Topical Collection "New Frontiers in Nucleic Acid Chemistry"
Prof. Dr. Ramon Eritja
Institute for Advanced Chemistry of Catalonia, IQAC-CSIC, CIBER-BBN, Jordi Girona 18-26, 08034 Barcelona, Spain
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Interests: nucleic acid chemistry; DNA and RNA analogs: synthesis applications, molecular tools; RNA interference; DNA nanotechnology; G-quadruplex; Triplex, artificial DNA
Prof. Dr. Lajos Kovacs
Nucleic Acids Laboratory, Department of Medicinal Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
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Fax: +36 62 42 59 71
Interests: G quadruplexes; supramolecular chemistry; synthetic organic chemistry of carbohydrates; nucleobases; nucleosides; C-nucleosides; peptide nucleic acids; heterocycles; protecting groups
Prof. Daniela Montesarchio
Department of Chemical Sciences, University of Naples Federico II, via Cintia 4, 80126 Naples, Italy
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Interests: Oligonucleotides; Nucleoside analogues; Unusual structures of DNA; G-quadruplex; Ru(III)-complexes; Pt(II)-complexes; Metal–DNA interactions; Small Molecule–DNA interactions
After the success of the Special Issues “Nucleic Acid Analogs”, edited by Molecules in 2012, and “Frontiers in Nucleic Acid Chemistry”, edited in 2015, we are happy to announce the launch of a Topical Collection on these topics. Synthetic oligonucleotides have become essential tools for biological, biomedical, and nanotechnology researches and have also shown promising results in therapeutics and diagnostics. Novel oligonucleotide derivatives with tailored properties are being continuously developed since their specific recognition and unique folding characteristics allow to obtain potential drugs or drug delivery agents, biosensors, diagnostic agents, etc. Along with this development, nucleic acid research is taking new directions as well: synthesis and applications of even more complex molecules, like synthetic RNA analogues (peptide nucleic acids, locked nucleic acids, morpholino oligos, conjugates, etc.), highly informative analytical methods (e.g., those based on mass spectrometry), study of higher-order structures (triple and quadruple helices), investigation of molecular electronic devices based on smart, self-assembling oligonucleotide analogues, to name just a few. The study of the properties of modified nucleic acids brings together many different branches of science, such as molecular biology, chemistry, biochemistry, medicinal chemistry, medicine, materials science, and synthetic biology.
The Topical Collection of Molecules, “New Frontiers in Nucleic Acid Chemistry”, will concentrate on the latest developments in nucleic acids chemistry. We cordially invite all the researchers involved in this exciting field to contribute to the continuing success of the Topical Collection “New Frontiers in Nucleic Acid Chemistry”.
Dr. Ramon Eritja
Dr. Lajos Kovács
Dr. Daniela Montesarchio
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 papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection 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 1800 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.
- modified oligonucleotides
- artificial nucleic acids
- xeno nucleic acids
- synthetic genes
- oligonucleotide conjugates
- nucleoside/nucleotide analogs
- RNA interference
- antiviral activity
- anticancer activity
- DNA nanobiotechnology
- surface-plasmon resonance
- fluorescent nucleic acids
- locked nucleic acids
- unlocked nucleic acids
- peptide nucleic acids
- DNA repair
- base-modified DNA
- DNA polymerase
- circular nucleic acids
- NMR of nucleic acids
- mass spectrometry of nucleic acids
- biophysical studies
- Aptamers: Past, Present, and Future in Molecules (20 articles - displayed below)
- Frontiers in Nucleic Acid Chemistry in Molecules (22 articles - displayed below)
- Nucleic Acid Analogs in Molecules (28 articles - displayed below)
- Catalytic Nucleic Acids in Molecules (21 articles - displayed below)
- Nucleic Acids in Molecules (24 articles - displayed below)
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.
Title: Fragment-based expansion for the development of highly stabilizing HIV LTR G-quadruplex ligands
Author: Sara N. Richter
Affiliation: Department of Molecular Medicine, University of Padua, Italy
Email: [email protected]
Abstract: Stabilization of G-quadruplex (G4) structures in the HIV-1 LTR promoter region suppresses viral transcription, which suggests the use of selective G4 ligands as a novel anti-HIV therapeutic approach. However, sufficient selectivity for the viral versus the cellular G4s needs to be reached to adopt this strategy. Here, we describe the design of new heterocyclic ligands identified by a fragment-based drug discovery (FBDD) approach. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We started with the screening of around 150 molecules, composed of structurally and chemically different fragments, selected from in-house libraries; further synthetic elaboration yielded several G4 ligands and two final potent and selective LTR G4 binders. This work highlights the possibility to apply a fragment-based approach to target G4s.
Title: Polyetheroaryl oxadiazole/pyridine-based ligands: a structural tuning for enhancing G-quadruplex binding
Author: Filippo Doria, Daniela Verga, Valentina Pirota, Marie-Paule Teulade-Fichou and Mauro Freccero
Affiliation: Università di Pavia, Dipartimento di Chimica , Pavia, Italy
Email: [email protected]
Abstract: Acyclic olygoheteroaryl-based compounds represent a valuable class of ligands for nucleic acid recognition. In this regard, acyclic pyridyl polyoxazoles and polyoxadiazoles were recently identified as selective G-quadruplex stabilizing compounds with high cytotoxicity and promising anticancer activity. Herein, we describe the synthesis of a new family of polyheteroaryl oxadiazole/pyridine-ligands targeting DNA G-quadruplexes. In order to perform a structure-activity analysis to identify determinants of activity and selectivity, we followed a convergent synthetic pathway to modulate the nature of the heterocycles, their number, and the effect of protonable lateral chains. Each ligand was evaluated towards secondary nucleic acid structures chosen as a prototype to mimic cancer-associated G-quadruplex structures (e.g., the human telomeric sequence, C-myc and C-kit promoters). Interesting, heptapyridyl-oxadiazole compounds showed preferential binding towards the telomeric sequence (22AG) and the C-myc oncogene promoter in competition conditions versus duplex DNA. In addition, G4-FID assays suggest a different binding mode from the classical stacking on the external G-quartet. Additionally, CD titrations in the presence of the two most promising compounds, TOxAzaPy and TOxAzaPhen, display a structural transition of 22AG in K-rich buffer. This investigation suggests that the pyridyl-oxadiazole motif is a promising recognition element for G-quadruplexes, combining seven heteroaryls in a single binding unit.
Title: Linking Temperature, Cation Concentration and Water Activity for the B to Z Conformational Transition in DNA
Author: Jaime M. Ferreira1# and Richard D. Sheardy2*
Affiliation: 1 Department of Chemistry and Biochemistry, Seton Hall University, South Orange, NJ 07079
2 Department of Chemistry and Biochemistry, Texas Woman’s University, Denton, TX 76204
Email: [email protected]
Abstract: High concentrations of Na+ or [Co(NH3)6]3+ can induce the B to Z conformational transition in alternating (dC-dG) oligo and polynucleotides. The use of short DNA oligomers (dC-dG)4 and (dm5C-dG)4 as models allows thermodynamic characterization of the transition. Both form right handed double helical structures in standard phosphate buffer with 115 mM Na+ at 25 oC. However, at 2.0 M Na+ or 200 μM [Co(NH3)6]3+, (dm5C-dG)4 assumes a left handed double helical structure while the unmethylated (dC-dG)4 analogue remains right handed. Here, isothermal titration calorimetry (ITC) is used to determine the linkages between temperature, cation concentration, water activity and the enthalpy of the conformational change. The results are discussed in terms of solvent accessible surface areas, electrostatic interactions and the role of water.