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

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 72807

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Special Issue Editors

Dr. Vaclav Brazda

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Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
Interests: relationship between DNA structure and function; interaction of proteins with DNA, local DNA structures and DNA damage; p53 protein and carcinogenesis; bioinformatics; immunology; neurosciences; neurodegeneration
Special Issues, Collections and Topics in MDPI journals

Dr. Richard Bowater

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Guest Editor

School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
Interests: relationship between DNA structure and function; interaction of proteins with nucleic acids; genome damage and repair mechanisms; nucleic acid ligases; biochemical and biophysical chemistry education

Special Issue Information

Dear Colleagues,

Interactions between nucleic acids and proteins are some of the most important interactions in biology because many are essential requirements for the viability of cellular life. These interactions are indispensable for many basic biological processes, such as replication, transcription, and recombination. DNA is typically presented as a double stranded B-DNA structure, which is usually referred to as its canonical structure, but nucleic acids have great structural flexibility. This is especially true for RNA, but it is also clear that DNA can adopt many structural variations. Current knowledge demonstrates that the structural conformations of nucleic acids—their topologies—play critical roles in protein–DNA interactions. Several non-canonical structures have been shown to be effective targets for proteins, and they are implicated to play important roles in a range of human diseases, including cancer.

Building on recent research findings, we aim to cover important and new aspects of protein binding to sequence-specific nucleic acid targets, with emphasis on interactions that involve non-canonical DNA structures, such as G-quadruplexes, i-motifs, triplexes, and cruciform structures. We welcome contributions that involve biophysical, biochemical, and molecular biological, as well as bioinformatics, approaches for analyses of these systems. Authors are invited to submit original research in all areas of protein–nucleic acids research and/or reviews of recent work in this area. Topics considered to be appropriate include all impacts of non-canonical structures of nucleic acids, from biological activity to structure, from detection methods to their protein targeting, providing molecular insight and novel physiological and pathological functions or regulatory mechanisms of non-canonical DNA structures and their protein recognition. Submitted papers can refer to in vitro studies or can involve any cellular system or model organism.

We look forward to receiving your contributions to this Special Issue on “Impacts of Molecular Structure on Nucleic Acid–Protein Interactions”.

Dr. Vaclav Brazda
Dr. Richard Bowater
Guest Editors

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Keywords

protein-DNA
recognition sequence
DNA topology
DNA structure
G-quadruplex
i-motif
inverted repeat
cruciform structure
sequence analysis
non-canonical DNA

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Published Papers (13 papers)

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Editorial

Jump to: Research, Review

4 pages, 637 KiB

Open AccessEditorial

Impacts of Molecular Structure on Nucleic Acid–Protein Interactions

by Richard P. Bowater and Václav Brázda

Int. J. Mol. Sci. 2023, 24(1), 407; https://doi.org/10.3390/ijms24010407 - 26 Dec 2022

Viewed by 1697

Abstract

Interactions between nucleic acids and proteins are some of the most important interactions in biology because they are the cornerstones for fundamental biological processes, such as replication, transcription, and recombination [...] Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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Research

Jump to: Editorial, Review

16 pages, 3448 KiB

Open AccessArticle

Cellular Computational Logic Using Toehold Switches

by Seungdo Choi, Geonhu Lee and Jongmin Kim

Int. J. Mol. Sci. 2022, 23(8), 4265; https://doi.org/10.3390/ijms23084265 - 12 Apr 2022

Cited by 5 | Viewed by 4610

Abstract

The development of computational logic that carries programmable and predictable features is one of the key requirements for next-generation synthetic biological devices. Despite considerable progress, the construction of synthetic biological arithmetic logic units presents numerous challenges. In this paper, utilizing the unique advantages of RNA molecules in building complex logic circuits in the cellular environment, we demonstrate the RNA-only bitwise logical operation of XOR gates and basic arithmetic operations, including a half adder, a half subtractor, and a Feynman gate, in Escherichia coli. Specifically, de-novo-designed riboregulators, known as toehold switches, were concatenated to enhance the functionality of an OR gate, and a previously utilized antisense RNA strategy was further optimized to construct orthogonal NIMPLY gates. These optimized synthetic logic gates were able to be seamlessly integrated to achieve final arithmetic operations on small molecule inputs in cells. Toehold-switch-based ribocomputing devices may provide a fundamental basis for synthetic RNA-based arithmetic logic units or higher-order systems in cells. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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12 pages, 3763 KiB

Open AccessCommunication

Hidden Information Revealed Using the Orthogonal System of Nucleic Acids

by Viktor Víglaský

Int. J. Mol. Sci. 2022, 23(3), 1804; https://doi.org/10.3390/ijms23031804 - 4 Feb 2022

Cited by 3 | Viewed by 1784

Abstract

In this study, the organization of genetic information in nucleic acids is defined using a novel orthogonal representation. Clearly defined base pairing in DNA allows the linear base chain and sequence to be mathematically transformed into an orthogonal representation where the G–C and A–T pairs are displayed in different planes that are perpendicular to each other. This form of base allocation enables the evaluation of any nucleic acid and predicts the likelihood of a particular region to form non-canonical motifs. The G4Hunter algorithm is currently a popular method of identifying G-quadruplex forming sequences in nucleic acids, and offers promising scores despite its lack of a substantial rational basis. The orthogonal representation described here is an effort to address this incongruity. In addition, the orthogonal display facilitates the search for other sequences that are capable of adopting non-canonical motifs, such as direct and palindromic repeats. The technique can also be used for various RNAs, including any aptamers. This powerful tool based on an orthogonal system offers considerable potential for a wide range of applications. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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18 pages, 4004 KiB

Open AccessCommunication

Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

by Martin Bartas, Kristyna Slychko, Václav Brázda, Jiří Červeň, Christopher A. Beaudoin, Tom L. Blundell and Petr Pečinka

Int. J. Mol. Sci. 2022, 23(2), 768; https://doi.org/10.3390/ijms23020768 - 11 Jan 2022

Cited by 14 | Viewed by 8183

Abstract

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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19 pages, 4655 KiB

Open AccessArticle

Chromatin Structure and “DNA Sequence View”: The Role of Satellite DNA in Ectopic Pairing of the Drosophila X Polytene Chromosome

by Aleksandr V. Zhuravlev, Gennadii A. Zakharov, Ekaterina V. Anufrieva, Anna V. Medvedeva, Ekaterina A. Nikitina and Elena V. Savvateeva-Popova

Int. J. Mol. Sci. 2021, 22(16), 8713; https://doi.org/10.3390/ijms22168713 - 13 Aug 2021

Cited by 2 | Viewed by 1916

Abstract

Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with different epigenetic properties, protein compositions and transcription activity. This leaves specific DNA sequences that affect chromosome interactions. The Drosophila melanogaster polytene chromosomes are involved in non-allelic ectopic pairing. The mutant strain agn^ts3, a Drosophila model for Williams–Beuren syndrome, has an increased frequency of ectopic contacts (FEC) compared to the wild-type strain Canton-S (CS). Ectopic pairing can be mediated by some specific DNA sequences. In this study, using our Homology Segment Analysis software, we estimated the correlation between FEC and frequency of short matching DNA fragments (FMF) for all sections of the X chromosome of Drosophila CS and agn^ts3 strains. With fragment lengths of 50 nucleotides (nt), CS showed a specific FEC–FMF correlation for 20% of the sections involved in ectopic contacts. The correlation was unspecific in agn^ts3, which may indicate the alternative epigenetic mechanisms affecting FEC in the mutant strain. Most of the fragments that specifically contributed to FMF were related to 1.688 or 372-bp middle repeats. Thus, middle repetitive DNA may serve as an organizer of ectopic pairing. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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23 pages, 8297 KiB

Open AccessArticle

The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity

by Martin Bartas, Václav Brázda, Adriana Volná, Jiří Červeň, Petr Pečinka and Joanna E. Zawacka-Pankau

Int. J. Mol. Sci. 2021, 22(16), 8512; https://doi.org/10.3390/ijms22168512 - 7 Aug 2021

Cited by 14 | Viewed by 16561

Abstract

Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remain unexplained. The p53 protein plays a crucial role in tumor suppression, tissue homeostasis, and aging. Long-lived, cancer-free African elephants have 20 copies of the TP53 gene, including 19 retrogenes (38 alleles), which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality rate of 11–25%. The mechanism through which p53 contributes to the resolution of the Peto’s paradox in Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in their lifespans. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespans have certain characteristic amino acid substitutions in the p53 DNA-binding domain that alter its function, as depicted from the Phenotypic Annotation of p53 Mutations, using the PROVEAN tool or SWISS-MODEL workflow. In addition, the loop 2 region of the human p53 DNA-binding domain was identified as the longest region that was associated with longevity. The 3D model revealed variations in the loop 2 structure in long-lived species when compared with human p53. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality, and the extended animal lifespan, and further highlight the importance of p53 protein in aging. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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15 pages, 3345 KiB

Open AccessArticle

Rhodamine 6G-Ligand Influencing G-Quadruplex Stability and Topology

by Lukáš Trizna, Ladislav Janovec, Andrea Halaganová and Viktor Víglaský

Int. J. Mol. Sci. 2021, 22(14), 7639; https://doi.org/10.3390/ijms22147639 - 16 Jul 2021

Cited by 6 | Viewed by 4735

Abstract

The involvement of G-quadruplex (G4) structures in nucleic acids in various molecular processes in cells such as replication, gene-pausing, the expression of crucial cancer-related genes and DNA damage repair is well known. The compounds targeting G4 usually bind directly to the G4 structure, but some ligands can also facilitate the G4 folding of unfolded G-rich sequences and stabilize them even without the presence of monovalent ions such as sodium or potassium. Interestingly, some G4-ligand complexes can show a clear induced CD signal, a feature which is indirect proof of the ligand interaction. Based on the dichroic spectral profile it is not only possible to confirm the presence of a G4 structure but also to determine its topology. In this study we examine the potential of the commercially available Rhodamine 6G (RhG) as a G4 ligand. RhG tends to convert antiparallel G4 structures to parallel forms in a manner similar to that of Thiazole Orange. Our results confirm the very high selectivity of this ligand to the G4 structure. Moreover, the parallel topology of G4 can be verified unambiguously based on the specific induced CD profile of the G4-RhG complex. This feature has been verified on more than 50 different DNA sequences forming various non-canonical structural motifs. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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13 pages, 3738 KiB

Open AccessCommunication

G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story

by Adriana Volná, Martin Bartas, Václav Karlický, Jakub Nezval, Kristýna Kundrátová, Petr Pečinka, Vladimír Špunda and Jiří Červeň

Int. J. Mol. Sci. 2021, 22(14), 7381; https://doi.org/10.3390/ijms22147381 - 9 Jul 2021

Cited by 14 | Viewed by 6725

Abstract

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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12 pages, 3116 KiB

Open AccessArticle

Tracing dsDNA Virus–Host Coevolution through Correlation of Their G-Quadruplex-Forming Sequences

by Natália Bohálová, Alessio Cantara, Martin Bartas, Patrik Kaura, Jiří Šťastný, Petr Pečinka, Miroslav Fojta and Václav Brázda

Int. J. Mol. Sci. 2021, 22(7), 3433; https://doi.org/10.3390/ijms22073433 - 26 Mar 2021

Cited by 13 | Viewed by 4139

Abstract

The importance of gene expression regulation in viruses based upon G-quadruplex may point to its potential utilization in therapeutic targeting. Here, we present analyses as to the occurrence of putative G-quadruplex-forming sequences (PQS) in all reference viral dsDNA genomes and evaluate their dependence on PQS occurrence in host organisms using the G4Hunter tool. PQS frequencies differ across host taxa without regard to GC content. The overlay of PQS with annotated regions reveals the localization of PQS in specific regions. While abundance in some, such as repeat regions, is shared by all groups, others are unique. There is abundance within introns of Eukaryota-infecting viruses, but depletion of PQS in introns of bacteria-infecting viruses. We reveal a significant positive correlation between PQS frequencies in dsDNA viruses and corresponding hosts from archaea, bacteria, and eukaryotes. A strong relationship between PQS in a virus and its host indicates their close coevolution and evolutionarily reciprocal mimicking of genome organization. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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22 pages, 4425 KiB

Open AccessArticle

CNBP Binds and Unfolds In Vitro G-Quadruplexes Formed in the SARS-CoV-2 Positive and Negative Genome Strands

by Georgina Bezzi, Ernesto J. Piga, Andrés Binolfi and Pablo Armas

Int. J. Mol. Sci. 2021, 22(5), 2614; https://doi.org/10.3390/ijms22052614 - 5 Mar 2021

Cited by 36 | Viewed by 5222

Abstract

The Coronavirus Disease 2019 (COVID-19) pandemic has become a global health emergency with no effective medical treatment and with incipient vaccines. It is caused by a new positive-sense RNA virus called severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). G-quadruplexes (G4s) are nucleic acid secondary structures involved in the control of a variety of biological processes including viral replication. Using several G4 prediction tools, we identified highly putative G4 sequences (PQSs) within the positive-sense (+gRNA) and negative-sense (−gRNA) RNA strands of SARS-CoV-2 conserved in related betacoronaviruses. By using multiple biophysical techniques, we confirmed the formation of two G4s in the +gRNA and provide the first evidence of G4 formation by two PQSs in the −gRNA of SARS-CoV-2. Finally, biophysical and molecular approaches were used to demonstrate for the first time that CNBP, the main human cellular protein bound to SARS-CoV-2 RNA genome, binds and promotes the unfolding of G4s formed by both strands of SARS-CoV-2 RNA genome. Our results suggest that G4s found in SARS-CoV-2 RNA genome and its negative-sense replicative intermediates, as well as the cellular proteins that interact with them, are relevant factors for viral genes expression and replication cycle, and may constitute interesting targets for antiviral drugs development. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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Review

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18 pages, 4195 KiB

Open AccessReview

Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids

by Richard P. Bowater, Natália Bohálová and Václav Brázda

Int. J. Mol. Sci. 2022, 23(11), 6171; https://doi.org/10.3390/ijms23116171 - 31 May 2022

Cited by 12 | Viewed by 4628

Abstract

Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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15 pages, 1214 KiB

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(Dys)function Follows Form: Nucleic Acid Structure, Repeat Expansion, and Disease Pathology in FMR1 Disorders

by Xiaonan Zhao and Karen Usdin

Int. J. Mol. Sci. 2021, 22(17), 9167; https://doi.org/10.3390/ijms22179167 - 25 Aug 2021

Cited by 11 | Viewed by 3163

Abstract

Fragile X-related disorders (FXDs), also known as FMR1 disorders, are examples of repeat expansion diseases (REDs), clinical conditions that arise from an increase in the number of repeats in a disease-specific microsatellite. In the case of FXDs, the repeat unit is CGG/CCG and the repeat tract is located in the 5′ UTR of the X-linked FMR1 gene. Expansion can result in neurodegeneration, ovarian dysfunction, or intellectual disability depending on the number of repeats in the expanded allele. A growing body of evidence suggests that the mutational mechanisms responsible for many REDs share several common features. It is also increasingly apparent that in some of these diseases the pathologic consequences of expansion may arise in similar ways. It has long been known that many of the disease-associated repeats form unusual DNA and RNA structures. This review will focus on what is known about these structures, the proteins with which they interact, and how they may be related to the causative mutation and disease pathology in the FMR1 disorders. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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11 pages, 4379 KiB

Open AccessReview

Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins

by Martin Bartas, Jiří Červeň, Simona Guziurová, Kristyna Slychko and Petr Pečinka

Int. J. Mol. Sci. 2021, 22(2), 922; https://doi.org/10.3390/ijms22020922 - 18 Jan 2021

Cited by 17 | Viewed by 6789

Abstract

Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category. Full article

(This article belongs to the Special Issue Impacts of Molecular Structure on Nucleic Acid-Protein Interactions)

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