DNA(去氧核糖核酸)分析被廣泛地應用在生物醫學測試以及許多日常生活中相關應用的生物鑑定。因為DNA本身具有專一性的特點，所以我們可以藉由DNA分析來檢驗樣本內是否含有目標DNA以及它在樣本中的含量。

滾環擴增法(Rolling Circle Amplification)是用於DNA定性和定量分析的新穎技術。不同於傳統的聚合酶鏈鎖反應(Polymers Chain Reaction)，這種滾環式擴增法可以在室溫下針對從檢體中取出的微量目標DNA進行大量複製。此外，固定式滾環擴增法可以藉由3-氨基丙基三甲氧基甲矽烷(APTES)修飾矽化物表面進而讓該反應能在其上進行。在本論文中，我們將使用CMOS元件即時檢測目標DNA在進行固定式滾環擴增法時的濃度變化。不同於以往使用螢光標定法或是進行電泳實驗，我們使用一個具有氮化矽絕緣層的CMOS延伸閘極場效電晶體(CMOS-compatible Extended-Gate Field-Effect-Transistor)即時感測目標DNA在固定式滾環擴增法中的濃度變化。此外我們也使用另一種CMOS開閘極離子感測電晶體 (CMOS-compitable open-gate Ion-Sensitive Field-Effect-Transistor)來測試DNA的電性量測。 最後我們提出並量測三種用來直接讀取表面電位變化的嵌入式延伸閘極電晶體讀值電路。

It is well known that the DNA (Deoxyribonucleic Acid) assays have been used widely in bio-medical tests and in many applications of bio-identification. Because DNA has the specific property, we can use DNA assays to justify if the target DNA exists and how many it is in the samples.

Rolling Circle Amplification (RCA) is a novel technology in both quantitative and qualitative DNA assays. Unlike the conventional Polymerase Chain Reaction (PCR) process, the RCA process can be proceeded in the room temperature to amplify a few of target DNAs which are extracted from the samples. Besides, the immobilized RCA can occur on the surface of silicon-based material with the modification of 3-Aminopropyltriethoxysilane (APTES). In this work, we are devoted to real-time detecting the changes of DNA concentrations in the immobilized RCA process with the current CMOS devices. Instead of using the fluorescence-labeling or doing the electrophoresis, a CMOS-compatible Extended-Gate Field Effect Transistor (EGFET) with its native passivation (silicon nitride) is employed to monitor the concentration change of the target DNA in the immobilized RCA process. Besides, the other CMOS-compatible open-gate ISFET is also proposed to do the pilot test of the DNA detection. Finally, three types of readout circuits with embedded EGFETs are proposed to read the surface potential of the embedded EGFETs directly and characterized electrically.

Chapter 1 ：Introduction
1.1 Motivation
1.2 Contribution to Knowledge
1.3 Chapter Layout
Chapter 2 ：Literature Review
2.1 DNA Amplification Methods
2.1.1 The Polymerase Chain Reaction
2.1.2 The Rolling Circle Amplification
2.2 Label-Free DNA Detection
2.2.1 Detecting the Intrinsic Charge of DNAs
2.2.2 The Charge Redistribution within The Intermolecular Space of DNAs
2.3 Label-Free DNA Detection Devices
2.3.1 Electrical-Gap Devices
2.3.2 FETs
2.3.3 Impedance Measurement
Chapter 3 ：Label-Free Detection of DNA with CMOS- Compatible ISFETs
3.1 Pilot experiments with Open-Gate ISFETs
3.1.1 Post-CMOS Micromachining Process of Open-Gate ISFETs
3.1.2 Electrical Tests
3.1.3 Methodology of ds-DNA Immobilization
3.2 Design of Extend-Gate ISFETs
3.3 Measurement Setup
3.4 Experimental Results with EGFETs
3.5 Discussion
3.6 Summary
Chapter 4 ：Detecting the Rolling Circle Amplification with EGFETs
4.1 The Immobilization of RCA Primers
4.2 Measurement Setup
4.3 Experimental Results
4.4 Discussion
4.5 Summary
Chapter 5 ：EGFETs Integrated with Detection Circuitry on a Single Chip
5.1 Design Considerations
5.1.1 Sensor Structure
5.1.2 Integrated Circuitry
5.2 Simulation & Layout
5.2.1 First Edition CVCC Readout Circuit
5.2.2 Second Edition CVCC Readout Circuit
5.2.3 Embedded EGFET OP Readout Circuit
5.2.4 The Tunable Resistor
5.2.5 The Whole Chip Layout
5.3 Characterization of EGFETs and Detection Circuitries 75
5.3.1 The Capacitance of CMOS Passivation Layer
5.3.2 The Input Dynamic Range and Noise Level of The Readout Circuits without The Extended Gate
5.3.3 The Input Dynamic Range of The Readout Circuits with EGFETs
5.3.4 The Long Term Measurement
5.4 Summary
Chapter 6 ：Conclusion and Future Work
6.1 Conclusion
6.2 Future Work
Appendix
1. The coupling ratio measurement of EGFET sensors with the external CVCC circuit
2. Measurement results with the fluorescent photographs of the EGFET sensors which are used in the RCA process
3. The Atomic Force Microscopy (AFM) photographs of RCA
Bibliography

[1] K. Dong-Sun, et al., "Field Effect Transistor-based Bimolecular Sensor Employing a Pt Reference Electrode for the Detection of Deoxyribonucleic Acid Sequence," Japanese Journal of Applied Physics, vol. 43, pp. 3855-3859, 2004.
[2] Y. Ishige, et al., "Immobilization of DNA Probes onto Gold Surface and its Application to Fully Electric Detection of DNA Hybridization using Field-Effect Transistor Sensor," Japanese Journal of Applied Physics, vol. 45, p. 3776, 2006.
[3] S. Ingebrandt, et al., "Label-free detection of single nucleotide polymorphisms utilizing the differential transfer function of field-effect transistors," Biosensors and Bioelectronics, vol. 22, pp. 2834-2840, 2007.
[4] K. Kleppe, et al., "Studies on polynucleotides. 96. Repair replication of short synthetic DNAs as catalyzed by DNA polymerases," Journal of molecular biology, vol. 56, 1971.
[5] R. Saiki, "Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia," Science, vol. 230, pp. 1350-1354, 1985.
[6] A. Chien, et al., "Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus," Journal of Bacteriology, vol. 127, p. 1550, 1976.
[7] “Principle of the PCR” [Online]. Available: http://users.ugent.be/~avierstr/principles/pcr.html."
[8] P. Lizardi, et al., "Mutation detection and single-molecule counting using isothermal rolling-circle amplification," Nature Genetics, vol. 19, pp. 225-232, 1998.
[9] D. Bunka and P. Stockley, "Aptamers come of age? at last," Nature Reviews Microbiology, vol. 4, pp. 588-596, 2006.
[10] D. Haible, et al., "Rolling circle amplification revolutionizes diagnosis and genomics of geminiviruses," Journal of virological methods, vol. 135, pp. 9-16, 2006.
[11] “RCA法的意義與原理” [Online]. Available: http://www.coa.gov.tw/view.php?catid=12672.
[12] Y. Cheng, et al., "An array-based CMOS biochip for electrical detection of DNA with multilayer self-assembly gold nanoparticles," Sensors and Actuators B: Chemical, vol. 109, pp. 249-255, 2005.
[13] S. Park, et al., "Array-based electrical detection of DNA with nanoparticle probes," Science, vol. 295, p. 1503, 2002.
[14] Y. Cheng, et al., "Development of an integrated CMOS DNA detection biochip," Sensors and Actuators B: Chemical, vol. 120, pp. 758-765, 2007.
[15] T. Sakata, et al., "DNA analysis chip based on field-effect transistors," Japanese Journal of Applied Physics, vol. 44, pp. 2854-2859, 2005.
[16] C. Tsai, et al., "Electrical detection of DNA hybridization with multilayer gold nanoparticles between nanogap electrodes," Microsystem Technologies, vol. 11, pp. 91-96, 2005.
[17] S. F. Liu, et al., "Electrochemical DNA biosensor fabrication with hollow gold nanospheres modified electrode and its enhancement in DNA immobilization and hybridization," Biosensors & Bioelectronics, vol. 25, pp. 1640-1645, Mar 2010.
[18] D. Braekenab, et al., "Electronic DNA hybridisation detection in low-ionic strength solutions," Journal of Experimental Nanoscience, vol. 3, pp. 157-169, 2008.
[19] A. Bonanni, et al., "Impedimetric genosensors for the detection of DNA hybridization," Analytical and Bioanalytical Chemistry, vol. 385, pp. 1195-1201, 2006.
[20] A. Poghossian, et al., "Label-free detection of charged macromolecules by using a field-effect-based sensor platform: Experiments and possible mechanisms of signal generation," Applied Physics A: Materials Science & Processing, vol. 87, pp. 517-524, 2007.
[21] J. Daniels and N. Pourmand, "Label-free impedance biosensors: Opportunities and challenges," Electroanalysis, vol. 19, p. 1239, 2007.
[22] R. Saiki, et al., "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase," Science(Washington), vol. 239, pp. 487-487, 1988.
[23] M. Schoning and A. Poghossian, "Recent advances in biologically sensitive field-effect transistors (BioFETs)," The Analyst, vol. 127, pp. 1137-1151, 2002.
[24] C. Tsai, et al., "An ultra sensitive DNA detection by using gold nanoparticle multilayer in nano-gap electrodes," Microelectronic Engineering, vol. 78, pp. 546-555, 2005.
[25] K. Park, et al., "Fabrication and characteristics of MOSFET protein chip for detection of ribosomal protein," Biosensors and Bioelectronics, vol. 20, pp. 2111-2115, 2005.
[26] A. Poghossian, et al., "Possibilities and limitations of label-free detection of DNA hybridization with field-effect-based devices," Sensors and Actuators B: Chemical, vol. 111, pp. 470-480, 2005.
[27] C. Lee, et al., "Ion-Sensitive Field-Effect Transistor for Biological Sensing," Sensors, vol. 9, p. 7111, 2009.
[28] P. Bergveld, "Development of an ion-sensitive solid-state device for neurophysiological measurements," IEEE Transactions on Bio-Medical Engineering, 1970.
[29] W. Chung, et al., "Drift Response Macromodel and Readout Circuit Development for ISFET and Its H+ Sensing Applications," Journal of Medical and Biological Engineering, vol. 26, 2006.
[30] S. Jamasb, et al., "A physical model for threshold voltage instability inSi 3 N 4-gate H-sensitive FET's (pHISFET's)," IEEE Transactions on Electron Devices, vol. 45, pp. 1239-1245, 1998.
[31] W. Siu and R. Cobbold, "Basic properties of the electrolyte!XSiO 2!XSi system: physical and theoretical aspects," IEEE Transactions on Electron Devices, vol. 26, pp. 1805-1815, 1979.
[32] W. Chung, et al., "ISFET interface circuit embedded with noise rejection capability," Electronics Letters, vol. 40, pp. 1115-1116, 2004.
[33] W. Chung, et al., "New ISFET interface circuit design with temperature compensation," Microelectronics Journal, vol. 37, pp. 1105-1114, 2006.
[34] David M Garner, et al., "A Multichannel DNA SoC for Rapid Point of Care Gene Detection," in Proc. Int. Solid-State Circuits Conf. (ISSCC’10), San Francisco, CA, Feb. 7-11, 2010, pp. 492-493.
[35] A. Zebda, et al., "Electrical resistivity dependence of semi-conductive oxide electrode on the label-free electrochemical detection of DNA," Sensors and Actuators B-Chemical, vol. 144, pp. 176-182, Jan 2010.
[36] A. Bard and L. Faulkner, Electrochemical methods: fundamentals and applications: Wiley New York, 1980.
[37] R. GhoshMoulick, et al., "Impedimetric detection of covalently attached biomolecules on field-effect transistors," physica status solidi (a), vol. 206, pp. 417-425, 2009.
[38] J. Macdonald, "Impedence Spectroscopy--Emphasizing Solid Materials and Systems," Wiley-Interscience, John Wiley and Sons, pp. 1-346, 1987.
[39] J. Jorcin, et al., "CPE analysis by local electrochemical impedance spectroscopy," Electrochimica Acta, vol. 51, pp. 1473-1479, 2006.
[40] T. Pajkossy, "Impedance of rough capacitive electrodes," Journal of Electroanalytical Chemistry, vol. 364, pp. 111-125, 1994.
[41] Z. Kerner and T. Pajkossy, "On the origin of capacitance dispersion of rough electrodes," Electrochimica Acta, vol. 46, pp. 207-211, 2000.
[42] BURGESS, et al., "Electric field driven protonation/deprotonation of self-assembled monolayers of acid-terminated thiols," Biomaterials, vol. 26, pp. 2695-2704, 2005.
[43] D. Macdonald, "Reflections on the history of electrochemical impedance spectroscopy," Electrochimica Acta, vol. 51, pp. 1376-1388, 2006.
[44] A. Hatch, et al., "Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection," Genetic Analysis: Biomolecular Engineering, vol. 15, pp. 35-40, 1999.
[45] C. Chang, et al., "A CMOS neuroelectronic interface based on two-dimensional transistor arrays with monolithically-integrated circuitry," Biosensors and Bioelectronics, vol. 24, pp. 1757-1764, 2009.
[46] F. Pouthas, et al., "DNA detection on transistor arrays following mutation-specific enzymatic amplification," Applied Physics Letters, vol. 84, p. 1594, 2004.
[47] Y. Han, et al., "Detection of DNA hybridization by a field-effect transistor with covalently attached catcher molecules," Surface and Interface Analysis, vol. 38, pp. 176-181, 2006.
[48] T. Uno, et al., "Direct Deoxyribonucleic Acid Detection Using Ion-Sensitive Field-Effect Transistors Based on Peptide Nucleic Acid," Japanese Journal of Applied Physics, vol. 43, p. 1584, 2004.
[49] A. Poghossian, et al., "Field-effect sensors for monitoring the layer-by-layer adsorption of charged macromolecules," Sensors and Actuators B: Chemical, vol. 118, pp. 163-170, 2006.
[50] M. Deen, et al., "High Sensitivity Detection of Biological Species via the Field-Effect," 2006, pp. 381-385.
[51] F. Uslu, et al., "Labelfree fully electronic nucleic acid detection system based on a field-effect transistor device," Biosensors and Bioelectronics, vol. 19, pp. 1723-1731, 2004.
[52] M. Waleed Shinwari, et al., "Study of the electrolyte-insulator-semiconductor field-effect transistor (EISFET) with applications in biosensor design," Microelectronics Reliability, vol. 47, pp. 2025-2057, 2007.
[53] S. Jamasb, et al., "A physical model for drift in pH ISFETs," Sensors and Actuators B: Chemical, vol. 49, pp. 146-155, 1998.
[54] L. Yang, et al., "Real-time rolling circle amplification for protein detection," Anal. Chem, vol. 79, pp. 3320-3329, 2007.
[55] P. Chan and D. Chen, "A CMOS ISFET interface circuit with dynamic current temperature compensation technique," IEEE Transactions on Circuits and Systems I: Regular Papers, vol. 54, pp. 119-129, 2007.
[56] W. Chung, et al., "ISFET performance enhancement by using the improved circuit techniques," Sensors and Actuators B: Chemical, vol. 113, pp. 555-562, 2006.
[57] S. Casans, et al., "Novel voltage-controlled conditioning circuit applied to the ISFETs temporary drift and thermal dependency," Sensors and Actuators B: Chemical, vol. 91, pp. 11-16, 2003.
[58] P. Allen and D. Holberg, CMOS analog circuit design: Oxford University Press New York, 2002.
[59] H. Wong and M. White, "A CMOS-integrated'ISFET-operational amplifier' chemical sensor employing differential sensing," IEEE Transactions on Electron Devices, vol. 36, pp. 479-487, 1989.
[60] I. Huang, et al., "Improvement of integrated Ag/AgCl thin-film electrodes by KCl-gel coating for ISFET applications," Sensors and Actuators B: Chemical, vol. 94, pp. 53-64, 2003.