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Special Issue "DNA Sensors and Biosensors"

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A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Chemical Sensors".

Deadline for manuscript submissions: closed (30 September 2009)

Special Issue Editor

Guest Editor
Prof. Dr. Heinz-Bernhard Kraatz (Website)

Department of Physical and Environmental Sciences, University of Toronto at Scarborough, 1265 Military Trail, Toronto M1C 1A4, Canada
Interests: electrochemical sensors; DNA and protein biosensors; chemical sensors; self-assembly; kinases; bioconjugates; secondary structure mimics

Special Issue Information

This special issue is devoted to DNA Sensors and Biosensors for the detection of DNA hybridization events, the detection of base-pair mismatches, and the detection of DNA-molecule interactions including aptamers, DNA-protein and DNA-small molecule interactions. Contributions are invited describing optical and electrochemical detection methods.

Related Special Issue: 2005 DNA Based Sensors: http://www.mdpi.com/journal/sensors/special_issues/dna-based-sensors

Keywords

  • DNA
  • single nucleotide mismatch
  • aptamers
  • bioconjugates
  • biosensors
  • impedance sensors
  • SPR
  • fluorescence sensors

Published Papers (6 papers)

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Research

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Open AccessArticle Real-time PCR Machine System Modeling and a Systematic Approach for the Robust Design of a Real-time PCR-on-a-Chip System
Sensors 2010, 10(1), 697-718; doi:10.3390/s100100697
Received: 7 December 2009 / Revised: 8 January 2010 / Accepted: 12 January 2010 / Published: 19 January 2010
Cited by 5 | PDF Full-text (1036 KB) | HTML Full-text | XML Full-text
Abstract
Chip-based DNA quantification systems are widespread, and used in many point-of-care applications. However, instruments for such applications may not be maintained or calibrated regularly. Since machine reliability is a key issue for normal operation, this study presents a system model of the [...] Read more.
Chip-based DNA quantification systems are widespread, and used in many point-of-care applications. However, instruments for such applications may not be maintained or calibrated regularly. Since machine reliability is a key issue for normal operation, this study presents a system model of the real-time Polymerase Chain Reaction (PCR) machine to analyze the instrument design through numerical experiments. Based on model analysis, a systematic approach was developed to lower the variation of DNA quantification and achieve a robust design for a real-time PCR-on-a-chip system. Accelerated lift testing was adopted to evaluate the reliability of the chip prototype. According to the life test plan, this proposed real-time PCR-on-a-chip system was simulated to work continuously for over three years with similar reproducibility in DNA quantification. This not only shows the robustness of the lab-on-a-chip system, but also verifies the effectiveness of our systematic method for achieving a robust design. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)
Open AccessArticle Chip-Oriented Fluorimeter Design and Detection System Development for DNA Quantification in Nano-Liter Volumes
Sensors 2010, 10(1), 146-166; doi:10.3390/s100100146
Received: 23 November 2009 / Revised: 11 December 2009 / Accepted: 22 December 2009 / Published: 28 December 2009
Cited by 2 | PDF Full-text (850 KB) | HTML Full-text | XML Full-text
Abstract
The chip-based polymerase chain reaction (PCR) system has been developed in recent years to achieve DNA quantification. Using a microstructure and miniature chip, the volume consumption for a PCR can be reduced to a nano-liter. With high speed cycling and a low [...] Read more.
The chip-based polymerase chain reaction (PCR) system has been developed in recent years to achieve DNA quantification. Using a microstructure and miniature chip, the volume consumption for a PCR can be reduced to a nano-liter. With high speed cycling and a low reaction volume, the time consumption of one PCR cycle performed on a chip can be reduced. However, most of the presented prototypes employ commercial fluorimeters which are not optimized for fluorescence detection of such a small quantity sample. This limits the performance of DNA quantification, especially low experiment reproducibility. This study discusses the concept of a chip-oriented fluorimeter design. Using the analytical model, the current study analyzes the sensitivity and dynamic range of the fluorimeter to fit the requirements for detecting fluorescence in nano-liter volumes. Through the optimized processes, a real-time PCR on a chip system with only one nano-liter volume test sample is as sensitive as the commercial real-time PCR machine using the sample with twenty micro-liter volumes. The signal to noise (S/N) ratio of a chip system for DNA quantification with hepatitis B virus (HBV) plasmid samples is 3 dB higher. DNA quantification by the miniature chip shows higher reproducibility compared to the commercial machine with respect to samples of initial concentrations from 103 to 105 copies per reaction. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)

Review

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Open AccessReview Nanomaterials as Analytical Tools for Genosensors
Sensors 2010, 10(1), 963-993; doi:10.3390/s100100963
Received: 12 December 2009 / Revised: 8 January 2010 / Accepted: 11 January 2010 / Published: 26 January 2010
Cited by 34 | PDF Full-text (361 KB) | HTML Full-text | XML Full-text
Abstract
Nanomaterials are being increasingly used for the development of electrochemical DNA biosensors, due to the unique electrocatalytic properties found in nanoscale materials. They offer excellent prospects for interfacing biological recognition events with electronic signal transduction and for designing a new generation of [...] Read more.
Nanomaterials are being increasingly used for the development of electrochemical DNA biosensors, due to the unique electrocatalytic properties found in nanoscale materials. They offer excellent prospects for interfacing biological recognition events with electronic signal transduction and for designing a new generation of bioelectronic devices exhibiting novel functions. In particular, nanomaterials such as noble metal nanoparticles (Au, Pt), carbon nanotubes (CNTs), magnetic nanoparticles, quantum dots and metal oxide nanoparticles have been actively investigated for their applications in DNA biosensors, which have become a new interdisciplinary frontier between biological detection and material science. In this article, we address some of the main advances in this field over the past few years, discussing the issues and challenges with the aim of stimulating a broader interest in developing nanomaterial-based biosensors and improving their applications in disease diagnosis and food safety examination. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)
Open AccessReview Aptamer-Functionalized Nano-Biosensors
Sensors 2009, 9(12), 10356-10388; doi:10.3390/s91210356
Received: 22 October 2009 / Revised: 3 December 2009 / Accepted: 3 December 2009 / Published: 21 December 2009
Cited by 61 | PDF Full-text (1369 KB) | HTML Full-text | XML Full-text
Abstract
Nanomaterials have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high surface energy and surface-to-volume ratio, and tunable surface properties. Aptamers are oligonucleotides that can bind their target ligands with high affinity. The [...] Read more.
Nanomaterials have become one of the most interesting sensing materials because of their unique size- and shape-dependent optical properties, high surface energy and surface-to-volume ratio, and tunable surface properties. Aptamers are oligonucleotides that can bind their target ligands with high affinity. The use of nanomaterials that are bioconjugated with aptamers for selective and sensitive detection of analytes such as small molecules, metal ions, proteins, and cells has been demonstrated. This review focuses on recent progress in the development of biosensors by integrating functional aptamers with different types of nanomaterials, including quantum dots, magnetic nanoparticles (NPs), metallic NPs, and carbon nanotubes. Colorimetry, fluorescence, electrochemistry, surface plasmon resonance, surface-enhanced Raman scattering, and magnetic resonance imaging are common detection modes for a broad range of analytes with high sensitivity and selectivity when using aptamer bioconjugated nanomaterials (Apt-NMs). We highlight the important roles that the size and concentration of nanomaterials, the secondary structure and density of aptamers, and the multivalent interactions play in determining the specificity and sensitivity of the nanosensors towards analytes. Advantages and disadvantages of the Apt-NMs for bioapplications are focused. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)
Open AccessReview DNA Hybridization Sensors Based on Electrochemical Impedance Spectroscopy as a Detection Tool
Sensors 2009, 9(12), 9513-9532; doi:10.3390/s91209513
Received: 30 September 2009 / Revised: 28 October 2009 / Accepted: 11 November 2009 / Published: 26 November 2009
Cited by 78 | PDF Full-text (651 KB) | HTML Full-text | XML Full-text
Abstract
Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e. [...] Read more.
Recent advances in label free DNA hybridization sensors employing electrochemical impedance spectroscopy (EIS) as a detection tool are reviewed. These sensors are based on the modulation of the blocking ability of an electrode modified with a probe DNA by an analyte, i.e., target DNA. The probe DNA is immobilized on a self-assembled monolayer, a conducting polymer film, or a layer of nanostructures on the electrode such that desired probe DNA would selectively hybridize with target DNA. The rate of charge transfer from the electrode thus modified to a redox indicator, e.g., [Fe(CN)6]3–/4–, which is measured by EIS in the form of charge transfer resistance (Rct), is modulated by whether or not, as well as how much, the intended target DNA is selectively hybridized. Efforts made to enhance the selectivity as well as the sensitivity of DNA sensors and to reduce the EIS measurement time are briefly described along with brief future perspectives in developing DNA sensors. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)
Open AccessReview DNA Sensors with Diamond as a Promising Alternative Transducer Material
Sensors 2009, 9(7), 5600-5636; doi:10.3390/s90705600
Received: 5 June 2009 / Revised: 2 July 2009 / Accepted: 3 July 2009 / Published: 14 July 2009
Cited by 18 | PDF Full-text (1144 KB) | HTML Full-text | XML Full-text
Abstract
Bio-electronics is a scientific field coupling the achievements in biology with electronics to obtain higher sensitivity, specificity and speed. Biosensors have played a pivotal role, and many have become established in the clinical and scientific world. They need to be sensitive, specific, [...] Read more.
Bio-electronics is a scientific field coupling the achievements in biology with electronics to obtain higher sensitivity, specificity and speed. Biosensors have played a pivotal role, and many have become established in the clinical and scientific world. They need to be sensitive, specific, fast and cheap. Electrochemical biosensors are most frequently cited in literature, often in the context of DNA sensing and mutation analysis. However, many popular electrochemical transduction materials, such as silicon, are susceptible to hydrolysis, leading to loss of bioreceptor molecules from the surface. Hence, increased attention has been shifted towards diamond, which surpasses silicon on many levels. Full article
(This article belongs to the Special Issue DNA Sensors and Biosensors)

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