Special Issue "Nucleic Acid Probes"


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
Department of Chemistry, University of Idaho, 875 Perimeter Drive MS 2343, Moscow, ID-83844, USA
Website: http://www.webpages.uidaho.edu/~hrdlicka/index.htm
E-Mail: hrdlicka@uidaho.edu
Phone: +1 208 885 0108
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


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.


  • 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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Displaying article 1-3
p. 36-54
by , , ,  and
Chemosensors 2015, 3(2), 36-54; doi:10.3390/chemosensors3020036 (registering DOI)
Received: 4 September 2014 / Revised: 7 March 2015 / Accepted: 9 March 2015 / Published: 27 March 2015
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(This article belongs to the Special Issue Nucleic Acid Probes)
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p. 267-286
by  and
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
Show/Hide Abstract | PDF Full-text (1311 KB) | HTML Full-text | XML Full-text | Supplementary Files
(This article belongs to the Special Issue Nucleic Acid Probes)
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p. 193-206
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
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Submitted Papers

Type of Paper: Article
Synthesis and Properties of 2'-deoxyuridine Analogues Bearing Various Azobenzene Derivatives at the C5-position
Shohei Mori 1, Kunihiko Morihiro 1,2,* and Satoshi Obika 1,2,*
Affiliations 1 Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
2 National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Osaka 567-0085, Japan
* Authors to whom correspondence should be addressed.
Nucleic acids that change its properties upon photo-irradiation could be powerful materials for molecular sensing with high spatiotemporal resolution. Recently, we reported a photoisomeric nucleoside bearing azobenzene at the C5-position of 2’–deoxyuridine (dUAz), of which hybridization ability can be reversibly controlled by the appropriate wavelength of light. In this paper, we synthesized and evaluated various dUAz analogues, which have various para-substitutions on the azobenzene moiety. Spectroscopic measurement and HPLC analysis revealed that the para-substitutions of azobenzene moiety strongly affect the photo-isomerization ability and thermal stability of dUAz. Theses results indicated that the proper substitution of azobenzene moiety could improve the properties of dUAz as the light-responsive nucleic acid probe.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Article
Angelika Swiatkowska and Bernard Juskowiak
Title: Effect of Cholesterol Anchoring Group on the Properties of G-Quadruplex—Based FRET Probes for Potassium Ion
: Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland
: In this contribution we report on the spectral properties and G-quadruplex folding ability of fluorescent oligonucleotide probes modified by the attachment cholesterol moiety. These probes were designed and studied in order to verify their potential as potassium sensing devices that could be incorporated into the cellular membrane. The 19-meric guanine-rich deoxyoligonucleotide was labeled with reporter fluorescent FRET groups (FAM and TAMRA) and 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 oligonucleotide are separated, thus fluorophores do not interact with each other and probe exhibits unperturbed fluorescence spectrum. In the presence of K+, the quadruplex structure is developed that enables fluorophores to be arranged in a close proximity causing generation of different fluorescence spectrum (FRET signal). Folding properties of probes and their spectral behavior were examined by recording UV-vis spectra, fluorescence emission and excitation spectra (FRET efficiency), and temperature stability of G-quadruplex structures adopted by probes (melting profiles). Fluorescence energy transfer efficiency increased with increase in concentration of sodium or potassium ion in aqueous solution, which indicated that the probes retained their cation-binding properties and could be promissing candidate for the potassium sensing at the cell membrane interface.

Last update: 13 August 2014

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