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Biophysical Study of the 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 Biophysics".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 17545

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

Dear Colleagues,

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

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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 and RNA–protein interactions

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Related Special Issues

Published Papers (7 papers)

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Editorial

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2 pages, 188 KiB  
Editorial
New Understandings from the Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0
by Joon-Hwa Lee
Int. J. Mol. Sci. 2022, 23(24), 15822; https://doi.org/10.3390/ijms232415822 - 13 Dec 2022
Cited by 1 | Viewed by 1023
Abstract
Nucleic acids play an essential role in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [...] Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)

Research

Jump to: Editorial

11 pages, 2236 KiB  
Article
Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3
by Ho-Seong Jin, Juyeon Son, Yeo-Jin Seo, Seo-Ree Choi, Hye-Bin Ahn, Youyeon Go, Juhee Lim, Kwang-Im Oh, Kyoung-Seok Ryu and Joon-Hwa Lee
Int. J. Mol. Sci. 2022, 23(16), 9497; https://doi.org/10.3390/ijms23169497 - 22 Aug 2022
Cited by 2 | Viewed by 1683
Abstract
Distal-less 3 (Dlx3) is a homeobox-containing transcription factor and plays a crucial role in the development and differentiation process. Human Dlx3 consists of two transactivation domains and a homeobox domain (HD) that selectively binds to the consensus site (5′-TAATT-3′) of the DNA duplex. [...] Read more.
Distal-less 3 (Dlx3) is a homeobox-containing transcription factor and plays a crucial role in the development and differentiation process. Human Dlx3 consists of two transactivation domains and a homeobox domain (HD) that selectively binds to the consensus site (5′-TAATT-3′) of the DNA duplex. Here, we performed chemical shift perturbation experiments on Dlx3-HD in a complex with a 10-base-paired (10-bp) DNA duplex under various salt conditions. We also acquired the imino proton spectra of the 10-bp DNA to monitor the changes in base-pair stabilities during titration with Dlx3-HD. Our study demonstrates that Dlx3-HD selectively recognizes its consensus DNA sequences through the α3 helix and L1 loop regions with a unique dynamic feature. The dynamic properties of the binding of Dlx3-HD to its consensus DNA sequence can be modulated by varying the salt concentrations. Our study suggested that this unique structural and dynamic feature of Dlx3-HD plays an important role in target DNA recognition, which might be associated with tricho-dento-osseous syndrome. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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13 pages, 6356 KiB  
Article
Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque
by Stepan Dzhimak, Alexandr Svidlov, Anna Elkina, Eugeny Gerasimenko, Mikhail Baryshev and Mikhail Drobotenko
Int. J. Mol. Sci. 2022, 23(8), 4428; https://doi.org/10.3390/ijms23084428 - 17 Apr 2022
Cited by 8 | Viewed by 2094
Abstract
The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the [...] Read more.
The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm). Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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16 pages, 2387 KiB  
Article
Fluorescence-Based Binding Characterization of Small Molecule Ligands Targeting CUG RNA Repeats
by Zhihua Chang, Ya Ying Zheng, Johnsi Mathivanan, Vibhav A. Valsangkar, Jinxi Du, Reham A. I. Abou-Elkhair, Abdalla E. A. Hassan and Jia Sheng
Int. J. Mol. Sci. 2022, 23(6), 3321; https://doi.org/10.3390/ijms23063321 - 19 Mar 2022
Cited by 2 | Viewed by 2391
Abstract
Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some [...] Read more.
Pathogenic CUG and CCUG RNA repeats have been associated with myotonic dystrophy type 1 and 2 (DM1 and DM2), respectively. Identifying small molecules that can bind these RNA repeats is of great significance to develop potential therapeutics to treat these neurodegenerative diseases. Some studies have shown that aminoglycosides and their derivatives could work as potential lead compounds targeting these RNA repeats. In this work, sisomicin, previously known to bind HIV-1 TAR, is investigated as a possible ligand for CUG RNA repeats. We designed a novel fluorescence-labeled RNA sequence of r(CUG)10 to mimic cellular RNA repeats and improve the detecting sensitivity. The interaction of sisomicin with CUG RNA repeats is characterized by the change of fluorescent signal, which is initially minimized by covalently incorporating the fluorescein into the RNA bases and later increased upon ligand binding. The results show that sisomicin can bind and stabilize the folded RNA structure. We demonstrate that this new fluorescence-based binding characterization assay is consistent with the classic UV Tm technique, indicating its feasibility for high-throughput screening of ligand-RNA binding interactions and wide applications to measure the thermodynamic parameters in addition to binding constants and kinetics when probing such interactions. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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16 pages, 3507 KiB  
Article
NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus
by Min June Yang, Jinwoo Kim, Yeongjoon Lee, Woonghee Lee and Chin-Ju Park
Int. J. Mol. Sci. 2022, 23(6), 3099; https://doi.org/10.3390/ijms23063099 - 13 Mar 2022
Cited by 2 | Viewed by 3186
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various [...] Read more.
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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15 pages, 12811 KiB  
Article
Fractal Analysis of DNA Sequences Using Frequency Chaos Game Representation and Small-Angle Scattering
by Eugen Mircea Anitas
Int. J. Mol. Sci. 2022, 23(3), 1847; https://doi.org/10.3390/ijms23031847 - 6 Feb 2022
Cited by 14 | Viewed by 3395
Abstract
The fractal characteristics of DNA sequences are studied using the frequency chaos game representation (FCGR) and small-angle scattering (SAS) technique. The FCGR allows representation of the frequencies of occurrence of k-mers (oligonucleotides of length k) in the form of images. The [...] Read more.
The fractal characteristics of DNA sequences are studied using the frequency chaos game representation (FCGR) and small-angle scattering (SAS) technique. The FCGR allows representation of the frequencies of occurrence of k-mers (oligonucleotides of length k) in the form of images. The numerically encoded data are then used in a SAS analysis to enhance hidden features in DNA sequences. It is shown that the simulated SAS intensity allows us to obtain the fractal dimensions and scaling factors at various scales. These structural parameters can be used to distinguish unambiguously between the scaling properties of complex hierarchical DNA sequences. The validity of this approach is illustrated on several sequences from: Escherichia coli, Mouse mitochondrion, Homo sapiens mitochondrion and Human cosmid. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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12 pages, 2768 KiB  
Article
Incorporation of a FRET Pair into a Riboswitch RNA to Measure Mg2+ Concentration and RNA Conformational Change in Cell
by Yanyan Xue and Yu Liu
Int. J. Mol. Sci. 2022, 23(3), 1493; https://doi.org/10.3390/ijms23031493 - 27 Jan 2022
Cited by 3 | Viewed by 2829
Abstract
Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, [...] Read more.
Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, into a full-length adenine riboswitch RNA and its isolated aptamer domain to monitor the dynamics of the RNAs in vitro and in cell. The adenine riboswitch was sensitive to Mg2+ concentrations and could be used as a biosensor to measure cellular Mg2+ concentrations. Additionally, the TQ3/Cy3-labeled adenine riboswitch yielded a Mg2+ concentration that was similar to that measured using a commercial assay kit. Furthermore, the fluorescence response to the adenine of the TQ3/Cy3-labeled riboswitch RNA was applied to determine the proportions of multiple RNA conformational changes in cells. The strategy developed in this work can be used to probe the dynamics of other RNAs in cells and may facilitate the developments of RNA biosensors, drugs and engineering. Full article
(This article belongs to the Special Issue Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0)
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