Skip to main content

Advertisement

SpringerLink
Log in

Single-molecule emulsion PCR in microfluidic droplets

  • Review
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

Abstract

The application of microfluidic droplet PCR for single-molecule amplification and analysis has recently been extensively studied. Microfluidic droplet technology has the advantages of compartmentalizing reactions into discrete volumes, performing highly parallel reactions in monodisperse droplets, reducing cross-contamination between droplets, eliminating PCR bias and nonspecific amplification, as well as enabling fast amplification with rapid thermocycling. Here, we have reviewed the important technical breakthroughs of microfluidic droplet PCR in the past five years and their applications to single-molecule amplification and analysis, such as high-throughput screening, next generation DNA sequencing, and quantitative detection of rare mutations. Although the utilization of microfluidic droplet single-molecule PCR is still in the early stages, its great potential has already been demonstrated and will provide novel solutions to today’s biomedical engineering challenges in single-molecule amplification and analysis.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9
Fig. 10

Similar content being viewed by others

References

  1. Xie XS, Yu J, Yang WY (2006) Science 312:228–230

    Article  CAS  Google Scholar 

  2. Sims CE, Allbritton NL (2007) Lab Chip 7:423–440

    Article  CAS  Google Scholar 

  3. Li GW, Xie XS (2011) Nature 475:308–315

    Article  CAS  Google Scholar 

  4. Funatsu T, Harada Y, Tokunaga M, Saito K, Yanagida T (1995) Nature 374:555–559

    Article  CAS  Google Scholar 

  5. Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM (1998) Science 282:902–907

    Article  CAS  Google Scholar 

  6. Weiss S (1999) Science 283:1676–1683

    Article  CAS  Google Scholar 

  7. Check E (2005) Nature 437:1084–1086

    Article  CAS  Google Scholar 

  8. Raser JM, O'Shea EK (2005) Science 309:2010–2013

    Article  CAS  Google Scholar 

  9. Misteli T, Soutoglou E (2009) Nat Rev Mol Cell Biol 10:243–254

    Article  CAS  Google Scholar 

  10. Stratton MR, Campbell PJ, Futreal PA (2009) Nature 458:719–724

    Article  CAS  Google Scholar 

  11. Burkhart DL, Sage J (2008) Nat Rev Cancer 8:671–682

    Article  CAS  Google Scholar 

  12. Jeffreys AJ, Wilson V, Neumann R, Keyte J (1988) Nucleic Acids Res 16:10953–10971

    Article  CAS  Google Scholar 

  13. Jeffreys AJ, Neumann R, Wilson V (1990) Cell 60:473–485

    Article  CAS  Google Scholar 

  14. Li HH, Gyllensten UB, Cui XF, Saiki RK, Erlich HA, Arnheim N (1988) Nature 335:414–417

    Article  CAS  Google Scholar 

  15. Ruano G, Kidd KK, Stephens JC (1990) Proc Natl Acad Sci U S A 87:6296–6300

    Article  CAS  Google Scholar 

  16. Song H, Chen DL, Ismagilov RF (2006) Angew Chem Int Ed Engl 45:7336–7356

    Article  CAS  Google Scholar 

  17. Dittrich PS, Manz A (2006) Nat Rev Drug Discovery 5:210–218

    Article  CAS  Google Scholar 

  18. Price AK, Culbertson CT (2007) Anal Chem 79:2614–2621

    Article  CAS  Google Scholar 

  19. Chiu DT, Lorenz RM (2009) Acc Chem Res 42:649–658

    Article  CAS  Google Scholar 

  20. Lindstrom S, Andersson-Svahn H (2010) Lab Chip 10:3363–3372

    Article  CAS  Google Scholar 

  21. Teh SY, Lin R, Hung LH, Lee AP (2008) Lab Chip 8:198–220

    Article  CAS  Google Scholar 

  22. Huebner A, Sharma S, Srisa-Art M, Hollfelder F, Edel JB, Demello AJ (2008) Lab Chip 8:1244–1254

    Article  CAS  Google Scholar 

  23. Theberge AB, Courtois F, Schaerli Y, Fischlechner M, Abell C, Hollfelder F, Huck WTS (2010) Angew Chem Int Edit 49:5846–5868

    CAS  Google Scholar 

  24. Baroud CN, Gallaire F, Dangla R (2010) Lab Chip 10:2032–2045

    Article  CAS  Google Scholar 

  25. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Science 230:1350–1354

    Article  CAS  Google Scholar 

  26. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Cold Spring Harbor Symp Quant Biol 51:263–273

    Article  CAS  Google Scholar 

  27. Zhang C, Da X (2010) Chem Rev (Washington, DC, U S) 110:4910–4947

    Article  CAS  Google Scholar 

  28. Kemp DJ, Smith DB, Foote SJ, Samaras N, Peterson MG (1989) Proc Natl Acad Sci U S A 86:2423–2427

    Article  CAS  Google Scholar 

  29. Porterjordan K, Rosenberg EI, Keiser JF, Gross JD, Ross AM, Nasim S, Garrett CT (1990) J Med Virol 30:85–91

    Article  CAS  Google Scholar 

  30. Kalinina O, Lebedeva I, Brown J, Silver J (1997) Nucleic Acids Res 25:1999–2004

    Article  CAS  Google Scholar 

  31. Lagally ET, Medintz I, Mathies RA (2001) Anal Chem 73:565–570

    Article  CAS  Google Scholar 

  32. Nakano M, Komatsu J, Matsuura S, Takashima K, Katsura S, Mizuno A (2003) J Biotechnol 102:117–124

    Article  CAS  Google Scholar 

  33. Shao KK, Ding WF, Wang F, Li HQ, Ma D, Wang HM (2011) PLoS One 6

  34. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Proc Natl Acad Sci U S A 100:8817–8822

    Article  CAS  Google Scholar 

  35. Diehl F, Li M, He YP, Kinzler KW, Vogelstein B, Dressman D (2006) Nat Methods 3:551–559

    Article  CAS  Google Scholar 

  36. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Science 309:1728–1732

    Article  CAS  Google Scholar 

  37. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Nature 437:376–380

    CAS  Google Scholar 

  38. Kumaresan P, Yang CJ, Cronier SA, Blazej RG, Mathies RA (2008) Anal Chem 80:3522–3529

    Article  CAS  Google Scholar 

  39. Thorsen T, Roberts RW, Arnold FH, Quake SR (2001) Phys Rev Lett 86:4163–4166

    Article  CAS  Google Scholar 

  40. Nisisako T, Torii T, Higuchi T (2002) Lab Chip 2:24–26

    Article  CAS  Google Scholar 

  41. Zagnoni M, Anderson J, Cooper JM (2010) Langmuir 26:9416–9422

    Article  CAS  Google Scholar 

  42. Gupta A, Kumar R (2010) Microfluid Nanofluid 8:799–812

    Article  Google Scholar 

  43. van Steijn V, Kleijn CR, Kreutzer MT (2010) Lab Chip 10:2513–2518

    Article  CAS  Google Scholar 

  44. Schneider T, Burnham DR, VanOrden J, Chiu DT (2011) Lab Chip 11:2055–2059

    Article  CAS  Google Scholar 

  45. Sivasamy J, Wong TN, Nguyen NT, Kao LTH (2011) Microfluid Nanofluid 11:1–10

    Article  Google Scholar 

  46. Liu HH, Zhang YH (2009) J Appl Phys 106

  47. Anna SL, Bontoux N, Stone HA (2003) Appl Phys Lett 82:364–366

    Article  CAS  Google Scholar 

  48. Ward T, Faivre M, Abkarian M, Stone HA (2005) Electrophoresis 26:3716–3724

    Article  CAS  Google Scholar 

  49. Nie ZH, Seo MS, Xu SQ, Lewis PC, Mok M, Kumacheva E, Whitesides GM, Garstecki P, Stone HA (2008) Microfluid Nanofluid 5:585–594

    Article  CAS  Google Scholar 

  50. Yobas L, Martens S, Ong WL, Ranganathan N (2006) Lab Chip 6:1073–1079

    Article  CAS  Google Scholar 

  51. Peng L, Yang M, Guo SS, Liu W, Zhao XZ (2011) Biomed Microdevices 13:559–564

    Article  Google Scholar 

  52. Takeuchi S, Garstecki P, Weibel DB, Whitesides GM (2005) Adv Mater (Weinheim, Ger) 17:1067

    Article  CAS  Google Scholar 

  53. Utada AS, Lorenceau E, Link DR, Kaplan PD, Stone HA, Weitz DA (2005) Science 308:537–541

    Article  CAS  Google Scholar 

  54. Tan YC, Fisher JS, Lee AI, Cristini V, Lee AP (2004) Lab Chip 4:292–298

    Article  CAS  Google Scholar 

  55. Link DR, Anna SL, Weitz DA, Stone HA (2004) Phys Rev Lett 92:054503

    Article  CAS  Google Scholar 

  56. Hatch AC, Fisher JS, Tovar AR, Hsieh AT, Lin R, Pentoney SL, Yang DL, Lee AP (2011) Lab Chip 11:3838–3845

    Article  CAS  Google Scholar 

  57. Link DR, Grasland-Mongrain E, Duri A, Sarrazin F, Cheng Z, Cristobal G, Marquez M, Weitz DA (2006) Angew Chem Int Ed Engl 45:2556–2560

    Article  CAS  Google Scholar 

  58. Cho SK, Moon HJ, Kim CJ (2003) J Microelectromech S 12:70–80

    Article  Google Scholar 

  59. Song H, Tice JD, Ismagilov RF (2003) Angew Chem Int Edit 42:768–772

    Article  CAS  Google Scholar 

  60. Hung LH, Choi KM, Tseng WY, Tan YC, Shea KJ, Lee AP (2006) Lab Chip 6:174–178

    Article  CAS  Google Scholar 

  61. Kohler JM, Henkel T, Grodrian A, Kirner T, Roth M, Martin K, Metze J (2004) Chem Eng J (Lausanne) 101:201–216

    CAS  Google Scholar 

  62. Fidalgo LM, Abell C, Huck WTS (2007) Lab Chip 7:984–986

    Article  CAS  Google Scholar 

  63. Mazutis L, Araghi AF, Miller OJ, Baret JC, Frenz L, Janoshazi A, Taly V, Miller BJ, Hutchison JB, Link D, Griffiths AD, Ryckelynck M (2009) Anal Chem 81:4813–4821

    Article  CAS  Google Scholar 

  64. Tresset G, Takeuchi S (2005) Anal Chem 77:2795–2801

    Article  CAS  Google Scholar 

  65. Tan WH, Takeuchi S (2006) Lab Chip 6:757–763

    Article  CAS  Google Scholar 

  66. Stroock AD, Dertinger SKW, Ajdari A, Mezic I, Stone HA, Whitesides GM (2002) Science 295:647–651

    Article  CAS  Google Scholar 

  67. Bringer MR, Gerdts CJ, Song H, Tice JD, Ismagilov RF (2004) Philos T Roy Soc A 362:1087–1104

    Article  CAS  Google Scholar 

  68. Liau A, Karnik R, Majumdar A, Cate JHD (2005) Anal Chem 77:7618–7625

    Article  CAS  Google Scholar 

  69. Cabral JT, Hudson SD (2006) Lab Chip 6:427–436

    Article  CAS  Google Scholar 

  70. Paik P, Pamula VK, Pollack MG, Fair RB (2003) Lab Chip 3:28–33

    Article  CAS  Google Scholar 

  71. Chatterjee D, Hetayothin B, Wheeler AR, King DJ, Garrell RL (2006) Lab Chip 6:199–206

    Article  CAS  Google Scholar 

  72. Tan YC, Ho YL, Lee AP (2008) Microfluid Nanofluid 4:343–348

    Article  CAS  Google Scholar 

  73. Huh D, Bahng JH, Ling YB, Wei HH, Kripfgans OD, Fowlkes JB, Grotberg JB, Takayama S (2007) Anal Chem 79:1369–1376

    Article  CAS  Google Scholar 

  74. Baret JC, Miller OJ, Taly V, Ryckelynck M, El-Harrak A, Frenz L, Rick C, Samuels ML, Hutchison JB, Agresti JJ, Link DR, Weitz DA, Griffiths AD (2009) Lab Chip 9:1850–1858

    Article  CAS  Google Scholar 

  75. Boukellal H, Selimovic S, Jia YW, Cristobal G, Fraden S (2009) Lab Chip 9:331–338

    Article  CAS  Google Scholar 

  76. Edgar JS, Milne G, Zhao YQ, Pabbati CP, Lim DSW, Chiu DT (2009) Angew Chem Int Edit 48:2719–2722

    Article  CAS  Google Scholar 

  77. Wang W, Yang C, Li CM (2009) Lab Chip 9:1504–1506

    Article  CAS  Google Scholar 

  78. Bai YP, He XM, Liu DS, Patil SN, Bratton D, Huebner A, Hollfelder F, Abell C, Huck WTS (2010) Lab Chip 10:1281–1285

    Article  CAS  Google Scholar 

  79. Huebner A, Bratton D, Whyte G, Yang M, deMello AJ, Abell C, Hollfelder F (2009) Lab Chip 9:692–698

    Article  CAS  Google Scholar 

  80. Frenz L, Blank K, Brouzes E, Griffiths AD (2009) Lab Chip 9:1344–1348

    Article  CAS  Google Scholar 

  81. Mary P, Abate AR, Agresti JJ, Weitz DA (2011) Biomicrofluidics 5

  82. Hettiarachchi K, Talu E, Longo ML, Dayton PA, Lee AP (2007) Lab Chip 7:463–468

    Article  CAS  Google Scholar 

  83. Malic L, Veres T, Tabrizian M (2009) Lab Chip 9:473–475

    Article  CAS  Google Scholar 

  84. Marz A, Henkel T, Cialla D, Schmitt M, Popp J (2011) Lab Chip 11:3584–3592

    Article  CAS  Google Scholar 

  85. Beer NR, Hindson BJ, Wheeler EK, Hall SB, Rose KA, Kennedy IM, Colston BW (2007) Anal Chem 79:8471–8475

    Article  CAS  Google Scholar 

  86. Beer NR, Wheeler EK, Lee-Houghton L, Watkins N, Nasarabadi S, Hebert N, Leung P, Arnold DW, Bailey CG, Colston BW (2008) Anal Chem 80:1854–1858

    Article  CAS  Google Scholar 

  87. Kiss MM, Ortoleva-Donnelly L, Beer NR, Warner J, Bailey CG, Colston BW, Rothberg JM, Link DR, Leamon JH (2008) Anal Chem 80:8975–8981

    Article  CAS  Google Scholar 

  88. Schaerli Y, Wootton RC, Robinson T, Stein V, Dunsby C, Neil MAA, French PMW, deMello AJ, Abell C, Hollfelder F (2009) Anal Chem 81:302–306

    Article  CAS  Google Scholar 

  89. Zeng Y, Novak R, Shuga J, Smith MT, Mathies RA (2010) Anal Chem 82:3183–3190

    Article  CAS  Google Scholar 

  90. Leng XF, Zhang WH, Wang CM, Cui LA, Yang CJ (2010) Lab Chip 10:2841–2843

    Article  CAS  Google Scholar 

  91. Novak R, Zeng Y, Shuga J, Venugopalan G, Fletcher DA, Smith MT, Mathies RA (2011) Angew Chem Int Edit 50:390–395

    Article  CAS  Google Scholar 

  92. Hua ZS, Rouse JL, Eckhardt AE, Srinivasan V, Pamula VK, Schell WA, Benton JL, Mitchell TG, Pollack MG (2010) Anal Chem 82:2310–2316

    Article  CAS  Google Scholar 

  93. Zhong Q, Bhattacharya S, Kotsopoulos S, Olson J, Taly V, Griffiths AD, Link DR, Larson JW (2011) Lab Chip 11:2167–2174

    Article  CAS  Google Scholar 

  94. Pekin D, Skhiri Y, Baret JC, Le Corre D, Mazutis L, Ben Salem C, Millot F, El Harrak A, Hutchison JB, Larson JW, Link DR, Laurent-Puig P, Griffiths AD, Taly V (2011) Lab Chip 11:2156–2166

    Article  CAS  Google Scholar 

  95. Reetz MT, Jaeger KE (1999) Biocatalysis - from Discovery to Application 200:31–57

    Article  CAS  Google Scholar 

  96. Pluckthun A, Schaffitzel C, Hanes J, Jermutus L (2001) Advances in Protein Chemistry 55(55):367–403

    Article  Google Scholar 

  97. Paegel BM (2010) Curr Opin Chem Biol 14:568–573

    Article  CAS  Google Scholar 

  98. Ellington AD, Szostak JW (1990) Nature 346:818–822

    Article  CAS  Google Scholar 

  99. Tuerk C, Gold L (1990) Science 249:505–510

    Article  CAS  Google Scholar 

  100. Robertson DL, Joyce GF (1990) Nature 344:467–468

    Article  CAS  Google Scholar 

  101. Nutiu R, Li Y (2005) Angew Chemie Int Ed 44:1061–1065

    Article  CAS  Google Scholar 

  102. Fang X, Tan W (2010) Acc Chem Res 43:48–57

    Article  CAS  Google Scholar 

  103. Zhang WY, Zhang WH, Liu ZY, Li C, Zhu Z, Yang CJ (2012) Anal Chem 84:350–355

  104. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Dontin MJ, D'Souza CA, Fox DS, Grinberg V, Fu JM, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJM, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW (2005) Science 307:1321–1324

    Article  Google Scholar 

  105. Zhao SY, Shetty J, Hou LH, Delcher A, Zhu BL, Osoegawa K, de Jong P, Nierman WC, Strausberg RL, Fraser CM (2004) Genome Res 14:1851–1860

    Article  CAS  Google Scholar 

  106. Blazej RG, Kumaresan P, Cronier SA, Mathies RA (2007) Anal Chem 79:4499–4506

    Article  CAS  Google Scholar 

  107. Ronaghi M, Uhlen M, Nyren P (1998) Science 281:363–365

    Article  CAS  Google Scholar 

  108. Goldberg SMD, Johnson J, Busam D, Feldblyum T, Ferriera S, Friedman R, Halpern A, Khouri H, Kravitz SA, Lauro FM, Li K, Rogers YH, Strausberg R, Sutton G, Tallon L, Thomas T, Venter E, Frazier M, Venter JC (2006) Proc Natl Acad Sci U S A 103:11240–11245

    Article  CAS  Google Scholar 

  109. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM (2008) Nature 452:U872–U875

    Article  CAS  Google Scholar 

  110. Vogelstein B, Kinzler KW (2004) Nat Med (N Y, NY, U S) 10:789–799

    CAS  Google Scholar 

  111. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang SL, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW (2011) Anal Chem 83:8604–8610

    Article  CAS  Google Scholar 

Download references

Acknowledgment

This work is supported by the National Basic Research Program of China (Grant 2010CB732402), National Scientific Foundation of China (Grants 21075104 and 20805038), and the Natural Science Foundation of Fujian Province for Distinguished Young Scholars (Grant 2010 J06004)

Author information

Authors and Affiliations

  1. State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, Key Laboratory of Analytical Science, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China

    Zhi Zhu, Gareth Jenkins, Wenhua Zhang, Mingxia Zhang, Zhichao Guan & Chaoyong James Yang

Authors
  1. Zhi Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gareth Jenkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenhua Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Mingxia Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Zhichao Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chaoyong James Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Chaoyong James Yang.

Additional information

Published in the special issue Young Investigators in Analytical and Bioanalytical Science with guest editors S. Daunert, J. Bettmer, T. Hasegawa, Q. Wang and Y. Wei.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhu, Z., Jenkins, G., Zhang, W. et al. Single-molecule emulsion PCR in microfluidic droplets. Anal Bioanal Chem 403, 2127–2143 (2012). https://doi.org/10.1007/s00216-012-5914-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-012-5914-x

Keywords

Search

Navigation