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Structure, Dynamics, and Function of Nucleic Acids: 2nd Edition

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: closed (30 September 2024) | Viewed by 6282

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 Due to the importance of these molecules and their broad applications, unpublished theoretical or experimental studies on the physical, chemical and biochemical aspects of nucleic acids, including bases, nucleosides, nucleotides, DNA and RNA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

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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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Related Special Issue

Published Papers (4 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 1623
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: 2nd Edition)
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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: 2nd Edition)
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Review

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12 pages, 3411 KiB  
Review
Riboswitch Mechanisms for Regulation of P1 Helix Stability
by Jason R. Stagno and Yun-Xing Wang
Int. J. Mol. Sci. 2024, 25(19), 10682; https://doi.org/10.3390/ijms251910682 - 4 Oct 2024
Viewed by 416
Abstract
Riboswitches are highly structured RNA regulators of gene expression. Although found in all three domains of life, they are particularly abundant and widespread in bacteria, including many human pathogens, thus making them an attractive target for antimicrobial development. Moreover, the functional versatility of [...] Read more.
Riboswitches are highly structured RNA regulators of gene expression. Although found in all three domains of life, they are particularly abundant and widespread in bacteria, including many human pathogens, thus making them an attractive target for antimicrobial development. Moreover, the functional versatility of riboswitches to recognize a myriad of ligands, including ions, amino acids, and diverse small-molecule metabolites, has enabled the generation of synthetic aptamers that have been used as molecular probes, sensors, and regulatory RNA devices. Generally speaking, a riboswitch consists of a ligand-sensing aptamer domain and an expression platform, whose genetic control is achieved through the formation of mutually exclusive secondary structures in a ligand-dependent manner. For most riboswitches, this involves formation of the aptamer’s P1 helix and the regulation of its stability, whose competing structure turns gene expression ON/OFF at the level of transcription or translation. Structural knowledge of the conformational changes involving the P1 regulatory helix, therefore, is essential in understanding the structural basis for ligand-induced conformational switching. This review provides a summary of riboswitch cases for which ligand-free and ligand-bound structures have been determined. Comparative analyses of these structures illustrate the uniqueness of these riboswitches, not only in ligand sensing but also in the various structural mechanisms used to achieve the same end of regulating switch helix stability. In all cases, the ligand stabilizes the P1 helix primarily through coaxial stacking interactions that promote helical continuity. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids: 2nd Edition)
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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 2070
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: 2nd Edition)
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