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Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 3.0

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 (31 July 2023) | Viewed by 9279

Special Issue Editor

Prof. Dr. Joon-Hwa Lee

E-Mail Website
Guest Editor
Department of Chemistry, Gyeongsang National University, Jinju, Gyeongnam 52828, Korea
Interests: NMR, Z-DNA; DNA-protein interaction; RNA dynamics; microRNA; transcription factor; protein dynamics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Nucleic acids play an important role in all biological processes related to genetic information such as replication, transcription, translation, repair, and recombination. Over the years, biophysical tools such as X-ray crystallography, NMR spectroscopy, and cryo-EM have been employed to study the structure of nucleic acids to understand their biological functions. In addition, biophysical studies of the dynamic features of nucleic acids should be conducted, because their less populated conformations can contribute to folding, stability, and biological functions. Recently, many experimental and theoretical approaches have been reported to understand the correlation between the structure and dynamics of nucleic acids and their biological functions. This Special Issue will introduce new interesting developments in the field of structure and dynamics of nucleic acids and complexes with target proteins.

Prof. Dr. Joon-Hwa Lee
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.

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Keywords

  • Structure of nucleic acids
  • Biophysical study of nucleic acids including NMR
  • X-ray
  • FRET
  • cryo-EM
  • computation/ Structure–function relationship of nucleic acids
  • Dynamics of nucleic acids
  • DNA–protein 
  • RNA–protein interactions/

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Published Papers (4 papers)

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Research

11 pages, 2188 KiB  
Article
Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR
by Omar Eladl, Yudai Yamaoki, Keiko Kondo, Takashi Nagata and Masato Katahira
Int. J. Mol. Sci. 2023, 24(10), 9069; https://doi.org/10.3390/ijms24109069 - 22 May 2023
Cited by 1 | Viewed by 1896
Abstract
An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living [...] Read more.
An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living cells. We examined an RNA aptamer for HIV-1 Tat (TA), which had been found to trap Tat and repress its function in living human cells. We first used in vitro NMR to examine the interaction between TA and a part of Tat containing the binding site for trans-activation response element (TAR). It was revealed that two U-A∗U base triples are formed in TA upon binding of Tat. This was assumed to be critical for strong binding. Then, TA in complex with a part of Tat was incorporated into living human cells. The presence of two U-A∗U base triples was also revealed for the complex in living human cells by in-cell NMR. Thus, the activity of TA in living human cells was rationally elucidated by in-cell NMR. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 3.0)
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14 pages, 4099 KiB  
Article
G-QINDER Tool: Bioinformatically Predicted Formation of Different Four-Stranded DNA Motifs from (GT)n and (GA)n Repeats
by Lukáš Trizna, Branislav Osif and Viktor Víglaský
Int. J. Mol. Sci. 2023, 24(8), 7565; https://doi.org/10.3390/ijms24087565 - 20 Apr 2023
Cited by 2 | Viewed by 1686
Abstract
The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs [...] Read more.
The recently introduced semi-orthogonal system of nucleic acid imaging offers a greatly improved method of identifying DNA sequences that are capable of adopting noncanonical structures. This paper uses our newly developed G-QINDER tool to identify specific repeat sequences that adopt unique structural motifs in DNA: TG and AG repeats. The structures were found to adopt a left-handed G-quadruplex form under extreme crowding conditions and a unique tetrahelical motif under certain other conditions. The tetrahelical structure likely consists of stacked AGAG-tetrads but, unlike G-quadruplexes, their stability does not appear to be dependent on the type of monovalent cation present. The occurrence of TG and AG repeats in genomes is not rare, and they are also found frequently in the regulatory regions of nucleic acids, so it is reasonable to assume that putative structural motifs, like other noncanonical forms, could play an important regulatory role in cells. This hypothesis is supported by the structural stability of the AGAG motif; its unfolding can occur even at physiological temperatures since the melting temperature is primarily dependent on the number of AG repeats in the sequence. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 3.0)
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11 pages, 2369 KiB  
Communication
The Anticancer Drug Daunomycin Directly Affects Gene Expression and DNA Structure
by Takashi Nishio, Yohji Shimada, Yuko Yoshikawa, Takahiro Kenmotsu, Helmut Schiessel and Kenichi Yoshikawa
Int. J. Mol. Sci. 2023, 24(7), 6631; https://doi.org/10.3390/ijms24076631 - 1 Apr 2023
Cited by 2 | Viewed by 1903
Abstract
Daunomycin (DM), an anthracycline antibiotic, is frequently used to treat various cancers, but the direct effects of DM on gene expression and DNA structure are unclear. We used an in vitro cell-free system, optimized with spermine (SP), to study the effect of DM [...] Read more.
Daunomycin (DM), an anthracycline antibiotic, is frequently used to treat various cancers, but the direct effects of DM on gene expression and DNA structure are unclear. We used an in vitro cell-free system, optimized with spermine (SP), to study the effect of DM on gene expression. A bimodal effect of DM on gene expression, weak promotion followed by inhibition, was observed with increasing concentration of DM. We also performed atomic force microscopy observation to measure how DM affects the higher-order structure of DNA induced with SP. DM destroyed SP-induced flower-like conformations of DNA by generating double-strand breaks, and this destructive conformational change of DNA corresponded to the inhibitory effect on gene expression. Interestingly, the weakly enhanced cell-free gene expression occurred as DNA conformations were elongated or relaxed at lower DM concentrations. We expect these newly unveiled DM effects on gene expression and the higher-order structure of DNA will contribute further to the development and refinement of useful anticancer therapy chemicals. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 3.0)
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18 pages, 4351 KiB  
Article
Targeting MYC Regulation with Polypurine Reverse Hoogsteen Oligonucleotides
by Simonas Valiuska, Alexandra Maria Psaras, Véronique Noé, Tracy A. Brooks and Carlos J. Ciudad
Int. J. Mol. Sci. 2023, 24(1), 378; https://doi.org/10.3390/ijms24010378 - 26 Dec 2022
Cited by 7 | Viewed by 2518
Abstract
The oncogene MYC has key roles in transcription, proliferation, deregulating cellular energetics, and more. Modulating the expression or function of the MYC protein is a viable therapeutic goal in an array of cancer types, and potential inhibitors of MYC with high specificity and [...] Read more.
The oncogene MYC has key roles in transcription, proliferation, deregulating cellular energetics, and more. Modulating the expression or function of the MYC protein is a viable therapeutic goal in an array of cancer types, and potential inhibitors of MYC with high specificity and selectivity are of great interest. In cancer cells addicted to their aberrant MYC function, suppression can lead to apoptosis, with minimal effects on non-addicted, non-oncogenic cells, providing a wide therapeutic window for specific and efficacious anti-tumor treatment. Within the promoter of MYC lies a GC-rich, G-quadruplex (G4)-forming region, wherein G4 formation is capable of mediating transcriptional downregulation of MYC. Such GC-rich regions of DNA are prime targets for regulation with Polypurine Reverse Hoogsteen hairpins (PPRHs). The current study designed and examined PPRHs targeting the G4-forming and four other GC-rich regions of DNA within the promoter or intronic regions. Six total PPRHs were designed, examined in cell-free conditions for target engagement and in cells for transcriptional modulation, and correlating cytotoxic activity in pancreatic, prostate, neuroblastoma, colorectal, ovarian, and breast cancer cells. Two lead PPRHs, one targeting the promoter G4 and one targeting Intron 1, were identified with high potential for further development as an innovative approach to both G4 stabilization and MYC modulation. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 3.0)
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