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Structure, Dynamics, and Function of Nucleic Acids

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

Deadline for manuscript submissions: closed (15 July 2023) | Viewed by 18350

Special Issue Editor

Special Issue Information

Dear Colleagues,

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 Due to the importance of these molecules and their broad applications, unpublished theoretical or experimental studies on the physical, chemical and biochemical aspects of nucleic acids–bases, nucleosides, nucleotides, DNA and RNA helices,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

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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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Published Papers (11 papers)

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Research

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13 pages, 14307 KiB  
Article
Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species
by Qing Xian, Suyin Wang, Yanyan Liu, Shenglong Kan and Wei Zhang
Int. J. Mol. Sci. 2023, 24(9), 7716; https://doi.org/10.3390/ijms24097716 - 23 Apr 2023
Cited by 2 | Viewed by 1479
Abstract
Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, [...] Read more.
Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 Corydalis species, and their GC contents were comparatively investigated in the context of ITS2’s characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2’s concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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12 pages, 1961 KiB  
Article
Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes
by Luca Bertini, Valeria Libera, Francesca Ripanti, Francesca Natali, Marco Paolantoni, Andrea Orecchini, Alessandro Nucara, Caterina Petrillo, Lucia Comez and Alessandro Paciaroni
Int. J. Mol. Sci. 2023, 24(5), 4280; https://doi.org/10.3390/ijms24054280 - 21 Feb 2023
Cited by 4 | Viewed by 1381
Abstract
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3) [...] Read more.
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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12 pages, 9966 KiB  
Article
cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities
by Fengfei Wang, Wei Li, Baiyi Li, Liangxu Xie, Yunguang Tong and Xiaojun Xu
Int. J. Mol. Sci. 2023, 24(4), 3822; https://doi.org/10.3390/ijms24043822 - 14 Feb 2023
Cited by 1 | Viewed by 1573
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5′ and 3′ ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in [...] Read more.
Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5′ and 3′ ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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10 pages, 8611 KiB  
Article
Evolutionary Dynamics of Avian Influenza Viruses Isolated from Wild Birds in Moscow
by Yulia Postnikova, Anastasia Treshchalina, Alexandra Gambaryan, Alla Belyakova, Aydar Ishmukhametov, Mikhail Matrosovich, Galina Sadykova, Alexey Prilipov, Natalia Lomakina and Elizaveta Boravleva
Int. J. Mol. Sci. 2023, 24(3), 3020; https://doi.org/10.3390/ijms24033020 - 3 Feb 2023
Viewed by 1579
Abstract
Forty-five strains of AIVs were isolated from wild aquatic birds during their autumn migration through Moscow (Russia). The aim of this work is to study the dynamics of AIV genomes in their natural habitat. Viruses were isolated from fecal sample in embryonated chicken [...] Read more.
Forty-five strains of AIVs were isolated from wild aquatic birds during their autumn migration through Moscow (Russia). The aim of this work is to study the dynamics of AIV genomes in their natural habitat. Viruses were isolated from fecal sample in embryonated chicken eggs; their complete genomes were sequenced, and a phylogenetic analysis was performed. The gene segments of the same lineage persisted over the years in the absence of persistence of complete viral genomes. The genes for internal proteins of the same lineage were often maintained by the viruses over few years; however, they were typically associated with the genes of novel HA and NA subtypes. Although frequent reassortment events were observed for any pair of internal genes, there was no reassortment between HA and NA segments. The differences in the persistence of phylogenetic lineages of surface and internal proteins and the different evolutionary strategy for these two types of genes of AIVs in primary hosts are discussed. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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12 pages, 2069 KiB  
Article
Unique Features of Satellite DNA Transcription in Different Tissues of Caenorhabditis elegans
by Juan A. Subirana and Xavier Messeguer
Int. J. Mol. Sci. 2023, 24(3), 2970; https://doi.org/10.3390/ijms24032970 - 3 Feb 2023
Cited by 1 | Viewed by 1338
Abstract
A large part of the genome is known to be transcribed as non-coding DNA including some tandem repeats (satellites) such as telomeric/centromeric satellites in different species. However, there has been no detailed study on the eventual transcription of the interspersed satellites found in [...] Read more.
A large part of the genome is known to be transcribed as non-coding DNA including some tandem repeats (satellites) such as telomeric/centromeric satellites in different species. However, there has been no detailed study on the eventual transcription of the interspersed satellites found in many species. In the present paper, we studied the transcription of the abundant DNA satellites in the nematode Caenorhabditis elegans using available RNA-Seq results. We found that many of them have been transcribed, but usually in an irregular manner; different regions of a satellite have been transcribed with variable efficiency. Satellites with a similar repeat sequence also have a different transcription pattern depending on their position in the genome. We also describe the peculiar features of satellites associated with Helitron transposons in C. elegans. Our demonstration that some satellite RNAs are transcribed adds a new family of non-coding RNAs, a new element in the world of RNA interference, with new paths for the control of mRNA translation. This is a field that requires further investigation and will provide a deeper understanding of gene expression and control. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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14 pages, 2822 KiB  
Article
Study on the Interaction of a Peptide Targeting Specific G-Quadruplex Structures Based on Chromatographic Retention Behavior
by Ju Wang, Junqin Qiao, Weijuan Zheng and Hongzhen Lian
Int. J. Mol. Sci. 2023, 24(2), 1438; https://doi.org/10.3390/ijms24021438 - 11 Jan 2023
Cited by 2 | Viewed by 1417
Abstract
G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to [...] Read more.
G-quadruplexes (G4s) are of vital biological significance and G4-specific ligands with conformational selectivity show great application potential in disease treatment and biosensing. RHAU, a RNA helicase associated with AU-rich element, exerts biological functions through the mediation of G4s and has been identified to be a G4 binder. Here, we investigated the interactions between the RHAU peptide and G4s with different secondary structures using size exclusion chromatography (SEC) in association with circular dichroism (CD), ultraviolet-visible (UV-Vis) absorption, and native polyacrylamide gel electrophoresis (Native-PAGE). Spectral results demonstrated that the RHAU peptide did not break the main structure of G4s, making it more reliable for G4 structural analysis. The RHAU peptide was found to display a structural selectivity for a preferential binding to parallel G4s as reflected by the distinct chromatographic retention behaviors. In addition, the RHAU peptide exhibited different interactions with intermolecular parallel G4s and intramolecular parallel G4s, providing a novel recognition approach to G4 structures. The findings of this study enriched the insight into the binding of RHAU to G4s with various conformations. It is noteworthy that SEC technology can be easy and reliable for elucidating G4–peptide interactions, especially for a multiple G4 coexisting system, which supplied an alternative strategy to screen novel specific ligands for G4s. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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12 pages, 1459 KiB  
Article
New DNA Plasmid Model for Studying DNA Mismatch Repair Response to the G4 Structure
by Anzhela V. Pavlova, Nina G. Dolinnaya, Maria I. Zvereva, Elena A. Kubareva and Mayya V. Monakhova
Int. J. Mol. Sci. 2023, 24(2), 1061; https://doi.org/10.3390/ijms24021061 - 5 Jan 2023
Viewed by 1832
Abstract
G-quadruplexes (G4s), the most widely studied alternative DNA structures, are implicated in the regulation of the key cellular processes. In recent years, their involvement in DNA repair machinery has become the subject of intense research. Here, we evaluated the effect of G4 on [...] Read more.
G-quadruplexes (G4s), the most widely studied alternative DNA structures, are implicated in the regulation of the key cellular processes. In recent years, their involvement in DNA repair machinery has become the subject of intense research. Here, we evaluated the effect of G4 on the prokaryotic DNA mismatch repair (MMR) pathway from two bacterial sources with different mismatch repair mechanisms. The G4 folding, which competes with the maintenance of double-stranded DNA, is known to be controlled by numerous opposing factors. To overcome the kinetic barrier of G4 formation, we stabilized a parallel G4 formed by the d(GGGT)4 sequence in a DNA plasmid lacking a fragment complementary to the G4 motif. Unlike commonly used isolated G4 structures, our plasmid with an embedded stable G4 structure contained elements, such as a MutH cleavage site, required to initiate the repair process. G4 formation in the designed construct was confirmed by Taq polymerase stop assay and dimethyl sulfate probing. The G4-carrying plasmid, together with control ones (lacking a looped area or containing unstructured d(GT)8 insert instead of the G4 motif), were used as new type models to answer the question of whether G4 formation interferes with DNA cleavage as a basic function of MMR. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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18 pages, 6542 KiB  
Article
Conformational Preferences of Pyridone Adenine Dinucleotides from Molecular Dynamics Simulations
by David P. Buckley, Marie E. Migaud and John J. Tanner
Int. J. Mol. Sci. 2022, 23(19), 11866; https://doi.org/10.3390/ijms231911866 - 6 Oct 2022
Cited by 2 | Viewed by 1463
Abstract
Pyridone adenine dinucleotides (ox-NADs) are redox inactive derivatives of the enzyme cofactor and substrate nicotinamide adenine dinucleotide (NAD) that have a carbonyl group at the C2, C4, or C6 positions of the nicotinamide ring. These aberrant cofactor analogs accumulate in cells under stress [...] Read more.
Pyridone adenine dinucleotides (ox-NADs) are redox inactive derivatives of the enzyme cofactor and substrate nicotinamide adenine dinucleotide (NAD) that have a carbonyl group at the C2, C4, or C6 positions of the nicotinamide ring. These aberrant cofactor analogs accumulate in cells under stress and are potential inhibitors of enzymes that use NAD(H). We studied the conformational landscape of ox-NADs in solution using molecular dynamics simulations. Compared to NAD+ and NADH, 2-ox-NAD and 4-ox-NAD have an enhanced propensity for adopting the anti conformation of the pyridone ribose group, whereas 6-ox-NAD exhibits greater syn potential. Consequently, 2-ox-NAD and 4-ox-NAD have increased preference for folding into compact conformations, whereas 6-ox-NAD is more extended. ox-NADs have distinctive preferences for the orientation of the pyridone amide group, which are driven by intramolecular hydrogen bonding and steric interactions. These conformational preferences are compared to those of protein-bound NAD(H). Our results may help in identifying enzymes targeted by ox-NADs. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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11 pages, 2537 KiB  
Article
Formation Mechanism of Inter-Crosslink in DNA by Nitrogen Oxides Pollutants through A Diazonium Intermediate
by Noemi Hernandez-Haro, Christian Solis-Calero, Rodrigo Casasnovas, Christophe Morell, Andre Grand, Juan Frau and Joaquín Ortega-Castro
Int. J. Mol. Sci. 2022, 23(18), 10621; https://doi.org/10.3390/ijms231810621 - 13 Sep 2022
Cited by 1 | Viewed by 1299
Abstract
Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able [...] Read more.
Outdoor air pollution is a mixture of multiple atmospheric pollutants, among which nitrogen oxide (NOx) stands out due to its association with several diseases. NOx reactivity can conduct to DNA damage as severe as interstrand crosslinks (ICL) formation, that in turn is able to block DNA replication and transcription. Experimental studies have suggested that the ICL formation due to NOx is realized through a diazonium intermediate (DI). In this work, we have modeled the DI structure, including a DNA double-strand composed of two base pairs GC/CG, being diazotized as one of the guanine nucleotides. The structural stability of DNA with DI lesion was essayed through 500 ns molecular dynamics simulations. It was found that the DNA structure of the oligonucleotide is stable when the DI is present since the loss of a Guanine–Cytosine hydrogen bond is replaced by the presence of two cation-π interactions. Additionally, we have studied the mechanism of formation of a crosslink between the two guanine nucleobases from the modeled DI by carrying out DFT calculations at the M06-L/DNP+ level of theory. Our results show that the mechanism is thermodynamically favored by a strong stabilization of the ICL product, and the process is kinetically viable since its limiting stage is accessible. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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23 pages, 5549 KiB  
Article
2-Selenouridine, a Modified Nucleoside of Bacterial tRNAs, Its Reactivity in the Presence of Oxidizing and Reducing Reagents
by Katarzyna Kulik, Klaudia Sadowska, Ewelina Wielgus, Barbara Pacholczyk-Sienicka, Elzbieta Sochacka and Barbara Nawrot
Int. J. Mol. Sci. 2022, 23(14), 7973; https://doi.org/10.3390/ijms23147973 - 19 Jul 2022
Cited by 2 | Viewed by 1831
Abstract
The 5-substituted 2-selenouridines are natural components of the bacterial tRNA epitranscriptome. Because selenium-containing biomolecules are redox-active entities, the oxidation susceptibility of 2-selenouridine (Se2U) was studied in the presence of hydrogen peroxide under various conditions and compared with previously reported data for 2-thiouridine (S2U). [...] Read more.
The 5-substituted 2-selenouridines are natural components of the bacterial tRNA epitranscriptome. Because selenium-containing biomolecules are redox-active entities, the oxidation susceptibility of 2-selenouridine (Se2U) was studied in the presence of hydrogen peroxide under various conditions and compared with previously reported data for 2-thiouridine (S2U). It was found that Se2U is more susceptible to oxidation and converted in the first step to the corresponding diselenide (Se2U)2, an unstable intermediate that decomposes to uridine and selenium. The reversibility of the oxidized state of Se2U was demonstrated by the efficient reduction of (Se2U)2 to Se2U in the presence of common reducing agents. Thus, the 2-selenouridine component of tRNA may have antioxidant potential in cells because of its ability to react with both cellular ROS components and reducing agents. Interestingly, in the course of the reactions studied, we found that (Se2U)2 reacts with Se2U to form new ‘oligomeric nucleosides′ as linear and cyclic byproducts. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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Review

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12 pages, 2904 KiB  
Review
DNA Materials Assembled from One DNA Strand
by Jiezhong Shi, Ben Zhang, Tianyi Zheng, Tong Zhou, Min Guo, Ying Wang and Yuanchen Dong
Int. J. Mol. Sci. 2023, 24(9), 8177; https://doi.org/10.3390/ijms24098177 - 3 May 2023
Cited by 3 | Viewed by 1990
Abstract
Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based [...] Read more.
Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. The construction of DNA materials using only one DNA strand can not only save time and cost, but also avoid defects in final assemblies generated by the inaccuracy of DNA ratios, which potentially promote the large-scale production and practical application of DNA materials. In order to use one DNA strand to form assemblies, the sequences have to be palindromes with lengths that need to be controlled carefully. In this review, we introduced the development of DNA assembly and mainly summarized current reported materials formed by one DNA strand. We also discussed the principle for the construction of DNA materials using one DNA strand. Full article
(This article belongs to the Special Issue Structure, Dynamics, and Function of Nucleic Acids)
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