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Advances in DNA and RNA Sensing
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Advances in DNA and RNA Sensing

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 17545

Special Issue Editor

Prof. Dr. Ivo Piantanida

E-Mail Website
Guest Editor
Laboratory for Biomolecular Interactions and Spectroscopy, Head Division of Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
Interests: supramolecular and medicinal chemistry; design and synthesis of dyes; DNA/RNA recognition; small molecule/protein interactions; fluorescence spectroscopy and microscopy; circular dichroism; microcalorimetry methods (ITC; DSC); development of Raman probes for biomacromolecules
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nucleic acids are one of the most investigated scientific topics in the last 60 years. During this time, new types of DNA or RNA, their novel secondary and ternary structures, new functions (e.g. DNAzyme, etc.), and new artificial applications (DNA barcoding, DNA data storage, etc.…) were continuously being discovered. Low molecular weight dyes (MW<1000) targeting DNA/RNA were essential for performing the nucleic acid research—for instance, fluorescent techniques now represent about 70% of the detection-enabling technologies used in DNA/RNA-related biochemistry, molecular biology, and medicine. Such a viable field of research is hard to follow through only primary scientific publications, thus, books, reviews, and dedicated special issues are of great use for keeping up-to-date.

This Special Issue aims to summarize some recent advances in small molecules, which sense various DNAs or RNAs by sensitive and biologically applicable methods. Particularly, sensing is not limited only to fluorescence response but also to alternative and complemental methods (CD, Raman, and other), which would allow recognition of increasing diversity of DNA/RNA structures, while avoiding overlapping spectral properties of known fluorescent dyes selective to particular DNA/RNA structure. Also, theragnostic properties of small molecules shall be addressed in cases when selective DNA/RNA sensing is accompanied by intriguing biological activity.

Prof. Dr. Ivo Piantanida
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. Molecules 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 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 structure recognition
  • Fluorescence probes
  • Circular dichroism probes
  • Raman probes
  • Theragnostic DNA/RNA activity

Published Papers (6 papers)

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Research

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10 pages, 1720 KiB  
Article
Conditional Cooperativity in DNA Minor-Groove Recognition by Oligopeptides
by Jurij Lah and San Hadži
Molecules 2021, 26(17), 5188; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26175188 - 26 Aug 2021
Cited by 1 | Viewed by 1282
Abstract
The recognition of specific DNA sequences in processes such as transcription is associated with a cooperative binding of proteins. Some transcription regulation mechanisms involve additional proteins that can influence the binding cooperativity by acting as corepressors or coactivators. In a conditional cooperativity mechanism, [...] Read more.
The recognition of specific DNA sequences in processes such as transcription is associated with a cooperative binding of proteins. Some transcription regulation mechanisms involve additional proteins that can influence the binding cooperativity by acting as corepressors or coactivators. In a conditional cooperativity mechanism, the same protein can induce binding cooperativity at one concentration and inhibit it at another. Here, we use calorimetric (ITC) and spectroscopic (UV, CD) experiments to show that such conditional cooperativity can also be achieved by the small DNA-directed oligopeptides distamycin and netropsin. Using a global thermodynamic analysis of the observed binding and (un)folding processes, we calculate the phase diagrams for this system, which show that distamycin binding cooperativity is more pronounced at lower temperatures and can be first induced and then reduced by increasing the netropsin or/and Na+ ion concentration. A molecular interpretation of this phenomenon is suggested. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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18 pages, 1780 KiB  
Article
Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment
by Antonija Erben, Igor Sviben, Branka Mihaljević, Ivo Piantanida and Nikola Basarić
Molecules 2021, 26(14), 4315; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26144315 - 16 Jul 2021
Cited by 1 | Viewed by 2032
Abstract
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous [...] Read more.
A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH2N(CH3)2] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent ΦF = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logKa = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield ΦR = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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14 pages, 1793 KiB  
Article
Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA
by Peter Jonas Wickhorst and Heiko Ihmels
Molecules 2021, 26(9), 2566; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26092566 - 28 Apr 2021
Cited by 5 | Viewed by 2220
Abstract
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = [...] Read more.
A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2–7 × 105 M−1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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14 pages, 3036 KiB  
Article
Fluorimetric and CD Recognition between Various ds-DNA/RNA Depends on a Cyanine Connectivity in Cyanine-guanidiniocarbonyl-pyrrole Conjugate
by Tamara Šmidlehner, Marta Košćak, Ksenija Božinović, Dragomira Majhen, Carsten Schmuck and Ivo Piantanida
Molecules 2020, 25(19), 4470; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules25194470 - 29 Sep 2020
Cited by 4 | Viewed by 2469
Abstract
Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism [...] Read more.
Two novel isosteric conjugates of guanidiniocarbonyl-pyrrole and 6-bromo-TO (thiazole orange) were prepared, differing only in linker connectivity to cyanine (benzothiazole nitrogen vs. quinoline nitrogen). The quinoline analog was significantly more susceptible to aggregation in an aqueous medium, which resulted in induced circular dichroism (ICD; λ = 450–550 nm) recognition between A-T(U) and G-C basepair containing polynucleotides. The benzothiazole-isostere showed pronounced (four-fold) fluorimetric selectivity toward ds-RNA in comparison to any ds-DNA, at variance to its quinoline-analogue fluorescence being weakly selective to GC-DNA. Preliminary screening on human tumor and normal lung cell lines showed that both dyes very efficiently enter living cells and accumulate in mitochondria, causing moderate cytotoxic effects, and thus could be considered as lead compounds toward novel theragnostic mitochondrial dyes. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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Review

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17 pages, 3399 KiB  
Review
Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules
by Tarita Biver
Molecules 2022, 27(13), 4165; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27134165 - 29 Jun 2022
Cited by 7 | Viewed by 2887
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, [...] Read more.
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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17 pages, 2872 KiB  
Review
Selected In Situ Hybridization Methods: Principles and Application
by Dominika Veselinyová, Jana Mašlanková, Katarina Kalinová, Helena Mičková, Mária Mareková and Miroslava Rabajdová
Molecules 2021, 26(13), 3874; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26133874 - 24 Jun 2021
Cited by 24 | Viewed by 5797
Abstract
We are experiencing rapid progress in all types of imaging techniques used in the detection of various numbers and types of mutation. In situ hybridization (ISH) is the primary technique for the discovery of mutation agents, which are presented in a variety of [...] Read more.
We are experiencing rapid progress in all types of imaging techniques used in the detection of various numbers and types of mutation. In situ hybridization (ISH) is the primary technique for the discovery of mutation agents, which are presented in a variety of cells. The ability of DNA to complementary bind is one of the main principles in every method used in ISH. From the first use of in situ techniques, scientists paid attention to the improvement of the probe design and detection, to enhance the fluorescent signal intensity and inhibition of cross-hybrid presence. This article discusses the individual types and modifications, and is focused on explaining the principles and limitations of ISH division on different types of probes. The article describes a design of probes for individual types of in situ hybridization (ISH), as well as the gradual combination of several laboratory procedures to achieve the highest possible sensitivity and to prevent undesirable events accompanying hybridization. The article also informs about applications of the methodology, in practice and in research, to detect cell to cell communication and principles of gene silencing, process of oncogenesis, and many other unknown processes taking place in organisms at the DNA/RNA level. Full article
(This article belongs to the Special Issue Advances in DNA and RNA Sensing)
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