Question? Leave a message!




Introduction to BioMEMS & Bionanotechnology

Introduction to BioMEMS & Bionanotechnology
Introduction to BioMEMS Bionanotechnology Lecture 1 R. Bashir R. Bashir Laboratory of Integrated Biomedical Micro/Nanotechnology and Applications (LIBNA), Discovery Park School of Electrical and Computer Engineering, Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana http://engineering.purdue.edu/LIBNA 1Key Topics • Biochips/Biosensors and Device Fabrication • Cells, DNA, Proteins • Microfluidics • Biochip Sensors Detection Methods • Microarrays • Labonachip Devices Cells Bacteria Viruses Proteins DNA Molecules 2Definitions • BioMEMS are biomedical or biological applications of MEMS (micro electro mechanical systems) • BioNanotechnology is biological applications of nanotechnology (science and technology of miniaturization at scales of 100nm) 3BioMEMS and Bionanotechnology Apply micro/nanotechnology to develop novel devices and systems that have a biomedical impact or are bioinspired Micro/Nanotechnology and Systems Biology Biomedicine Novel Solutions for Novel Solutions for Frontiers in Medicine Frontiers in Materials and Biology and Information 4 ProcessingOn Size and Scale Topdown 100µm Plant and Animal Cells 10µm MEMS Microfluidics Molecular Most Bacteria Devices Molecule Specific Memory 1µm MEMS/ Sensors NEMS 2D CMOS platform 100nm Min Feature Virus of MOST (in 2004) 10nm Integrated Proteins One Helical Turn of DNA BioChips (Macro, Micro, 1nm Gate Insulator Nano) for 100nm MOST Atoms 0.1nm BottomsUp 5 Feature Size MicroElectronics Nanoscale functional MEMS elementsMore Definitions • Biosensors are ‘analytical devices that combine a biologically sensitive element with a physical or chemical transducer to selectively and quantitatively detect the presence of specific compounds in a given external environment’ VoDinh and Cullum, 2000. • Biochips can be defined as ‘microelectronicinspired devices that are used for delivery, processing, analysis, or detection of biological molecules and species’ Bashir, 2004. These devices are used to detect cells, microorganisms, viruses, proteins, DNA and related nucleic acids, and small molecules of biochemical importance and interest. 6Overview of Biosensor System Data Analysis/ Sample Processing/ Detection/ Results Separation ID • Water • Food • Air • Body Fluids 7Introduction Key Attributes of Biochips 1. Small length scale 2. Small thermal mass 3. Laminar flow, Re 1 4. High surfacetovolume ratio W.J. Chang, D. Akin, M. Sedlek, M. Ladisch, R. Bashir, Biomedical Microdevices, vol. 5, no. 4, pp. 281290, 2003. Whitesides Harvard University 8Reasons for Miniaturization • In general, the use of micro and nanoscale detection technologies is justified by, – (i) reducing the sensor element to the scale of the target species and hence providing a higher sensitivity à single entity/molecule – (ii) reduced reagent volumes and associated costs, – (iii) reduced time to result due to small volumes resulting in higher effective concentrations, – (iv) amenability of portability and miniaturization of the entire system – (v) pointofcare diagnostic, – (vi) Multiagent detection capability – (vii) Potential for use in vitro as well as in vivo 9Biochips for Detection • Applications o Medicine o Pharmaceuticals o Food Safety o Homeland Security, etc. • Integrated, Sensitive, Rapid, Cost x Performance • Commercialized; Nanogen, Affymetrix, Caliper, Others…. Cells Bacteria Viruses Proteins DNA Molecules 10Novel Tools for NanoBiology Transcription factors: Controlled Microenvironment Proteins that control the in a Biochip transcription of specific genes stimulus DNA Cell Transcription Real Real time time cell cell mRNA bio bio chemical chemical communication communication Translation Electrical Electrical Proteins or Optical Signals • Analysis of single cells and the study of their function in real time. • Increase understanding of signaling pathways inside the cell. • Basic cell functions such as differentiation, reproduction, apoptosis, etc. and their implications on various disease states. • Focus of the postgenomic era and systems biology 11BioChip/BioMEMS Materials • Silicon and microelectronic materials • Glass, Quartz • Polymers – Poly (dimethylsiloxane) (PDMS) – Poly (methyl methacrylate) (PMMA) – Teflon, etc. • Biological Entities – Cells, Proteins, DNA – Frontier of BioMEMS 12Introduction to Device Fabrication • MEMS/NEMS Silicon Fabrication – Formation of structures that could be used to form sensors and actuators. – Processing of electrical or nonelectrical signals. – Conventional and new semiconductor processing technology modules are used. – Etching, Deposition, Photolithography, Oxidation, Epitaxy, etc. – Deep RIE, Thick Plating, etc • Bulk and Surface Micromachining 13MEMS Examples From Dec 1996, Electron IC Design Probes for AFM Bulk Micromachined Accelerometer from Silicon Microstructures. Inc. DMD Chip from Texas Instruments 14MEMS Examples Single Chip Single Chip Microphone Au backplate Accelerometer (Analog Devices) Sensor Etch Cavity Chip Si Membrane Deployment of airbag Draper Labs, 15 National Semiconductor, 1998Silicon BioMEMS Examples Kumetrix IBM Zurich Research Purdue Silicon BioChip 16BioMEMS/Biochip Fabrication • In addition to Silicon…. • Biocompatibility, ideal for biomedical devices • Transparent within the visible spectrum • Rapid fabrication • Photodefinable • Chemically modifiable • Possible choices – PDMS polydimethylsiloxane, – Hydrogels – PMAA, – Teflon – SU8, etc. Lab on Chip (Caliper) 17Alternative Fabrication Methods • Soft Lithography – Replication and molding – Microcontact printing – Micromolding in capillaries – Microtransfer molding – Solvent assisted micromolding – Dip Pen Lithography • Compression Molding – Hot Embossing – Injection Molding • Inkjet Printing 18Replication and Molding • Master mold made from silicon, glass, metal, SU8 • Surface treatment of master • Pour PDMS (mix, oligomer, and CL agent) • Cure (60C, 1 hr) • Peel off PDMS structure • Mold can be used again • Y. Gia, and G. M. Whitesides, Annu. Rev. Mater. Sci. 1998, 28, 15384 19μContact Printing • Ink the PDMS structure with molecules (alkylthiols, proteins, DNA, etc.) • Transfer the layer through physical contact (optimize time) • Inking is performed via covalent binding on substrate • Can be performed on flat surface or curved surface 20PDMS/Glass (Silicon) Hybrid Biochip st (a) PDMS 1 layer Vertical channels (e) Silanized silicon mold (b) Teflon tubing (f) (f) Bonding on top of nd (c) silicon chip PDMS 2 layer (g) Connection of tubings (d) Horizontal channel for the flow of liquid Opening sealed with PDMS 21Silicon Base, 3 PDMS layers, Glass Base, 3 PDMS layers, Top I/O port, Valves Top I/O port Input Reservoir nd rd 2 Layer in 3 Layer of PDMS of PDMS st 1 Layer of PDMS Chip Underneath Input Reservoir rd Bonding Output in 3 Layer with PDMS Tube of PDMS nd 2 Layer Air channels of PDMS st 1 Layer of PDMS Metal Oxide Silicon 22Dip Pen Lithography • AFM Tip used to ‘write’ molecules • Being commercialized by Nanoink, Inc. • SAMs, DNA, Proteins, etc. • Serial (need array of cantilevers for parallel writing) • Continuous source of molecules – microfluidics Lee, K.B.; Park, S.J.; Mirkin , C.A. ; Smith, J.C.; Mrksich, M. 23 Protein nanoarrays generated by dippen nanolithography Science 2002 , 295, 17021705. Compression Molding Precision Injection Hot Embossing Molding Mold Heat Pressure Polymer (thermoplastic Features down to 0.1um material) deep and 0.6um wide (for CDR) Substrate 24NanoImprint Lithography Imprint mold with 10nm diameter holes imprinted in 10nm diameter pillars PMMA Substrate Substrate 10nm diameter metal dots • Nanoscale extension of hot embossing • Need a nanoscale master mold • Added to ITRS Roadmap 25 Steve Chou, Princeton U.Key Topics • Biochips/Biosensors and Device Fabrication • Cells, DNA, Proteins • Microfluidics • Biochip Sensors Detection Methods • Microarrays • Labonachip Devices Cells Bacteria Viruses Proteins DNA Molecules 26Cells – Brief Overview • Genetic information is contained in chromatin (a diffused mass which distinguishes to a chromosome when cell is ready to divide) • Humans have 46 chromosomes in each cell (except in reproductive cells) • Chromosomes are long, uninterrupted, packed, supercoiled linear polymer strands of DNA (deoxyribonucleic acid) 6 cm long when extended • In humans, each chromosome is 50400 x 6 10 units long 27 From: Biology, 4th Edition by CampbellCells – Brief Overview Surface Proteins Transcription factors: (could be specific to cells) Proteins that control the transcription of specific genes DNA Cell Transcription mRNA Translation Proteins 28 http://gslc.genetics.utah.edu/units/basics/transcribe/ Y YDNA to Proteins • Transcription – double stranded DNA is converted to a single stranded mRNA – RNA polymerase synthesizes the mRNA • Translation – Ribosomes ‘translate’ the sequence of bases in the mRNA to proteins. – These proteins than perform various functions inside and outside the cell 29Chromosomes à DNA 30 Decreasing complexityStructure of DNA • DNA is composed of; – a phosphate backbone where each phosphate radical has a negative charge – a Deoxyribose (D in DNA) sugar – 4 types of bases or nucleotides. These are adenine (A), thymine (T), cytosine (C), Guanine (G) • A binds to T and G binds to C complementary base pairs 31Structure of DNA 32 Pyrimidines Purines (T, C) (A, G) 2 rings 1 ringDNA Hybridization • When DNA is heated to a temperature (90°C) or exposed to pH 12, the complementary strands dissociates DNA denaturation • Process is reversible (exposure to a melting temperature T m 65°C) and 2 complementary ssDNA will hybridize to each other and join to form dsDNA • Hybridization can happen between any two complementary single stranded molecules (DNA/DNA, DNA/RNA, RNA/RNA) • Can provide a very sensitive means to detect specific nucleotide sequences • Factors affecting hybridizaton : temperature, Salt and buffer concentration, G C content T can be calculated m • Rate of hybridization is proportional to concentration of target and probe and limited by the lower concentration material 33DNA Hybridization 34DNA Hybridization Stringency A T A C T Reduced C G G C Stringency G A T A G C A Hybridization C C A T A C T G C G C Stringent T A T A G G Hybridization T G C 35PCR Polymerase Chain Reaction • Technique to amplify (make multiple copies) of known DNA molecules invented in 1985 • Use enzyme called DNA polymerase and primers (short ssDNA strands) • Billions of copies can be made within hours in laboratory • Very useful in research, diagnosis, forensics, etc where large samples are required from very small concentrations. 36PCR Sequence • Primers are short strands of nucleotides which are complementary to specific regions of the target DNA to the amplified hence the ‘end’ sequence of short regions of the target DNA to be 1. Denature 1. Denature 90C 90C copied is needed 3. Extend 3. Extend • DNA Polymerase is an enzyme 70C 70C which takes nucleotides from the 55C 55C ambient solution and starts to 2. Anneal 2. Anneal construct the complementary RT sequence • An adequate supply of nucleotides are needed (dNTPs 1530 1530 3060 Time sec sec sec deoxyribonucleose triphosphates dATP, dCTP, dGTP, dTTP) 37 TemperatureProtein Structure NH 2 NH 2 H R C H R1 C COOH Peptide Bond C H R2 Peptide Bond R3 C H Peptide Bond R4 C H COOH http://www.umass.edu/microbio/rasmol/rotating.htm 38 http://www.umass.edu/microbio/chime/antibody/
Website URL
Comment