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Recent Advances in Nucleic Acid Sensors
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Recent Advances in Nucleic Acid Sensors

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

Deadline for manuscript submissions: closed (30 April 2018) | Viewed by 28205

Special Issue Editor

Prof. Dr. Ramon Eritja

E-Mail Website
Guest Editor
Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, CIBER-BBN, Jordi Girona 18-26, 08034 Barcelona, Spain
Interests: nucleic acid chemistry; DNA and RNA analogs: synthesis applications, molecular tools; RNA interference; DNA nanotechnology; G-quadruplex; Triplex, artificial DNA
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nucleic acids are the key molecules for the transmission of genetic inheritance. The identification of DNA as the basis of genetic material and the elucidation of its structure stimulated the development of protocols for the synthesis of defined oligonucleotides carrying a large number of chemical entities that are optimal for nucleic acid immobilization on sensing surfaces. Combinatorial methods, such as SELEX, have generated a large number of DNA/RNA molecules or aptamers with high affinity to ions, small molecules, peptides, proteins and cells. Moreover, the human genome sequencing project has open the path towards personalized medicine that has increased the need of identifying genetic mutations. All these activities have generated large expectations in the field of nucleic acids sensing technologies. The development of nucleic acids sensors brings together many different branches of science, such as molecular biology, organic chemistry, biochemistry, pharmacy, medicine, material science, electrochemistry, and engineering.

This Special Issue of Sensors will concentrate on the latest developments of Nucleic Acids Sensors. We encourage authors to submit research papers and comprehensive reviews for this Special Issue describing the fabrication and use of nucleic acids sensing devices including optical and electrochemical sensors, such as electrochemical impedance spectroscopy (EIS), nanotube field effect transistors (FETs), quartz crystal microbalance (QCM), surface plasmon resonance (SPR) for the detection of nucleic acids hybridization, detection of point mutations or aptamer binding including all types of enhancement such as fluorescent probes, colorimetric reagents, antibodies, nanoparticles and so on. If you are interested in forming part of this Special Issue, we would appreciate very much receiving the tentative tile of your contribution.

Dr. Ramon Eritja
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. Sensors is an international peer-reviewed open access semimonthly 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 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

  • aptamers,
  • electrochemical impedance spectroscopy (EIS)
  • surface plasmon resonance (SPR),
  • quartz crystal microbalance (QCM),
  • field effect transistors (FETs),
  • molecular beacons,
  • opticals sensors,
  • electrochemical sensors,
  • aptamer-based sensors,
  • DNAzymes and ribozymes

Published Papers (6 papers)

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Research

17 pages, 3858 KiB  
Article
The Application of ATR-FTIR Spectroscopy and the Reversible DNA Conformation as a Sensor to Test the Effectiveness of Platinum(II) Anticancer Drugs
by Khansa Al-Jorani, Anja Rüther, Miguela Martin, Rukshani Haputhanthri, Glen B. Deacon, Hsiu Lin Li and Bayden R. Wood
Sensors 2018, 18(12), 4297; https://doi.org/10.3390/s18124297 - 06 Dec 2018
Cited by 13 | Viewed by 5465
Abstract
Platinum(II) complexes have been found to be effective against cancer cells. Cisplatin curbs cell replication by interacting with the deoxyribonucleic acid (DNA), reducing cell proliferation and eventually leading to cell death. In order to investigate the ability of platinum complexes to affect cancer [...] Read more.
Platinum(II) complexes have been found to be effective against cancer cells. Cisplatin curbs cell replication by interacting with the deoxyribonucleic acid (DNA), reducing cell proliferation and eventually leading to cell death. In order to investigate the ability of platinum complexes to affect cancer cells, two examples from the class of polyfluorophenylorganoamidoplatinum(II) complexes were synthesised and tested on isolated DNA. The two compounds trans-[N,N′-bis(2,3,5,6-tetrafluorophenyl)ethane-1,2-diaminato(1-)](2,3,4,5,6-pentafluorobenzoato)(pyridine)platinum(II) (PFB) and trans-[N,N′-bis(2,3,5,6-tetrafluorophenyl)ethane-1,2-diaminato(1-)](2,4,6-trimethylbenzoato)(pyridine)platinum(II) (TMB) were compared with cisplatin through their reaction with DNA. Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy was applied to analyse the interaction of the Pt(II) complexes with DNA in the hydrated, dehydrated and rehydrated states. These were compared with control DNA in acetone/water (PFB, TMB) and isotonic saline (cisplatin) under the same conditions. Principle Component Analysis (PCA) was applied to compare the ATR-FTIR spectra of the untreated control DNA with spectra of PFB and TMB treated DNA samples. Disruptions in the conformation of DNA treated with the Pt(II) complexes upon rehydration were mainly observed by monitoring the position of the IR-band around 1711 cm−1 assigned to the DNA base-stacking vibration. Furthermore, other intensity changes in the phosphodiester bands of DNA at ~1234 cm−1 and 1225 cm−1 and shifts in the dianionic phosphodiester vibration at 966 cm−1 were observed. The isolated double stranded DNA (dsDNA) or single stranded DNA (ssDNA) showed different structural changes when incubated with the studied compounds. PCA confirmed PFB had the most dramatic effect by denaturing both dsDNA and ssDNA. Both compounds, along with cisplatin, induced changes in DNA bands at 1711, 1088, 1051 and 966 cm−1 indicative of DNA conformation changes. The ability to monitor conformational change with infrared spectroscopy paves the way for a sensor to screen for new anticancer therapeutic agents. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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11 pages, 1779 KiB  
Article
A Label-Free Fluorescent AND Logic Gate Aptasensor for Sensitive ATP Detection
by Jingjing Zhang, Chunzheng Yang, Chaoqun Niu, Chen Liu, Xuepin Cai, Jie Du and Yong Chen
Sensors 2018, 18(10), 3281; https://doi.org/10.3390/s18103281 - 29 Sep 2018
Cited by 6 | Viewed by 3617
Abstract
In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and [...] Read more.
In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and single-stranded DNA were used as input signals. Fluorescence intensity of PicoGreen dye was used as an output signal. The biosensor-related performances, including the logic gate construction, reaction time, linearity, sensitivity, and specificity, were investigated and the results showed that an AND logic gate was successfully constructed. The ATP detection range was found to be 20 to 400 nM (R2 = 0.9943) with limit of detection (LOD) of 142.6 pM, and the sensitivity range was 1.846 × 106 to 2.988 × 106 M−1. This method for the detection of ATP has the characteristics of being simple, low cost, and highly sensitive. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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Graphical abstract

11 pages, 1495 KiB  
Article
Microplate Chemiluminescent Assay for DNA Detection Using Apoperoxidase-Oligonucleotide as Capture Conjugate and HRP-Streptavidin Signaling System
by Ivan Sakharov
Sensors 2018, 18(4), 1289; https://doi.org/10.3390/s18041289 - 23 Apr 2018
Cited by 5 | Viewed by 5080
Abstract
A covalent conjugate of horseradish apoperoxidase and amino-containing oligonucleotide was synthesized for the first time. Using the obtained conjugate as a capture reagent chemiluminescent microtiter plate-based assay for detection of 35-mer fragment of hepatitis B virus (HBV) DNA (proof-of-concept analyte) was developed. To [...] Read more.
A covalent conjugate of horseradish apoperoxidase and amino-containing oligonucleotide was synthesized for the first time. Using the obtained conjugate as a capture reagent chemiluminescent microtiter plate-based assay for detection of 35-mer fragment of hepatitis B virus (HBV) DNA (proof-of-concept analyte) was developed. To detect the target DNA, a signaling system consisted of biotinylated reporter oligonucleotide and HRP-streptavidin conjugate was used. The high sensitivity of the assay was due to the enhanced chemiluminescence reaction, where 3-(10′-phenothiazinyl)propane-1-sulfonate/N-morpholinopyridine pair was used as an enhancer. Under the optimized conditions the limit of detection and a working range of the assay were 3 pM and 6–100 pM, respectively. The assay sensitivity was 1.6 × 105 RLU/pM of target. The coefficient of variation (CV) for determination of HBV DNA within the working range was lower than 6%. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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12 pages, 5171 KiB  
Article
Metal Nanoparticles/Porous Silicon Microcavity Enhanced Surface Plasmon Resonance Fluorescence for the Detection of DNA
by Jiajia Wang and Zhenhong Jia
Sensors 2018, 18(2), 661; https://doi.org/10.3390/s18020661 - 23 Feb 2018
Cited by 23 | Viewed by 5062
Abstract
A porous silicon microcavity (PSiMC) with resonant peak wavelength of 635 nm was fabricated by electrochemical etching. Metal nanoparticles (NPs)/PSiMC enhanced fluorescence substrates were prepared by the electrostatic adherence of Au NPs that were distributed in PSiMC. The Au NPs/PSiMC device was used [...] Read more.
A porous silicon microcavity (PSiMC) with resonant peak wavelength of 635 nm was fabricated by electrochemical etching. Metal nanoparticles (NPs)/PSiMC enhanced fluorescence substrates were prepared by the electrostatic adherence of Au NPs that were distributed in PSiMC. The Au NPs/PSiMC device was used to characterize the target DNA immobilization and hybridization with its complementary DNA sequences marked with Rhodamine red (RRA). Fluorescence enhancement was observed on the Au NPs/PSiMC device substrate; and the minimum detection concentration of DNA ran up to 10 pM. The surface plasmon resonance (SPR) of the MC substrate; which is so well-positioned to improve fluorescence enhancement rather the fluorescence enhancement of the high reflection band of the Bragg reflector; would welcome such a highly sensitive in biosensor. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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11 pages, 2876 KiB  
Article
Detection of Ammonia-Oxidizing Bacteria (AOB) Using a Porous Silicon Optical Biosensor Based on a Multilayered Double Bragg Mirror Structure
by Hongyan Zhang, Jie Lv and Zhenhong Jia
Sensors 2018, 18(1), 105; https://doi.org/10.3390/s18010105 - 01 Jan 2018
Cited by 15 | Viewed by 3723
Abstract
We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure [...] Read more.
We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure is quite easy to prepare and exhibits interesting optical properties. The width of high reflectivity stop band of the PS double Bragg mirror is about 761 nm with a sharp and deep resonance peak at 1328 nm in the reflectance spectrum, which gives a high sensitivity and distinguishability for sensing performance. The detection sensitivity of such a double Bragg mirror structure is illustrated through the investigation of AOB DNA hybridization in the PS pores. The redshifts of the reflectance spectra show a good linear relationship with both complete complementary and partial complementary DNA. The lowest detection limit for complete complementary DNA is 27.1 nM and the detection limit of the biosensor for partial complementary DNA is 35.0 nM, which provides the feasibility and effectiveness for the detection of AOB in a real environment. The PS double Bragg mirror structure is attractive for widespread biosensing applications and provides great potential for the development of optical applications. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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1903 KiB  
Article
Facile Determination of Sodium Ion and Osmolarity in Artificial Tears by Sequential DNAzymes
by Eun Hye Kim, Eun-Song Lee, Dong Yun Lee and Young-Pil Kim
Sensors 2017, 17(12), 2840; https://doi.org/10.3390/s17122840 - 07 Dec 2017
Cited by 5 | Viewed by 4645
Abstract
Despite high relevance of tear osmolarity and eye abnormality, numerous methods for detecting tear osmolarity rely upon expensive osmometers. We report a reliable method for simply determining sodium ion-based osmolarity in artificial tears using sequential DNAzymes. When sodium ion-specific DNAzyme and peroxidase-like DNAzyme [...] Read more.
Despite high relevance of tear osmolarity and eye abnormality, numerous methods for detecting tear osmolarity rely upon expensive osmometers. We report a reliable method for simply determining sodium ion-based osmolarity in artificial tears using sequential DNAzymes. When sodium ion-specific DNAzyme and peroxidase-like DNAzyme were used as a sensing and detecting probe, respectively, the concentration of Na+ in artificial tears could be measured by absorbance or fluorescence intensity, which was highly correlated with osmolarity over the diagnostic range (R2 > 0.98). Our approach is useful for studying eye diseases in relation to osmolarity. Full article
(This article belongs to the Special Issue Recent Advances in Nucleic Acid Sensors)
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