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Biomolecules
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Polynucleotides
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Polynucleotides

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Nucleic Acids".

Deadline for manuscript submissions: closed (1 October 2022) | Viewed by 11153

Special Issue Editor

Dr. Ivo Crnolatac

E-Mail Website
Guest Editor
Laboratory for Biomolecular Interactions and Spectroscopy, Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54, 10000 Zagreb, Croatia
Interests: biomolecular interaction; DNA binding; DNA structure; protein structure; peptide; click-chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The time when polynucleotides will be out of the research focus cannot be foreseen. The structure of these biomolecular preparation manuals, written in the simplest possible yet perfectly understandable code, was proposed more than 100 years ago. The central dogma of biology involving different polynucleotides and their system of exchanging information was proposed in 1958. However, their impact in the biological sense is yet to be fully described and understood. Recently, the roles and structural characteristics of G-quadruplexes and hybrid polynucleotide structures have been extensively investigated.

Furthermore, as polynucleotides’ preparation has become technologically and commercially more affordable, their utilization in biosensor production is becoming unavoidable due to their molecular recognition ability with remarkable specificity and sensitivity. Aptamers, DNAzymes, and intricate DNA origami structures are currently being built and intensively studied for various applications.

Polynucleotides are also scientifically attractive as polyelectrolytes or simply as models for studies of polymer configurations and dynamics.

This Special Issue of Biomolecules will cover some of the fascinating features and application potentials of polynucleotides.

Dr. Ivo Crnolatac
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. Biomolecules is an international peer-reviewed open access monthly 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

  • Polynucleotide
  • DNA
  • RNA
  • Hybrid polynucleotide
  • G-quadruplex
  • Aptamer
  • DNAzyme

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Published Papers (3 papers)

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Research

20 pages, 3979 KiB  
Article
Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential
by Ivana Fabijanić, Atanas Kurutos, Ana Tomašić Paić, Vanja Tadić, Fadhil S. Kamounah, Lucija Horvat, Anamaria Brozovic, Ivo Crnolatac and Marijana Radić Stojković
Biomolecules 2023, 13(1), 128; https://doi.org/10.3390/biom13010128 - 7 Jan 2023
Cited by 5 | Viewed by 3294
Abstract
The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the [...] Read more.
The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect. Full article
(This article belongs to the Special Issue Polynucleotides)
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20 pages, 2822 KiB  
Article
Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands
by Iva Zonjić, Lidija-Marija Tumir, Ivo Crnolatac, Filip Šupljika, Livio Racané, Sanja Tomić and Marijana Radić Stojković
Biomolecules 2022, 12(3), 374; https://doi.org/10.3390/biom12030374 - 27 Feb 2022
Cited by 3 | Viewed by 3491
Abstract
Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential [...] Read more.
Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences. Full article
(This article belongs to the Special Issue Polynucleotides)
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20 pages, 5405 KiB  
Article
Polycationic Monomeric and Homodimeric Asymmetric Monomethine Cyanine Dyes with Hydroxypropyl Functionality—Strong Affinity Nucleic Acids Binders
by Ivana Mikulin, Ivana Ljubić, Ivo Piantanida, Aleksey Vasilev, Mihail Mondeshki, Meglena Kandinska, Lidija Uzelac, Irena Martin-Kleiner, Marijeta Kralj and Lidija-Marija Tumir
Biomolecules 2021, 11(8), 1075; https://doi.org/10.3390/biom11081075 - 21 Jul 2021
Cited by 6 | Viewed by 2840
Abstract
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities [...] Read more.
New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA–poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents. Full article
(This article belongs to the Special Issue Polynucleotides)
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