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Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides

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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 (30 November 2020) | Viewed by 15038

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Prof. Dr. Mauricio Alcolea Palafox

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Departamento de Química-Fisica, Universidad Complutense de Madrid, Madrid, Spain
Interests: DFT applications to different systems; infrared and Raman vibrational wavenumbers; scaling the wavenumbers; molecular structure of DNA-RNA microhelices; molecular structure of nucleobases and nucleosides
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Dr. Saber Mohammadi

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Universidad Complutense de Madrid, Departamento de Química-Fisica, Madrid, Spain

Special Issue Information

Dear Colleague,

Nucleic acids are the most important macromolecules for the continuity of life. With them, DNA and RNA strands are formed, which carry the genetic model of a cell and carry instructions for the functioning of the cell. Due to the importance of these molecules and the extensive applications of their derivatives, unpublished theoretical or experimental manuscripts that report the physical, chemical, and biochemical aspects of nucleic acids bases, nucleosides, nucleotides, DNA and RNA helices, and interactions involved with them are welcome for this Special Issue. In addition, computational studies that deal with structure predictions, molecular modeling, docking calculations, and tautomerism are also collected.

Prof. Mauricio Palafox
Dr. Saber Mohammadi
Guest Editors

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Keywords

nucleic acid structure and dynamics
nucleobases pairs
nucleotides
molecular simulations
computer calculations
DNA structure

Published Papers (5 papers)

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Research

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14 pages, 2909 KiB

Open AccessArticle

MD-TSPC4: Computational Method for Predicting the Thermal Stability of I-Motif

by Amen Shamim, Maria Razzaq and Kyeong Kyu Kim

Int. J. Mol. Sci. 2021, 22(1), 61; https://doi.org/10.3390/ijms22010061 - 23 Dec 2020

Cited by 1 | Viewed by 2405

Abstract

I-Motif is a tetrameric cytosine-rich DNA structure with hemi-protonated cytosine: cytosine base pairs. Recent evidence showed that i-motif structures in human cells play regulatory roles in the genome. Therefore, characterization of novel i-motifs and investigation of their functional implication are urgently needed for comprehensive understanding of their roles in gene regulation. However, considering the complications of experimental investigation of i-motifs and the large number of putative i-motifs in the genome, development of an in silico tool for the characterization of i-motifs in the high throughput scale is necessary. We developed a novel computation method, MD-TSPC4, to predict the thermal stability of i-motifs based on molecular modeling and molecular dynamic simulation. By assuming that the flexibility of loops in i-motifs correlated with thermal stability within certain temperature ranges, we evaluated the correlation between the root mean square deviations (RMSDs) of model structures and the thermal stability as the experimentally obtained melting temperature (Tm). Based on this correlation, we propose an equation for Tm prediction from RMSD. We expect this method can be useful for estimating the overall structure and stability of putative i-motifs in the genome, which can be a starting point of further structural and functional studies of i-motifs. Full article

(This article belongs to the Special Issue Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides)

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26 pages, 3458 KiB

Open AccessArticle

Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure

by Anzhela V. Pavlova, Mayya V. Monakhova, Anna M. Ogloblina, Natalia A. Andreeva, Gennady Yu. Laptev, Vladimir I. Polshakov, Elizaveta S. Gromova, Maria I. Zvereva, Marianna G. Yakubovskaya, Tatiana S. Oretskaya, Elena A. Kubareva and Nina G. Dolinnaya

Int. J. Mol. Sci. 2020, 21(22), 8773; https://doi.org/10.3390/ijms21228773 - 20 Nov 2020

Cited by 13 | Viewed by 3429

Abstract

DNA mismatch repair (MMR) plays a crucial role in the maintenance of genomic stability. The main MMR protein, MutS, was recently shown to recognize the G-quadruplex (G4) DNA structures, which, along with regulatory functions, have a negative impact on genome integrity. Here, we studied the effect of G4 on the DNA-binding activity of MutS from Rhodobacter sphaeroides (methyl-independent MMR) in comparison with MutS from Escherichia coli (methyl-directed MMR) and evaluated the influence of a G4 on the functioning of other proteins involved in the initial steps of MMR. For this purpose, a new DNA construct was designed containing a biologically relevant intramolecular stable G4 structure flanked by double-stranded regions with the set of DNA sites required for MMR initiation. The secondary structure of this model was examined using NMR spectroscopy, chemical probing, fluorescent indicators, circular dichroism, and UV spectroscopy. The results unambiguously showed that the d(GGGT)₄ motif, when embedded in a double-stranded context, adopts a G4 structure of a parallel topology. Despite strong binding affinities of MutS and MutL for a G4, the latter is not recognized by E. coli MMR as a signal for repair, but does not prevent MMR processing when a G4 and G/T mismatch are in close proximity. Full article

(This article belongs to the Special Issue Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides)

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15 pages, 3562 KiB

Open AccessArticle

Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons

by Nicholas J. Thornton and Tanja van Mourik

Int. J. Mol. Sci. 2020, 21(18), 6571; https://doi.org/10.3390/ijms21186571 - 08 Sep 2020

Cited by 4 | Viewed by 2156

Abstract

Halogen bonding is studied in different structures consisting of halogenated guanine DNA bases, including the Hoogsteen guanine–guanine base pair, two different types of guanine ribbons (R-I and R-II) consisting of two or three monomers, and guanine quartets. In the halogenated base pairs (except the Cl-base pair, which has a very non-planar structure with no halogen bonds) and R-I ribbons (except the At trimer), the potential N-X•••O interaction is sacrificed to optimise the N-X•••N halogen bond. In the At trimer, the astatines originally bonded to N1 in the halogen bond donating guanines have moved to the adjacent O6 atom, enabling O-At•••N, N-At•••O, and N-At•••At halogen bonds. The brominated and chlorinated R-II trimers contain two N-X•••N and two N-X•••O halogen bonds, whereas in the iodinated and astatinated trimers, one of the N-X•••N halogen bonds is lost. The corresponding R-II dimers keep the same halogen bond patterns. The G-quartets display a rich diversity of symmetries and halogen bond patterns, including N-X•••N, N-X•••O, N-X•••X, O-X•••X, and O-X•••O halogen bonds (the latter two facilitated by the transfer of halogens from N1 to O6). In general, halogenation decreases the stability of the structures. However, the stability increases with the increasing atomic number of the halogen, and the At-doped R-I trimer and the three most stable At-doped quartets are more stable than their hydrogenated counterparts. Significant deviations from linearity are found for some of the halogen bonds (with halogen bond angles around 150°). Full article

(This article belongs to the Special Issue Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides)

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18 pages, 5825 KiB

Open AccessArticle

Different Oxidation Pathways of 2-Selenouracil and 2-Thiouracil, Natural Components of Transfer RNA

by Katarzyna Kulik, Klaudia Sadowska, Ewelina Wielgus, Barbara Pacholczyk-Sienicka, Elzbieta Sochacka and Barbara Nawrot

Int. J. Mol. Sci. 2020, 21(17), 5956; https://doi.org/10.3390/ijms21175956 - 19 Aug 2020

Cited by 3 | Viewed by 2311

Abstract

Sulfur- and selenium-modified uridines present in the wobble position of transfer RNAs (tRNAs) play an important role in the precise reading of genetic information and tuning of protein biosynthesis in all three domains of life. Both sulfur and selenium chalcogens functionally operate as key elements of biological molecules involved in the protection of cells against oxidative damage. In this work, 2-thiouracil (S2Ura) and 2-selenouracil (Se2Ura) were treated with hydrogen peroxide at 1:0.5, 1:1, and 1:10 molar ratios and at selected pH values ranging from 5 to 8. It was found that Se2Ura was more prone to oxidation than its sulfur analog, and if reacted with H₂O₂ at a 1:1 or lower molar ratio, it predominantly produced diselenide Ura-Se-Se-Ura, which spontaneously transformed to a previously unknown Se-containing two-ring compound. Its deselenation furnished the major reaction product, a structure not related to any known biological species. Under the same conditions, only a small amount of S2Ura was oxidized to form Ura-SO₂H and uracil (Ura). In contrast, 10-fold excess hydrogen peroxide converted Se2Ura and S2Ura into corresponding Ura-SeO_nH and Ura-SO_nH intermediates, which decomposed with the release of selenium and sulfur oxide(s) to yield Ura as either a predominant or exclusive product, respectively. Our results confirmed significantly different oxidation pathways of 2-selenouracil and 2-thiouracil. Full article

(This article belongs to the Special Issue Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides)

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Review

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15 pages, 5974 KiB

Open AccessReview

On the Way to Understanding the Interplay between the RNA Structure and Functions in Cells: A Genome-Wide Perspective

by Angelika Andrzejewska, Małgorzata Zawadzka and Katarzyna Pachulska-Wieczorek

Int. J. Mol. Sci. 2020, 21(18), 6770; https://doi.org/10.3390/ijms21186770 - 15 Sep 2020

Cited by 15 | Viewed by 4184

Abstract

RNAs adopt specific structures in order to perform their biological activities. The structure of RNA is an important layer of gene expression regulation, and can impact a plethora of cellular processes, starting with transcription, RNA processing, and translation, and ending with RNA turnover. The development of high-throughput technologies has enabled a deeper insight into the sophisticated interplay between the structure of the cellular transcriptome and the living cells environment. In this review, we present the current view on the RNA structure in vivo resulting from the most recent transcriptome-wide studies in different organisms, including mammalians, yeast, plants, and bacteria. We focus on the relationship between the mRNA structure and translation, mRNA stability and degradation, protein binding, and RNA posttranscriptional modifications. Full article

(This article belongs to the Special Issue Molecular Structure and Biochemical Aspects of Nucleic Acids and Nucleosides)

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