一种基于SU8聚合物的基因测序芯片

韩伟静; 魏清泉; 李运涛; 周晓光; 俞育德

doi:10.7498/aps.62.148701

摘要

基因测序技术极大地推动了生物学和医学研究的发展. 结合了焦磷酸测序原理及阵列式微反应池芯片的高通量测序仪在从头测序和宏基因组测序方面有着不可替代的作用. 本文首次提出并研制了一种基于SU8聚合物的基因测序芯片. 选择了高传输效率、低耦合损耗的光纤面板作为基片, 通过改善SU8均匀性及释放应力, 在光纤面板上成功制备出百万数量级阵列式微反应池; 设计并制作侧壁镀膜装置, 实现了SU8阵列式微反应池侧壁选择性光学薄膜蒸镀, 有效地提高了微反应池的光学隔离度, 将相邻微反应池之间的光串扰率平均值从25%降低到了1%, 满足了高通量焦磷酸测序对测序芯片独立并行传输弱光信号的要求. 基于SU8聚合物的基因测序芯片制备工艺简单、成本低廉, 具有良好的应用前景.

关键词:

DNA测序 /
SU8 /
微反应池 /
光纤面板

Abstract

DNA sequencing technology has markedly advanced the development of biological and medicinal sciences. High-throughput pyrosequencing instruments that combine the pyrosequencing with microfabricated high-density picoliter reactors have been proved to be suitable for de novo sequencing and metagenome sequencing. In the present work, we report on an alternative sequencing chip consisting of hundreds of thousands of picoliter sized honeycombed SU8 reaction vessels on a fiber-optic slide by lithography technique for high-throughput pyrosequencing instruments. Highly reproducible fabrication process of SU8 sequencing chip is achieved through the improvement on SU8 film thickness uniformity and relaxation of SU8 residual stress during fabrication. To achieve the optical isolation required for SU8 reaction wells, metal film is selectively deposited on the side walls of the reaction vessels by reformating vacuum coating. With the metal coating, the average value of optical cross talking between SU8 reaction vessels is reduced from 25% to 1%. The SU8 sequencing chip demonstrates an excellent light transmission characteristic and meets the need of pyrosequencing application.

Keywords:

作者及机构信息

1.
中国科学院半导体研究所, 集成光电子学国家重点实验室, 北京 100083;

2.
中国科学院半导体研究所, 中国科学院北京基因组研究所, 生物信息获取与传感技术联合实验室, 北京 100083

基金项目: 中国科学院科研装备研制项目(批准号: YZ200823)和中国博士后科学基金(批准号: 2011M500371)资助的课题.

Authors and contacts

1.
State Key Laboratory of Integrated Optoelectronics, Institute of Semicnductorss, Chinese Academy of Sciences, Beijing 100083, China;

2.
The Joint Laboratory of Bioinformation Acquisition and Sensing Technology, Institute of Semicnductorss, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100083, China

Funds: Project supported by the Scientific Equipment Research Project of China Academy of Science (Grant No. YZ200823) and the China Postdoctoral Science Foundation (Grant No. 2011M500371).

参考文献

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[10]	Leamon J H, Lee W L, Tatrtaro K R, Lanza J R, Sarlis G J, de Winter A D, Berka J, Lohman K L 2003 Electrophoresis 24 3769
[11]	Pantano P, Walt D R 1995 Anal. Chem. 65 481A
[12]	Walt D R 2010 Chem. Soc. Rev. 39 38
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[14]	Wang J M, Kong D P, Wang L L 2012 Acta Phys. Sin. 61 054216 (in Chinese) [王金猛, 孔德鹏, 王丽莉 2012 物理学报 61 054216]
[15]	Ransley J H T, Watari M, Sukumaran D, McKendry R A, Seshia A A 2006 Microelectron. Eng. 83 1621
[16]	El-Ali J, Nielsen I R, Poulsen C R, Bang D D, Telleman P, Wolffa A 2004 Sens. Actuators. A: Phys. 110 3
[17]	Sanzaa F J, Lagunaa M F, Casquela R, Holgadoa M, Barriosb C A, Ortegac F J, Romerob D L, Ballesterosa J J, Banulsc M J, Maquieirac A, Puchadesc R 2011 Appl. Surf. Sci. 257 5403
[18]	Wang Y L, Sims C E, Marc P, Bachman M, Li G P, Allbritton N L 2006 Langmuir 22 8257
[19]	Mackay R E, Le H R, Keatch R P 2011 J. Micro-Nano Mech. 6 13
[20]	Verdoy D, Barrenetxeaa Z, Berganzoa J, Agirregabiriab M, Ruano-Lópezb J M, Marimónc J M, Olabarríaa G 2012 Biosens. Bioelectron. 32 259
[21]	Shaw M, Nawrocki D, Hurditch R, Johnoson D 2003 Microsyst. Technol. 10 1
[22]	Liu G, Tian Y, Kan Y 2005 Microsyst. Technol. 11 343
[23]	Hammacher J, Fuelle A, Flaemig J, Saupe J, Loechel B, Grimm J 2008 Microsyst. Technol. 14 1515
[24]	Feng R, Farris J 2002 J. Mater. Sci. 37 4793
[25]	Nguyen T T N, Nguyen Q L, Zyss J 2013 Appl. Phys. A DOI:10.1007/ s00339-012-7537-7
[26]	Tung K K, Wong W H, Pun E Y B 2005 Appl. Phys. A 80 621
[27]	Gunde M K, Hauptman N, Macek M, Kunaver M 2009 Appl. Phys. A 95 673
[28]	Dai W, Lian K, Wang W J 2005 Microsyst. Technol. 11 526
[29]	Macleod H A 1974 Thin-Film Optical Filter (London: Institute of Physics Publishing) p158

施引文献

[1]	Sanger F, Nicklen S, Coulson A R 1977 Proc. Natl. Acad. Sci. USA 74 5463
[2]	Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P 1996 Anal. Biochem. 242 84
[3]	Eid J, Fehr A, Gray J, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Winter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma X X, Marks P, Maxham M, Murphy M, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S 2009 Science 323 133
[4]	Branton D, Dreamer D W, Marziali A, Bayley H, Benner S A, Butler T, Ventra M D, Garaj S, Hibbs A, Huang X H, Jovanovich S B, KrsticP S, Lindsay S, Ling X S, Mastrangelo C H, Meller A, Oliver J S, Pershin Y V, Ramsey J M, Riehn R, Soni1 G V, Tabard C V, Wanunu M, Wiggin M, Schloss J A 2008 Nat. Biotechnol. 26 1146
[5]	Jiang S C, Zhang L X, Xia A G, Chen H P 2010 Acta Phys. Sin. 59 4337 (in Chinese) [江绍钏, 章林溪, 夏阿根, 陈宏平 2010 物理学报 59 4337]
[6]	Zhou X G, Ren L F, Li Y T, Zhang M, Yu Y D, Yu J 2010 Sci. China Life Sci. 53 44
[7]	Leamon J H, Rothberg J M 2007 Chem. Rev. 107 3367
[8]	Margulies M, Egholm M, Altman W E, Attiya1 S, Bader J S, Bemben L A, Berka J, Braverman M S, Chen Y J, Chen J T, Dewell S B, Du L, Fierro J M, Gomes X V, Godwin B C, He W, Helgesen S, Ho C H, Irzyk G P, Jando S C, Alenquer M L I, Jarvie T P, Jirage K B, Kim J B, Knight J R, Lanza J R, Leamon J H, Lefkowitz S M, Lei M, Li J, Lohman K L, Lu H, Makhijani V B, McDade K E, McKenna M P, Myers E W, Nickerson E, Nobile J R, Plant R, Puc B P, Ronan M T, Roth G T, Sarkis G J, Simons J F, Simpson J W, Srinivasan M, Tartaro K R, Tomasz A, Vogt K A, Volkmer G A, Wang S H, Wang Y, Weiner M P, Yu P G, Begley R F, Rothberg J M 2005 Nature 437 376
[9]	Yuan L N, Ren L F, Li Y T, Han W J, Yu Y, Chu Y N, Liu G M, Yu D, Teng M J, Wang L, Wang X M, Zhou X G, Yu Y D, Yu J 2011 Sci. China Life Sci. 54 835
[10]	Leamon J H, Lee W L, Tatrtaro K R, Lanza J R, Sarlis G J, de Winter A D, Berka J, Lohman K L 2003 Electrophoresis 24 3769
[11]	Pantano P, Walt D R 1995 Anal. Chem. 65 481A
[12]	Walt D R 2010 Chem. Soc. Rev. 39 38
[13]	Epstein J R, Leung P K, Lee K H, Walt D R 2003 Biosens. Bioelectron. 18 541
[14]	Wang J M, Kong D P, Wang L L 2012 Acta Phys. Sin. 61 054216 (in Chinese) [王金猛, 孔德鹏, 王丽莉 2012 物理学报 61 054216]
[15]	Ransley J H T, Watari M, Sukumaran D, McKendry R A, Seshia A A 2006 Microelectron. Eng. 83 1621
[16]	El-Ali J, Nielsen I R, Poulsen C R, Bang D D, Telleman P, Wolffa A 2004 Sens. Actuators. A: Phys. 110 3
[17]	Sanzaa F J, Lagunaa M F, Casquela R, Holgadoa M, Barriosb C A, Ortegac F J, Romerob D L, Ballesterosa J J, Banulsc M J, Maquieirac A, Puchadesc R 2011 Appl. Surf. Sci. 257 5403
[18]	Wang Y L, Sims C E, Marc P, Bachman M, Li G P, Allbritton N L 2006 Langmuir 22 8257
[19]	Mackay R E, Le H R, Keatch R P 2011 J. Micro-Nano Mech. 6 13
[20]	Verdoy D, Barrenetxeaa Z, Berganzoa J, Agirregabiriab M, Ruano-Lópezb J M, Marimónc J M, Olabarríaa G 2012 Biosens. Bioelectron. 32 259
[21]	Shaw M, Nawrocki D, Hurditch R, Johnoson D 2003 Microsyst. Technol. 10 1
[22]	Liu G, Tian Y, Kan Y 2005 Microsyst. Technol. 11 343
[23]	Hammacher J, Fuelle A, Flaemig J, Saupe J, Loechel B, Grimm J 2008 Microsyst. Technol. 14 1515
[24]	Feng R, Farris J 2002 J. Mater. Sci. 37 4793
[25]	Nguyen T T N, Nguyen Q L, Zyss J 2013 Appl. Phys. A DOI:10.1007/ s00339-012-7537-7
[26]	Tung K K, Wong W H, Pun E Y B 2005 Appl. Phys. A 80 621
[27]	Gunde M K, Hauptman N, Macek M, Kunaver M 2009 Appl. Phys. A 95 673
[28]	Dai W, Lian K, Wang W J 2005 Microsyst. Technol. 11 526
[29]	Macleod H A 1974 Thin-Film Optical Filter (London: Institute of Physics Publishing) p158

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