Special Issue "Nucleic Acid Probes"

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A special issue of Chemosensors (ISSN 2227-9040).

Deadline for manuscript submissions: closed (31 August 2014)

Special Issue Editor

Guest Editor
Dr. Patrick J. Hrdlicka (Website)

Department of Chemistry, University of Idaho, 875 Perimeter Drive MS 2343, Moscow, ID-83844, USA
Interests: DNA recognition; DNA diagnostics; in vivo imaging; FISH; SNP detection; antisense; oligonucleotides; LNA; pyrene and intercalators

Special Issue Information

Dear Colleagues,

Revolutionary advances in genome sequencing and nucleic acid biology over the past 15 years have resulted in an explosion of data and knowledge about the identity, function and regulation of cellular DNA and RNA. This insight is increasingly harnessed for applications in molecular biology, biotechnology, and medicine. In parallel with these advances, there has been a growing need for techniques that enable detection of nucleic acids. Cleverly designed probes and assays are already used to localize RNA expression in living cells, perform advanced karyotyping, detect disease-related single nucleotide polymorphisms (SNPs), monitor enzyme activity, detect biological threat agents, and monitor PCR in real-time, to name only but a few important examples.

In this special issue of Chemosensors, we welcome communications, full papers and focused reviews on topics that pertain to the use of reporter-modified oligonucleotides and analogues thereof for the detection of nucleic acids and other biomolecules. This includes - but is not limited to - development and characterization of novel reporter-modified oligonucleotides/PNA/polyamides, aptasensors, assays and biosensors. Emphasis should be on chemistry/technology development and proof-of-concept studies, rather than adaptation of a well-established probes/assays/sensors to a new biological target. Please join us in collecting some of the best work in this exciting area from laboratories worldwide.

Dr. Patrick J. Hrdlicka
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Chemosensors is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • DNA/RNA/triplex/quadruplex/i-DNA/Z-DNA/H-DNA detection
  • detection via fluorescence, electrochemistry or EPR spectroscopy
  • hybridization probes
  • SNP-discriminating probes
  • base-discriminating fluorescent nucleotides
  • intrinsically fluorescent probes
  • detection of abasic sites or insertion/deletion mutations
  • elucidation of protein function
  • aptasensors
  • molecular beacons
  • dual probes
  • FRET wires
  • biosensors
  • fluorescence in situ hybridization
  • tricomponent reactions
  • QUAL; ECHO; LNA; PNA; polyamides; TALEN; CRISPR
  • zinc fingers
  • Invaders
  • gold nanoparticles
  • nanomaterials

Published Papers (3 papers)

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Research

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Open AccessArticle Synthesis and Properties of 2'-Deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5 Position
Chemosensors 2015, 3(2), 36-54; doi:10.3390/chemosensors3020036
Received: 4 September 2014 / Revised: 7 March 2015 / Accepted: 9 March 2015 / Published: 27 March 2015
Cited by 1 | PDF Full-text (1048 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Nucleic acids that change their properties upon photo-irradiation could be powerful materials for molecular sensing with high spatiotemporal resolution. Recently, we reported a photo-isomeric nucleoside bearing azobenzene at the C5 position of 2'-deoxyuridine (dUAz), whose hybridization ability could be [...] Read more.
Nucleic acids that change their properties upon photo-irradiation could be powerful materials for molecular sensing with high spatiotemporal resolution. Recently, we reported a photo-isomeric nucleoside bearing azobenzene at the C5 position of 2'-deoxyuridine (dUAz), whose hybridization ability could be reversibly controlled by the appropriate wavelength of light. In this paper, we synthesized and evaluated dUAz analogues that have various para-substitutions on the azobenzene moiety. Spectroscopic measurements and HPLC analyses revealed that the para-substitutions of the azobenzene moiety strongly affect the photo-isomerization ability and thermal stability of the cis-form. The results suggest that proper substitution of the azobenzene moiety can improve the properties of dUAz as a light-responsive nucleic acid probe. Full article
(This article belongs to the Special Issue Nucleic Acid Probes)
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Open AccessArticle Effect of Cholesterol Anchoring Group on the Properties of G-Quadruplex-Based FRET Probes for Potassium Ion
Chemosensors 2014, 2(4), 267-286; doi:10.3390/chemosensors2040267
Received: 31 August 2014 / Revised: 13 October 2014 / Accepted: 15 October 2014 / Published: 21 November 2014
PDF Full-text (1311 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In this study we report on the spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes modified by the attachment of a cholesterol moiety. These probes were designed and studied in order to verify their potential as potassium-sensing devices that can [...] Read more.
In this study we report on the spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes modified by the attachment of a cholesterol moiety. These probes were designed and studied in order to verify their potential as potassium-sensing devices that can be incorporated into the cellular membrane. The 19-meric guanine-rich deoxyoligonucleotide was labeled with reporter fluorescent FRET groups (FAM and TAMRA) and a cholesterol anchor was attached using different approaches. The probes exhibited abilities to fold into a quadruplex structure and to bind metal cations (Na+ and K+). In an unbound state, both termini of the oligonucleotide are separated, thus fluorophores do not interact with each other and the probe exhibits an unperturbed fluorescence spectrum. In the presence of K+, the quadruplex structure is developed such that it enables fluorophores to be arranged in close proximity, causing generation of a different fluorescence spectrum (FRET signal). Folding properties of probes and their spectral behavior were examined by recording the UV-Vis, fluorescence emission, and excitation spectra (FRET efficiency), and the temperature stability of G-quadruplex structures adopted by probes (melting profiles). Fluorescence energy transfer efficiency increased with increases in sodium or potassium ion concentrations in an aqueous solution, which indicated that the probes retained their cation-binding properties and could be promising candidates for potassium sensing at the cell membrane interface. Full article
(This article belongs to the Special Issue Nucleic Acid Probes)
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Review

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Open AccessReview Toward Non-Enzymatic Ultrasensitive Identification of Single Nucleotide Polymorphisms by Optical Methods
Chemosensors 2014, 2(3), 193-206; doi:10.3390/chemosensors2030193
Received: 2 February 2014 / Revised: 7 July 2014 / Accepted: 8 July 2014 / Published: 22 July 2014
Cited by 1 | PDF Full-text (582 KB) | HTML Full-text | XML Full-text
Abstract
Single nucleotide polymorphisms (SNPs) are single nucleotide variations which comprise the most wide spread source of genetic diversity in the genome. Currently, SNPs serve as markers for genetic predispositions, clinically evident disorders and diverse drug responses. Present SNP diagnostics are primarily based [...] Read more.
Single nucleotide polymorphisms (SNPs) are single nucleotide variations which comprise the most wide spread source of genetic diversity in the genome. Currently, SNPs serve as markers for genetic predispositions, clinically evident disorders and diverse drug responses. Present SNP diagnostics are primarily based on enzymatic reactions in different formats including sequencing, polymerase-chain reaction (PCR) and microarrays. In these assays, the enzymes are applied to address the required sensitivity and specificity when detecting SNP. On the other hand, the development of enzyme-free, simple and robust SNP sensing methods is in a constant focus in research and industry as such assays allow rapid and reproducible SNP diagnostics without the need for expensive equipment and reagents. An ideal method for detection of SNP would entail mixing a DNA or RNA target with a probe to directly obtain a signal. Current assays are still not fulfilling these requirements, although remarkable progress has been achieved in recent years. In this review, current SNP sensing approaches are described with a main focus on recently introduced direct, enzyme-free and ultrasensitive SNP sensing by optical methods. Full article
(This article belongs to the Special Issue Nucleic Acid Probes)

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