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Figure 1: schematic of a biosensor Transduction must be done to translate the actual sensing event (DNA binding, oxidation/reduction, etc.) into a format understandable by a computer (voltage, light intensity, mass, etc.), which then enables additional analysis and processing to produce a final, human-readable output. The multiple technologies needed to make a successful biochip — from sensing chemistry, to microarraying, to signal processing — require a true multidisciplinary approach, making the barrier to entry steep. One of the first commercial biochips was introduced by Affymetrix. Their "GeneChip" products contain thousands of individual DNA sensors for use in sensing defects, or single nucleotide polymorphisms (SNPs), in genes such as p53 (a tumor suppressor) and BRCA1 and BRCA2 (related to breast cancer) [8]. The chips are produced using microlithography techniques traditionally used to fabricate integrated circuits (see below). Biochips are a platform that require, in addition to microarray technology, transduction and signal processing technologies to output the results of sensing experiments Today, a large variety of biochip technologies are either in development or being commercialized. Numerous advancements continue to be made in sensing research that enable new platforms to be developed for new applications. Cancer diagnosis through DNA typing is just one market opportunity. A variety of industries currently desire the ability to simultaneously screen for a wide range of chemical and biological agents, with purposes ranging from testing public water systems for disease agents to screening airline cargo for explosives. Pharmaceutical companies wish to combinatorially screen drug candidates against target enzymes. To achieve these ends, DNA, RNA, proteins, and even living cells are being employed as sensing
mediators on biochips. Numerous transduction methods can be employed including surface plasmon resonance, fluorescence, and chemiluminescence. The particular sensing and transduction techniques chosen depend on factors such as price, sensitivity, and reusability. Optical transduction is more and more used since photonic devices could be small, lightweight and thus portable due to the integrability of all optical components. Furthermore, optical devices do not require electric contacts. Fluorescence is by far the most used optical signalling method but a wide-use sensor can not be limited by the labelling of the probe nor the analyte, since this step is not always possible. Reagentless optical biosensors are monitoring devices which can detect a target analyte in a heterogeneous solution without the addition of anything than the sample. In the fields of genomics and proteomics this is a straightforward advantage since it allows real-time readouts and, thus, very high throughoutputs analysis. A label free optical biosensor can be realized by integrating the biological probe with a signalling material which directly transduces the molecular recognition event into an optical signal. There are many advantages of optical sensing. Optical sensing schemes are sensitive. By measuring differences in wavelengths or times, optical signals can be readily multiplexed. Some optical techniques, such as fluorescence, have intrinsic amplification in which a single label can lead to a million photons. In addition, some optical techniques are zero or “black” background in which the only source of signal is due to the presence of the species being measured, thereby enabling high sensitivity measurements. Finally, optical signals travel in an open path—no wires or other transmitting conduits are necessary. This feature enables remote measurements to be made. There are a variety of optical sensing transduction mechanisms including: • Luminescence • Fluorescence—intensity, lifetime, polarization • Phosphorescence • Fluorescence resonance energy transfer • Absorbance • Scattering • Raman-surface enhanced, resonance • Surface plasmon resonance • Interference Each of these techniques may have several variations. Another rubric for classifying optical sensors revolves around the categories of materials, surfaces, and arrays. In the materials field, there is a burgeoning effort in developing new materials for performing optical sensing. Such materials encompass work in the fields of polymers, ceramics, and semiconductors as well as more conventional inorganic and organic materials. These materials can be used as new recognition agents, as supports for immobilizing sensing materials, as materials for concentrating analytes, and as intrinsic optical sensors with integrated functionality including binding and signal transduction. This latter goal of creating materials that integrate binding with optical signal transduction is a major area of interest and investigation. In the surfaces area, a host of new phenomena are being discovered and employed for biosensing. It should be noted that there is a growing trend aimed at creating nanoscale devices. 3
Page 1: BIOCHIP AND LAB-ON-CHIP FOR GENOMIC
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Page 25: Introduction The development of bio
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Page 39 and 40: 23. Anderson SHC, Elliot H, Wallis
Page 41 and 42: phys. stat. sol. (c) 4, No. 6, 1966
Page 43 and 44: 1968 L. De Stefano et al.: Optical
Page 45 and 46: 1970 L. De Stefano et al.: Optical
Page 47 and 48: Introduction to the sensing mechani
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Page 59 and 60: • Oxidation of porous silicon Wit
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S2020 SD’Auriaet al Fluorescence
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S2028 SD’Auriaet al [36] Szmacins
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Introduction: proteins from extremo
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Figure 2. Experimental setup used t
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Chemical and biological functionali
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Oligonucleotides direct synthesis o
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cm -1 (Si-O-Si) and 1065, 880 cm -1
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Abstract Physica E 38 (2007) 188-19
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190 surface through Si-C bonds. We
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192 Acknowledgments The authors are
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Introduction: PSi hybrid systems Mu
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8. S.H.C. Anderson, H. Elliot, D.J.
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A polymer modified PSi optical devi
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The polymer solutions were prepared
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solution of 5(6)-Carboxyfluorescein
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5 CREATED USING THE RSC ARTICLE TEM
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5 10 15 20 25 30 35 The HFB biofilm
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5 10 15 20 25 Conclusions We have d
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Introduction to Lab-on-chip technol
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• Glass etching The technology fo
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Many lab-on-chip applications have
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Microsystems Based on Porous Silico
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Sensors 2006, 6 681 optical microca
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Sensors 2006, 6 683 changed with a
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Sensors 2006, 6 685 probably exists
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Sensors 2006, 6 687 6. Obermeier, E
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LASER OXIDATION MICROPATTERNING OF
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384 48mW, using a setup composed of
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386 APO fluorescence macroscopy sys
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PUBLICATIONS: J1. Luca De Stefano,
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P12. L. De Stefano, L. Rotiroti, I.
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C18. L. De Stefano, I. Rea, L. Roti
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Appendix
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White light source Gas channels Sea
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% Reflectance 110 100 90 80 70 60 5
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IOP PUBLISHING JOURNAL OF PHYSICS:
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J. Phys.: Condens. Matter 19 (2007)
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with a number of other sugar-bindin
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treatment in the range 600-800 nm,
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Sensors 2008, 8, 1-x manuscripts; D
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Sensors 2008 3 2. Experimental A hi
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Sensors 2008 5 Figure 3. Resonant p
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Sensors 2008 7 Figure 6. Resonance
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