017-2743-3
Sia SK, Whitesides GM (2003) Review microfluidic devices fabricated in poly (dimethylsiloxane) for biological studies, 3563–3576. https://doi.org/10.1002/elps.200305584
Sipos R, Sz AJ (2007) Effect of primer mismatch, annealing temperature and PCR cycle number on16S rRNA gene-targeting bacterial community analysis. https://doi.org/10.1111/j.1574-6941.2007.00283.x
Smith LM, Burgoyne LA (2004) Collecting, archiving and processing DNA from wildlife samples using FTA ® databasing paper, 11, pp 1–11
Song Y et al (2014) Visual detection of DNA on paper chips. Anal Chem 86(3):1575–1582. https://doi.org/10.1021/ac403196b
Stephen J, Lakes F, Smith PEF (1998) United States patent (19)
Tan SC, Yiap BC (2009) DNA, RNA, and protein extraction: the past and the present. https://doi.org/10.1155/2009/574398
Tang R et al (2017) A fully disposable and integrated paper-based device for nucleic acid extraction, amplification and detection. Lab Chip 17(7):1270–1279. https://doi.org/10.1039/C6LC01586G
Teengam P et al (2017) Multiplex paper-based colorimetric DNA sensor using pyrrolidinyl peptide nucleic acid-induced AgNPs aggregation for detecting MERS-CoV, MTB, and HPV Oligonucleotides. Anal Chem 89(10):5428–5435. https://doi.org/10.1021/acs.analchem.7b00255
Tian L, Cronin TM, Weizmann Y (2014) Enhancing-effect of gold nanoparticles on DNA strand displacement amplifications and their application to an isothermal telomerase assay. Chem Sci 5(11):4153–4162
Tomita N et al (2008) Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat Protoc 3(5):877–882. https://doi.org/10.1038/nprot.2008.57
Tsai TT et al (2013) Paper-based tuberculosis diagnostic devices with colorimetric gold nanoparticles. Sci Technol Adv Mater 14(4). https://doi.org/10.1088/1468-6996/14/4/044404
Tsaloglou MN et al (2018) Handheld isothermal amplification and electrochemical detection of DNA in resource-limited settings. Anal Biochem. 543(November 2017):116–121. https://doi.org/10.1016/j.ab.2017.11.025
Vagenende V, Yap MGS, Trout BL (2009) Mechanisms of protein stabilization and prevention of protein aggregation by glycerol †, 11084–11096. https://doi.org/10.1021/bi900649t
Vincent M, Xu Y, Kong H (2004) Helicase-dependent isothermal DNA amplification. EMBO Rep 5(8):795–800. https://doi.org/10.1038/sj.embor.7400200
Walker GT et al (1992) Strand displacement amplification-an isothermal, in vitro DNA amplification technique, 20(7):1691–1696
Wallenberger FT, Watson JC, Li H (2001) Glass fibers. Mater Park OH: ASM Int 2001:27–34
Weissensteiner T (1996) Strategy for controlling preferential amplification and avoiding false negatives in PCR typing, 21(6):1102–1108
Xu G et al (2016) Paper-Origami-based multiplexed malaria diagnostics from whole blood. Angew Chem Int Edit 55(49):15250–15253. https://doi.org/10.1002/anie.201606060
Yang Z et al (2018) Rapid veterinary diagnosis of bovine reproductive infectious diseases from semen using paper-origami DNA microfluidics. ACS Sens 3(2):403–409. https://doi.org/10.1021/acssensors.7b00825
Yetisen AK, Akram MS, Lowe CR (2013) Paper-based microfluidic point-of-care diagnostic devices. Lab Chip 13(12):2210–2251. https://doi.org/10.1039/c3lc50169h
Zhong ZW, Wang ZP, Huang GXD (2012) Investigation of wax and paper materials for the fabrication of paper-based microfluidic devices. Microsyst Technol 18(5):649–659
Zou Y et al (2017) Nucleic acid purification from plants, animals and microbes in under 30 s. PLoS Biol 15(11):1–22. https://doi.org/10.1371/journal.pbio.2003916
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Naik, P., Manna, R., Paul, D. (2019). Nucleic Acid Amplification on Paper Substrates. In: Bhattacharya, S., Kumar, S., Agarwal, A. (eds) Paper Microfluidics. Advanced Functional Materials and Sensors. Springer, Singapore. https://doi.org/10.1007/978-981-15-0489-1_8
Download citation
DOI: https://doi.org/10.1007/978-981-15-0489-1_8
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-0488-4
Online ISBN: 978-981-15-0489-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)