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Structure, Dynamics, and Function of Nucleic Acids 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 30 September 2024 | Viewed by 3900

Special Issue Editor

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue “Structure, Dynamics, and Function of Nucleic Acids” (https://www.mdpi.com/journal/ijms/special_issues/Nucleic_Acids_Structure).

Nucleic acids are the most important macromolecules for sustainable life. They form strands of DNA and RNA, which carry the genetic model of a cell and the instructions for its functioning. Due to the importance of these molecules and their broad applications, unpublished theoretical or experimental studies on the physical, chemical and biochemical aspects of nucleic acids, including bases, nucleosides, nucleotides, DNA and RNA helices, as well as their associated interactions and functions, are welcome for this Special Issue. In addition, computational studies that address structure predictions, molecular modeling, docking calculations and tautomerism are also welcome.

Dr. Mauricio Alcolea Palafox
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • structure predictions
  • molecular modeling
  • molecular systems and processes
  • electronic properties and structure
  • RNA structure
  • DNA structure and dynamics
  • docking calculations
  • nucleic acid structure and dynamics
  • biomolecular interactions

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Published Papers (3 papers)

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Research

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15 pages, 2096 KiB  
Article
Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3
by Miklós Cervenak, Orsolya Réka Molnár, Péter Horváth and László Smeller
Int. J. Mol. Sci. 2024, 25(5), 2482; https://doi.org/10.3390/ijms25052482 - 20 Feb 2024
Viewed by 938
Abstract
The G-quadruplex is one of the non-canonical structures formed by nucleic acids, which can be formed by guanine-rich sequences. They became the focus of much research when they were found in several oncogene promoter regions and also in the telomeres. Later on, they [...] Read more.
The G-quadruplex is one of the non-canonical structures formed by nucleic acids, which can be formed by guanine-rich sequences. They became the focus of much research when they were found in several oncogene promoter regions and also in the telomeres. Later on, they were discovered in viruses as well. Various ligands have been developed in order to stabilize DNA G-quadruplexes, which were believed to have an anti-cancer or antiviral effect. We investigated three of these ligands, and whether they can also affect the stability of the G-quadruplex-forming sequences of the RNA genome of SARS-CoV-2. All three investigated oligonucleotides showed the G-quadruplex form. We characterized their stability and measured their thermodynamic parameters using the Förster resonance energy transfer method. The addition of the ligands caused an increase in the unfolding temperature, but this effect was smaller compared to that found earlier in the case of G-quadruplexes of the hepatitis B virus, which has a DNA genome. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids 2.0)
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20 pages, 12105 KiB  
Article
Molecular Insights into the Specific Targeting of c-MYC G-Quadruplex by Thiazole Peptides
by Sen Cao, Qian Su, Yong-Hao Chen, Meng-Lu Wang, Yi Xu, Li-Hui Wang, Yan-Hua Lu, Jian-Feng Li, Jun Liu, Xiao-Jing Hong, Hong-Yan Wang, Jun-Ping Liu and Zhi-Guo Wang
Int. J. Mol. Sci. 2024, 25(1), 623; https://doi.org/10.3390/ijms25010623 - 3 Jan 2024
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Abstract
Stabilization of a G-quadruplex (G4) in the promotor of the c-MYC proto-oncogene leads to inhibition of gene expression, and it thus represents a potentially attractive new strategy for cancer treatment. However, most G4 stabilizers show little selectivity among the many G4s present in [...] Read more.
Stabilization of a G-quadruplex (G4) in the promotor of the c-MYC proto-oncogene leads to inhibition of gene expression, and it thus represents a potentially attractive new strategy for cancer treatment. However, most G4 stabilizers show little selectivity among the many G4s present in the cellular complement of DNA and RNA. Intriguingly, a crescent-shaped cell-penetrating thiazole peptide, TH3, preferentially stabilizes the c-MYC G4 over other promotor G4s, but the mechanisms leading to this selective binding remain obscure. To investigate these mechanisms at the atomic level, we performed an in silico comparative investigation of the binding of TH3 and its analogue TH1 to the G4s from the promotors of c-MYC, c-KIT1, c-KIT2, and BCL2. Molecular docking and molecular dynamics simulations, combined with in-depth analyses of non-covalent interactions and bulk and per-nucleotide binding free energies, revealed that both TH3 and TH1 can induce the formation of a sandwich-like framework through stacking with both the top and bottom G-tetrads of the c-MYC G4 and the adjacent terminal capping nucleotides. This framework produces enhanced binding affinities for c-MYC G4 relative to other promotor G4s, with TH3 exhibiting an outstanding binding priority. Van der Waals interactions were identified to be the key factor in complex formation in all cases. Collectively, our findings fully agree with available experimental data. Therefore, the identified mechanisms leading to specific binding of TH3 towards c-MYC G4 provide valuable information to guide the development of new selective G4 stabilizers. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids 2.0)
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Review

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19 pages, 2321 KiB  
Review
Multi-Scale Imaging of the Dynamic Organization of Chromatin
by Fabiola García Fernández, Sébastien Huet and Judith Miné-Hattab
Int. J. Mol. Sci. 2023, 24(21), 15975; https://doi.org/10.3390/ijms242115975 - 4 Nov 2023
Cited by 1 | Viewed by 1505
Abstract
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution [...] Read more.
Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids 2.0)
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