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Next-Generation Nucleic Acid Sensors
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Next-Generation Nucleic Acid Sensors

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

Deadline for manuscript submissions: closed (28 February 2015) | Viewed by 51279

Special Issue Editor

Dr. Matteo Castronovo

E-Mail Website
Guest Editor
1. Adjunct Assistant Professor, Department of Biology, Temple University, Philadelphia, PA, USA
2. Department of Medical and Biological Sciences, University of Udine, Piazzale Kolbe, 4, 33100 Udine, Italy
Interests: atomic force microscopy; crowding; denaturation; detection; DNA; electrochemistry; enzymes; fluorescence; hybridization; molecular device; nanoarray; nanomanipulation; nanomedicine; nanotechnology; nucleic acids; nucleases; RNA; self-assembled monolayers; self-assembly; steric hindrance; surfaces

Special Issue Information

Dear Colleagues,

The explosive development of nucleic acid (NA) nanotechnologies has underscored the importance of the inherent capacity of NAs to self-associate, thus providing an essentially limitless wellspring for the directed formation of complex assemblies with diverse functions.

DNA, RNA, and related NA polymers provide the building blocks for the bottoms-up fabrication of sensing devices. In addition, the high-throughput detection/analysis of NAs also requires the confinement of functional probes within highly dense microchips, which involves the top-down fabrication of microfluidic and electronic components. The development of next-generation of NA sensors will require functional integration between the bottom-up and top-down approaches, thus necessitating strongly interdisciplinary research approaches. This special issue aims to bring together, under one cover, innovative bottom-up and top-down approaches for NA detection and analysis.

Papers addressing a wide range of bottoms-up, top-down, and hybrid approaches for the quantitative detection or analysis of DNA and RNA molecules are sought; topics include, but are not necessarily limited to, recent developments in the following areas: the manipulation of long DNA or RNA molecules through single-molecule microscopy and spectroscopic approaches; biological and solid-state nanopores; microfluidic systems; DNA or RNA micro- and nano-arrays; DNA sequencing; solid-state PCR; digital PCR; DNA- or RNA-functionalized nanoparticles; and DNA origami.

Both review articles and original research papers relating to the development or the application of advanced technologies for sensing nucleic acids, as well as nanoscience studies relating to the novel behaviors of NA-based, self-assembled nanodevices are sought.

Dr. Matteo Castronovo
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 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 nanosensors
  • lab-on-a-chip DNA sensors
  • functional DNA nanotechnologies
  • DNA self-assembly
  • DNA nanoarrays
  • next-generation sequencing
  • nanopores
  • single molecule DNA/RNA detection
  • nanomedicine

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Published Papers (7 papers)

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Research

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4998 KiB  
Article
Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles
by Hassan Maktuff Jaber Al-Ta'ii, Vengadesh Periasamy and Yusoff Mohd Amin
Sensors 2015, 15(5), 11836-11853; https://doi.org/10.3390/s150511836 - 21 May 2015
Cited by 14 | Viewed by 7012
Abstract
Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky [...] Read more.
Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0–20 min) of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung’s and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung’s methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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1159 KiB  
Article
A mRNA-Responsive G-Quadruplex-Based Drug Release System
by Hidenobu Yaku, Takashi Murashima, Daisuke Miyoshi and Naoki Sugimoto
Sensors 2015, 15(4), 9388-9403; https://doi.org/10.3390/s150409388 - 21 Apr 2015
Cited by 13 | Viewed by 7425
Abstract
G-quadruplex-based drug delivery carriers (GDDCs) were designed to capture and release a telomerase inhibitor in response to a target mRNA. Hybridization between a loop on the GDDC structure and the mRNA should cause the G-quadruplex structure of the GDDC to unfold and release [...] Read more.
G-quadruplex-based drug delivery carriers (GDDCs) were designed to capture and release a telomerase inhibitor in response to a target mRNA. Hybridization between a loop on the GDDC structure and the mRNA should cause the G-quadruplex structure of the GDDC to unfold and release the bound inhibitor, anionic copper(II) phthalocyanine (CuAPC). As a proof of concept, GDDCs were designed with a 10-30-mer loop, which can hybridize with a target sequence in epidermal growth factor receptor (EGFR) mRNA. Structural analysis using circular dichroism (CD) spectroscopy showed that the GDDCs form a (3 + 1) type G-quadruplex structure in 100 mM KCl and 10 mM MgCl2 in the absence of the target RNA. Visible absorbance titration experiments showed that the GDDCs bind to CuAPC with Ka values of 1.5 × 105 to 5.9 × 105 M−1 (Kd values of 6.7 to 1.7 μM) at 25 °C, depending on the loop length. Fluorescence titration further showed that the G-quadruplex structure unfolds upon binding to the target RNA with Ka values above 1.0 × 108 M−1 (Kd values below 0.01 μM) at 25 °C. These results suggest the carrier can sense and bind to the target RNA, which should result in release of the bound drug. Finally, visible absorbance titration experiments demonstrated that the GDDC release CuAPC in response to the target RNA. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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Graphical abstract

10933 KiB  
Article
Calculation of the Electronic Parameters of an Al/DNA/p-Si Schottky Barrier Diode Influenced by Alpha Radiation
by Hassan Maktuff Jaber Al-Ta'ii, Yusoff Mohd Amin and Vengadesh Periasamy
Sensors 2015, 15(3), 4810-4822; https://doi.org/10.3390/s150304810 - 26 Feb 2015
Cited by 23 | Viewed by 7145
Abstract
Many types of materials such as inorganic semiconductors have been employed as detectors for nuclear radiation, the importance of which has increased significantly due to recent nuclear catastrophes. Despite the many advantages of this type of materials, the ability to measure direct cellular [...] Read more.
Many types of materials such as inorganic semiconductors have been employed as detectors for nuclear radiation, the importance of which has increased significantly due to recent nuclear catastrophes. Despite the many advantages of this type of materials, the ability to measure direct cellular or biological responses to radiation might improve detector sensitivity. In this context, semiconducting organic materials such as deoxyribonucleic acid or DNA have been studied in recent years. This was established by studying the varying electronic properties of DNA-metal or semiconductor junctions when exposed to radiation. In this work, we investigated the electronics of aluminium (Al)/DNA/silicon (Si) rectifying junctions using their current-voltage (I-V) characteristics when exposed to alpha radiation. Diode parameters such as ideality factor, barrier height and series resistance were determined for different irradiation times. The observed results show significant changes with exposure time or total dosage received. An increased deviation from ideal diode conditions (7.2 to 18.0) was observed when they were bombarded with alpha particles for up to 40 min. Using the conventional technique, barrier height values were observed to generally increase after 2, 6, 10, 20 and 30 min of radiation. The same trend was seen in the values of the series resistance (0.5889–1.423 Ω for 2–8 min). These changes in the electronic properties of the DNA/Si junctions could therefore be utilized in the construction of sensitive alpha particle detectors. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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440 KiB  
Article
Surface Plasmon Resonator Using High Sensitive Resonance Telecommunication Wavelengths for DNA Sensors of Mycobacterium Tuberculosis with Thiol-Modified Probes
by Shih-Hsiang Hsu, Shao-Chiang Hung, Yu-Kun Chen and Zhi-Hao Jian
Sensors 2015, 15(1), 331-340; https://doi.org/10.3390/s150100331 - 25 Dec 2014
Cited by 6 | Viewed by 5611
Abstract
Various analytes can be verified by surface plasmon resonance, thus continuous improvement of this sensing technology is crucial for better sensing selection and higher sensitivity. The SPR sensitivity on the wavelength modulation is enhanced with increasing wavelengths. The telecommunication wavelength range was then [...] Read more.
Various analytes can be verified by surface plasmon resonance, thus continuous improvement of this sensing technology is crucial for better sensing selection and higher sensitivity. The SPR sensitivity on the wavelength modulation is enhanced with increasing wavelengths. The telecommunication wavelength range was then utilized to detect Mycobacterium tuberculosis (MTB) deoxyribonucleic acid (DNA) under two situations, without immobilization and with 5'-thiol end labeled IS6100 DNA probes, for SPR sensitivity comparison. The experimental data demonstrated that the SPR sensitivity increased more than 13 times with the wavelength modulation after immobilization. Since the operating wavelength accuracy of a tunable laser source can be controlled within 0.001 nm, the sensitivity and resolution on immobilized MTB DNA were determined as 1.04 nm/(μg/mL) and 0.9 ng/mL, respectively. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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1911 KiB  
Article
HPV Genotyping 9G Membrane Test: A Point-of-Care Diagnostic Platform
by Keumsoo Song, Satish Balasaheb Nimse, Heejung An and Taisun Kim
Sensors 2014, 14(10), 19162-19175; https://doi.org/10.3390/s141019162 - 15 Oct 2014
Cited by 5 | Viewed by 6242
Abstract
The results of HPV detection in 550 cervical samples by cervical cytology were compared with the sequencing analysis and HPV genotyping 9G membrane test. The HPV genotyping 9G membrane test can efficiently identify and discriminate five HR-HPV genotypes. The 100% identical results of [...] Read more.
The results of HPV detection in 550 cervical samples by cervical cytology were compared with the sequencing analysis and HPV genotyping 9G membrane test. The HPV genotyping 9G membrane test can efficiently identify and discriminate five HR-HPV genotypes. The 100% identical results of HPV genotyping 9G membrane tests with the sequencing results in 550 clinical samples ensure its wide clinical applicability. The simple handling steps and the portable scanning device make the HPV genotyping 9G membrane test applicable in point-of-care settings. Moreover, the HPV genotyping 9G membrane test allows one to obtain final results in 30 min at 25 °C by simply loading the hybridization and washing solution and scanning the membranes without any drying steps or special handling. The clinical sensitivity and specificity of the HPV genotyping 9G membrane test was found to be 100%, which is much higher than cervical cytology. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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481 KiB  
Article
Ion-Channel Genosensor for the Detection of Specific DNA Sequences Derived from Plum Pox Virus in Plant Extracts
by Kamila Malecka, Lech Michalczuk, Hanna Radecka and Jerzy Radecki
Sensors 2014, 14(10), 18611-18624; https://doi.org/10.3390/s141018611 - 9 Oct 2014
Cited by 27 | Viewed by 6510
Abstract
A DNA biosensor for detection of specific oligonucleotides sequences of Plum Pox Virus (PPV) in plant extracts and buffer is proposed. The working principles of a genosensor are based on the ion-channel mechanism. The NH2-ssDNA probe was deposited onto a glassy [...] Read more.
A DNA biosensor for detection of specific oligonucleotides sequences of Plum Pox Virus (PPV) in plant extracts and buffer is proposed. The working principles of a genosensor are based on the ion-channel mechanism. The NH2-ssDNA probe was deposited onto a glassy carbon electrode surface to form an amide bond between the carboxyl group of oxidized electrode surface and amino group from ssDNA probe. The analytical signals generated as a result of hybridization were registered in Osteryoung square wave voltammetry in the presence of [Fe(CN)6]3−/4− as a redox marker. The 22-mer and 42-mer complementary ssDNA sequences derived from PPV and DNA samples from plants infected with PPV were used as targets. Similar detection limits of 2.4 pM (31.0 pg/mL) and 2.3 pM (29.5 pg/mL) in the concentration range 1–8 pM were observed in the presence of the 22-mer ssDNA and 42-mer complementary ssDNA sequences of PPV, respectively. The genosensor was capable of discriminating between samples consisting of extracts from healthy plants and leaf extracts from infected plants in the concentration range 10–50 pg/mL. The detection limit was 12.8 pg/mL. The genosensor displayed good selectivity and sensitivity. The 20-mer partially complementary DNA sequences with four complementary bases and DNA samples from healthy plants used as negative controls generated low signal. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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Review

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1466 KiB  
Review
Field Effect Sensors for Nucleic Acid Detection: Recent Advances and Future Perspectives
by Bruno Veigas, Elvira Fortunato and Pedro V. Baptista
Sensors 2015, 15(5), 10380-10398; https://doi.org/10.3390/s150510380 - 4 May 2015
Cited by 76 | Viewed by 10753
Abstract
In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new [...] Read more.
In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs’ greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab. Full article
(This article belongs to the Special Issue Next-Generation Nucleic Acid Sensors)
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