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Biosensors
Special Issues
Nano and Micro DNA/RNA Sensors
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Nano and Micro DNA/RNA Sensors

A special issue of Biosensors (ISSN 2079-6374).

Deadline for manuscript submissions: closed (30 June 2013) | Viewed by 57723

Special Issue Editor

Prof. Dr. Jeff Tza-Huei Wang

E-Mail Website
Guest Editor
Departments of Mechanical Engineering, Biomedical Engineering and Oncology, Johns Hopkins University, 108 Latrobe, 3400 N. Charles Street, Baltimore, MD 21218, USA
Interests: new technologies and methods for molecular analysis of diseases and biomedical research; nano-biosensors; single-molecule fluorescence spectroscopy; microfluidics; genetic and epigenetic biomarker detection of cancer and infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Quantitative and qualitative analysis of DNA/RNA sequences provides information essential to a variety of applications such as disease diagnostics, personalized medicine, environmental analysis, drug discovery, as well as, bio-warfare defense. The explosion in nano and micro-technologies has led to a surge of interest in designing sensors engineered at small length from molecular probes and nanomaterials as the basis for next-generation DNA/RNA biosensors to achieve even higher sensitivity, higher throughput, more flexible conjugation chemistries, lower cost, and more pervasive application.

In this special issue, we would like to discuss the latest developments and applications of nano and micro-structure based methods for nucleic acid detection. We plan to invite reviews and research articles related, but not limited to, the following topics: functional nanomaterials (e.g., nanoparticle, nanowire, nanotube and grapheme)-based DNA/RNA sensing, genetic variation detection, multiplexed detection, and microfluidic sample preparation for nucleic acid detection.

Prof. Dr. Tza-Huei “Jeff” Wang
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biosensors is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA/RNA detection
  • nanopartciles
  • nanowires
  • disease diagnostics
  • genetic variation detection
  • microfluidics

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Published Papers (6 papers)

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Editorial

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87 KiB  
Editorial
Micro and Nanotechnologies Enhanced Biomolecular Sensing
by Tza-Huei Wang
Biosensors 2013, 3(3), 283-285; https://doi.org/10.3390/bios3030283 - 5 Jul 2013
Cited by 4 | Viewed by 7095
Abstract
This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive [...] Read more.
This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)

Research

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133 KiB  
Communication
A Facile Inhibitor Screening of Hepatitis C Virus NS3 Protein Using Nanoparticle-Based RNA
by Changhyun Roh
Biosensors 2012, 2(4), 427-432; https://doi.org/10.3390/bios2040427 - 24 Oct 2012
Cited by 9 | Viewed by 7089
Abstract
Globally, over hundreds of million people are infected with the hepatitis C virus: the global rate of death as a direct result of the hepatitis C virus has increased remarkably. For this reason, the development of efficient drug treatments for the biological effects [...] Read more.
Globally, over hundreds of million people are infected with the hepatitis C virus: the global rate of death as a direct result of the hepatitis C virus has increased remarkably. For this reason, the development of efficient drug treatments for the biological effects of the hepatitis C virus is highly necessary. We have previously shown that quantum dots (QDs)-conjugated RNA oligonucleotide can recognize the hepatitis C virus NS3 protein specifically and sensitively. In this study, we elucidated that this biochip can analyze inhibitors to the hepatitis C virus NS3 protein using a nanoparticle-based RNA oligonucleotide. Among the polyphenolic compounds examined, 7,8,4'-trihydroxyisoflavone and 6,7,4'-trihydroxyisoflavone demonstrated a remarkable inhibition activity on the hepatitis C virus NS3 protein. Both 7,8,4'-trihydroxyisoflavone and 6,7,4'-trihydroxyisoflavone attenuated the binding affinity in a concentrated manner as evidenced by QDs conjugated RNA oligonucleotide. At a concentration of 0.01 μg·mL−1, 7,8,4'-trihydroxyisoflavone and 6,7,4'-trihydroxyisoflavone showed more than a 30% inhibition activity of a nanoparticle-based RNA oligonucleotide biochip system. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
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518 KiB  
Article
Microfluidic-Based Amplification-Free Bacterial DNA Detection by Dielectrophoretic Concentration and Fluorescent Resonance Energy Transfer Assisted in Situ Hybridization (FRET-ISH)
by Michelle M. Packard, Maxim Shusteff and Evangelyn C. Alocilja
Biosensors 2012, 2(4), 405-416; https://doi.org/10.3390/bios2040405 - 10 Oct 2012
Cited by 8 | Viewed by 7351
Abstract
Although real-time PCR (RT-PCR) has become a diagnostic standard for rapid identification of bacterial species, typical methods remain time-intensive due to sample preparation and amplification cycle times. The assay described in this work incorporates on-chip dielectrophoretic capture and concentration of bacterial cells, thermal [...] Read more.
Although real-time PCR (RT-PCR) has become a diagnostic standard for rapid identification of bacterial species, typical methods remain time-intensive due to sample preparation and amplification cycle times. The assay described in this work incorporates on-chip dielectrophoretic capture and concentration of bacterial cells, thermal lysis, cell permeabilization, and nucleic acid denaturation and fluorescence resonance energy transfer assisted in situ hybridization (FRET-ISH) species identification. Combining these techniques leverages the benefits of all of them, allowing identification to be accomplished completely on chip less than thirty minutes after receipt of sample, compared to multiple hours required by traditional RT-PCR and its requisite sample preparation. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
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395 KiB  
Article
Detection of Alpha-Methylacyl-CoA Racemase (AMACR), a Biomarker of Prostate Cancer, in Patient Blood Samples Using a Nanoparticle Electrochemical Biosensor
by Po-Yuan Lin, Kai-Lun Cheng, James D. McGuffin-Cawley, Fuh-Sheng Shieu, Anna C. Samia, Sanjay Gupta, Matthew Cooney, Cheryl L. Thompson and Chung Chiun Liu
Biosensors 2012, 2(4), 377-387; https://doi.org/10.3390/bios2040377 - 26 Sep 2012
Cited by 22 | Viewed by 11105
Abstract
Although still commonly used in clinical practice to screen and diagnose prostate cancer, there are numerous weaknesses of prostate-specific antigen (PSA) testing, including lack of specificity and the inability to distinguish between aggressive and indolent cancers. A promising prostate cancer biomarker, alpha-methylacyl-CoA racemase [...] Read more.
Although still commonly used in clinical practice to screen and diagnose prostate cancer, there are numerous weaknesses of prostate-specific antigen (PSA) testing, including lack of specificity and the inability to distinguish between aggressive and indolent cancers. A promising prostate cancer biomarker, alpha-methylacyl-CoA racemase (AMACR), has been previously demonstrated to distinguish cancer from healthy and benign prostate cells with high sensitivity and specificity. However, no accurate clinically useful assay has been developed. This study reports the development of a single use, disposable biosensor for AMACR detection. Human blood samples were used to verify its validity, reproducibility and reliability. Plasma samples from 9 healthy males, 10 patients with high grade prostatic intraepithelial neoplasia (HGPIN), and 5 prostate cancer patients were measured for AMACR levels. The average AMACR levels in the prostate cancer patients was 10 fold higher (mean(SD) = 0.077 (0.10)) than either the controls (mean(SD) = 0.005 (0.001)) or HGPIN patients (mean(SD) = 0.004 (0.0005)). At a cutoff of between 0.08 and 0.9, we are able to achieve 100% accuracy in separating prostate cancer patients from controls. Our results provide strong evidence demonstrating that this biosensor can perform as a reliable assay for prostate cancer detection and diagnosis. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
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339 KiB  
Article
Development of a Fish Cell Biosensor System for Genotoxicity Detection Based on DNA Damage-Induced Trans-Activation of p21 Gene Expression
by Deyu Geng, Zhixia Zhang and Huarong Guo
Biosensors 2012, 2(3), 318-340; https://doi.org/10.3390/bios2030318 - 10 Sep 2012
Cited by 13 | Viewed by 8494
Abstract
p21CIP1/WAF1 is a p53-target gene in response to cellular DNA damage. Here we report the development of a fish cell biosensor system for high throughput genotoxicity detection of new drugs, by stably integrating two reporter plasmids of pGL3-p21-luc (human [...] Read more.
p21CIP1/WAF1 is a p53-target gene in response to cellular DNA damage. Here we report the development of a fish cell biosensor system for high throughput genotoxicity detection of new drugs, by stably integrating two reporter plasmids of pGL3-p21-luc (human p21 promoter linked to firefly luciferase) and pRL-CMV-luc (CMV promoter linked to Renilla luciferase) into marine flatfish flounder gill (FG) cells, referred to as p21FGLuc. Initial validation of this genotoxicity biosensor system showed that p21FGLuc cells had a wild-type p53 signaling pathway and responded positively to the challenge of both directly acting genotoxic agents (bleomycin and mitomycin C) and indirectly acting genotoxic agents (cyclophosphamide with metabolic activation), but negatively to cyclophosphamide without metabolic activation and the non-genotoxic agents ethanol and D-mannitol, thus confirming a high specificity and sensitivity, fast and stable response to genotoxic agents for this easily maintained fish cell biosensor system. This system was especially useful in the genotoxicity detection of Di(2-ethylhexyl) phthalate (DEHP), a rodent carcinogen, but negatively reported in most non-mammalian in vitro mutation assays, by providing a strong indication of genotoxicity for DEHP. A limitation for this biosensor system was that it might give false positive results in response to sodium butyrate and any other agents, which can trans-activate the p21 gene in a p53-independent manner. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
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Review

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350 KiB  
Review
DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters
by Judy M. Obliosca, Cong Liu, Robert Austin Batson, Mark C. Babin, James H. Werner and Hsin-Chih Yeh
Biosensors 2013, 3(2), 185-200; https://doi.org/10.3390/bios3020185 - 23 Apr 2013
Cited by 71 | Viewed by 15137
Abstract
DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more [...] Read more.
DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more photostable. Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core. The preparation of DNA/Ag NCs is simple and there is no need to remove excess precursors as these precursors are non-fluorescent. Our recent discovery of the fluorogenic and color switching properties of DNA/Ag NCs have led to the invention of new molecular probes, termed NanoCluster Beacons (NCBs), for DNA detection, with the capability to differentiate single-nucleotide polymorphisms by emission colors. NCBs are inexpensive, easy to prepare, and compatible with commercial DNA synthesizers. Many other groups have also explored and taken advantage of the environment sensitivities of DNA/Ag NCs in creating new tools for DNA/RNA detection and single-nucleotide polymorphism identification. In this review, we summarize the recent trends in the use of DNA/Ag NCs for developing DNA/RNA sensors. Full article
(This article belongs to the Special Issue Nano and Micro DNA/RNA Sensors)
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