Journal articles on the topic 'Non-canonical crack'
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1
Leonovich, S. N. "Modeling of Capillary Shrinkage and Cracking in Early-Age Concrete." Science & Technique 17, no. 4 (July 31, 2018): 265–77. http://dx.doi.org/10.21122/2227-1031-2018-17-4-265-277.
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. Scientific hypothesis on moistening shrinkage mechanism for cement stone and concrete has been assumed as a basis for the present paper. Physical ideas on a mechanism for cracks volume increment in a concrete model presented as two-level structure have been accepted as a theoretical basis for a calculation method of crack resistance during capillary shrinkage. These ideas are the following: a matrix of hardening cement stone with inclusions and emptiness of various forms (cracks) as result of influences that change an intense deformed state in a point and a volume. The following assumptions have been accepted while making a theoretical justification for a calculation method of shrinkable concrete crack resistance. Following this methodology approaches of fracture mechanics according to a generalized criterion have been applied in the paper. Concrete is considered as an elastic quasi-homogeneous two-component medium which consists of the following parts:a) constructive part: a matrix – a cement stone with structural elements of crushed stone, sand; b) destructive part: emptiness – capillaries cracks and pores (cavities with initial cracks in walls). Emptiness in a matrix and contact zones are presented by a coordinated five-level system in the form and sizes which are multiple to a diameter due to impacts while reaching critical sizes. These critical sizes make it possible to pass from one level into another one according to the following scheme: size stabilization – accumulation delocalization – critical concentration in single volume – transition to the following level. Process of cracks formation and their growth are considered as a result of non-power influences on the basis of crack theory principles from a condition that fields of deformation and tension creating schemes of a normal separation and shift occur in the top part of each crack at its level in the initial concrete volume. Ксij(t) parameter as algebraic amount of critical values Kij in the whole system of all levels of cracks filling canonical volume up to critical concentration has been accepted as a generalized constant of property for concrete crack resistance in time, its resistance to formation, accumulation in volumes of micro-cracks and formation of trunk cracks with critical values. External temperature, moistening long influences create fields of tension in the top parts of cracks. Concrete destruction processes due to cracks are considered as generalized deformedintensed state in some initial volume having physical features which are inherent to a composite with strength and deformative properties. It is possible to realize analytical calculations for assessment of tension and crack resistance of concrete at early age on the basis of a generalized criterion in terms of stress intensity factor due to modern experimental data on capillary pressure value (70 kPa in 180 min after concrete placing). The developed algorithm of calculation allows to consider factors influencing on capillary pressure: type of cement, modifiers and mineral additives, concrete curing conditions.
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Rangadurai, Atul, Eric S. Szymanski, Isaac Kimsey, Honglue Shi, and Hashim M. Al-Hashimi. "Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion." Journal of Biomolecular NMR 74, no. 8-9 (August 12, 2020): 457–71. http://dx.doi.org/10.1007/s10858-020-00337-7.
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Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.
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Kozlov, Nicolay Nicolayevich, and Evgeny Ivanovich Kugushev. "Mathematical Phenomenon of Genetic Link G-U." Keldysh Institute Preprints, no. 10 (2021): 1–15. http://dx.doi.org/10.20948/prepr-2021-10.
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As you know, the secondary structure of RNA molecules, unlike DNA, in addition to canonical or Watson-Crick pairs, non-canonical G-U pairs, this is guanine - uracil. The last pairs were established experimentally by X-ray diffraction analysis and are still a mystery to researchers. The fact is that such pairs are 5-10 times energetically weaker than the canonical pairs A-U, C-G. The question arises: why are such pairs needed? The study was carried out in the framework of the strict mathematical analogy established earlier by the authors of some cases of genetic overlaps and stems of the secondary structure of messenger RNAs. In this work, it is shown that due to the non-canonical G-U pair, using the new ambiguities found, it is possible to substantially “regulate” the stem free energy (even for small stems) - the most important biochemical characteristic. It turned out that the discovered effect for G-U pairs significantly exceeds a similar effect for canonical pairs A-U, C-G.
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Johnson, Philip Z., Wojciech K. Kasprzak, Bruce A. Shapiro, and Anne E. Simon. "Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer." Nucleic Acids Research 50, no. 3 (February 1, 2022): 1601–19. http://dx.doi.org/10.1093/nar/gkac007.
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Abstract Canonical eukaryotic mRNA translation requires 5′cap recognition by initiation factor 4E (eIF4E). In contrast, many positive-strand RNA virus genomes lack a 5′cap and promote translation by non-canonical mechanisms. Among plant viruses, PTEs are a major class of cap-independent translation enhancers located in/near the 3′UTR that recruit eIF4E to greatly enhance viral translation. Previous work proposed a single form of PTE characterized by a Y-shaped secondary structure with two terminal stem-loops (SL1 and SL2) atop a supporting stem containing a large, G-rich asymmetric loop that forms an essential pseudoknot (PK) involving C/U residues located between SL1 and SL2. We found that PTEs with less than three consecutive cytidylates available for PK formation have an upstream stem-loop that forms a kissing loop interaction with the apical loop of SL2, important for formation/stabilization of PK. PKs found in both subclasses of PTE assume a specific conformation with a hyperreactive guanylate (G*) in SHAPE structure probing, previously found critical for binding eIF4E. While PTE PKs were proposed to be formed by Watson–Crick base-pairing, alternative chemical probing and 3D modeling indicate that the Watson–Crick faces of G* and an adjacent guanylate have high solvent accessibilities. Thus, PTE PKs are likely composed primarily of non-canonical interactions.
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Bhattacharyya, Dhananjay, Sukanya Halder, Sankar Basu, Debasish Mukherjee, Prasun Kumar, and Manju Bansal. "RNAHelix: computational modeling of nucleic acid structures with Watson–Crick and non-canonical base pairs." Journal of Computer-Aided Molecular Design 31, no. 2 (January 19, 2017): 219–35. http://dx.doi.org/10.1007/s10822-016-0007-0.
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LEONTIS, NEOCLES B., and ERIC WESTHOF. "Conserved geometrical base-pairing patterns in RNA." Quarterly Reviews of Biophysics 31, no. 4 (November 1998): 399–455. http://dx.doi.org/10.1017/s0033583599003479.
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1. INTRODUCTION 3992. DEFINITIONS 4013. CIS BASEPAIRS 4103.1 Cis Watson–Crick/Watson–Crick 4103.2 Wobble pairings 4113.3 Cis Watson–Crick/Hoogsteen pairings 4163.4 Bifurcated pairings 4173.5 Cis open and water-inserted 4214. TRANS BASEPAIRS 4234.1 Trans Watson–Crick/Watson–Crick 4234.2 Trans wobble pairs 4244.3 Trans Watson–Crick/Hoogsteen pairs 4244.4 Trans Hoogsteen/Hoogsteen pairs 4304.5 Trans bifurcated pairings 4325. SHALLOW-GROOVE PAIRINGS 4325.1 Hoogsteen/Shallow-groove pairs 4335.2 Watson–Crick/Shallow-groove pairings 4385.3 Shallow-groove/Shallow-groove pairings 4406. SIDE-BY-SIDE BASES 4467. DEFINING A LIBRARY OF ISOSTERIC PAIRINGS 4468. CONCLUSIONS 4519. ACKNOWLEDGEMENTS 45210. REFERENCES 452RNA molecules fold into a bewildering variety of complex 3D structures. Almost every new RNA structure obtained at high resolution reveals new, unanticipated structural motifs, which we are rarely able to predict at the current stage of our theoretical understanding. Even at the most basic level of specific RNA interactions – base-to-base pairing – new interactions continue to be uncovered as new structures appear. Compilations of possible non-canonical base-pairing geometries have been presented in previous reviews and monographs (Saenger, 1984; Tinoco, 1993). In these compilations, the guiding principle applied was the optimization of hydrogen-bonding. All possible pairs with two standard H-bonds were presented and these were organized according to symmetry or base type. However, many of the features of RNA base-pairing interactions that have been revealed by high-resolution crystallographic analysis could not have been anticipated and, therefore were not incorporated into these compilations. These will be described and classified in the present review. A recently presented approach for inferring basepair geometry from patterns of sequence variation (Gautheret & Gutell, 1997) relied on the 1984 compilation of basepairs (Saenger, 1984), and was extended to include all possible single H-bond combinations not subject to steric clashes. Another recent review may be consulted for a discussion of the NMR spectroscopy and thermodynamic effects of non-canonical (‘mismatched’) RNA basepairs on duplex stability (Limmer, 1997).
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Landy, Francis. "Noah's Ark and Mrs. Monkey." Biblical Interpretation 15, no. 4-5 (2007): 351–76. http://dx.doi.org/10.1163/156851507x230304.
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AbstractThe article traces the interpretation of the flood story in children's literature, from the apparently literal versions, in which imaginative reinterpretation is transferred to the illustrations, to the non-verbal crowded scenes of Peter Spier, the Midrashic retellings of Scholem Asch and Marc Gellman, feminist readings, like those of Bach and Exum, Madeleine L'Engle's teen novel, and versions which stress the annihilatory implications, including Janisch and Zwerger's Noah's Ark. It concludes with a discussion of Ruth Kerr's How Mrs. Monkey Missed the Ark, in which the canonical text is virtually eliminated, and only appears through the cracks.
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Ohlenschläger, Oliver, Jens Wöhnert, Ramadurai Ramachandran, Christian Sich, and Matthias Görlach. "Nuclear magnetic resonance studies of ribonucleic acids." Spectroscopy 17, no. 2-3 (2003): 537–47. http://dx.doi.org/10.1155/2003/378434.
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Ribonucleic acids (RNA) and RNA−protein complexes are essential components of biological information transfer, catalytic processes and are associated with regulatory functions. This broad range of biological functions is paralleled at the conformational level by a large number of non-canonical structural elements or sequences with non-standard backbone conformations, e.g., loops, bulges, pseudo-knots and complex tertiary folds. NMR spectroscopy has evolved to a powerful tool for the determination of ribonucleic acid structures of up to 20 kDa. Uniform or selective stable isotope labelling aids in solving assignment problems arising from the inherently limited chemical shift dispersion and overlap of resonances for larger nucleotide sequences. Recent developments of multi-dimensional heteronuclear NMR pulse sequences allow e.g., to directly observe the hydrogen bonding pattern of canonical Watson−Crick base pairs as well as of unusual types of base pairs, thereby opening up a fast access to secondary structure screening of RNA. Detailed conformational descriptions are obtained using conventional NOE andJcoupling-derived data, nowadays supplemented by information from residual dipolar couplings. The latter method also provides a new means for the probing of dynamical features of ribonucleic acids.
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Gorab, Eduardo. "Triple-Helical DNA in Drosophila Heterochromatin." Cells 7, no. 12 (November 23, 2018): 227. http://dx.doi.org/10.3390/cells7120227.
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Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences. The satellite probe hybridized to AAGAG-containing regions omitting chromosomal DNA denaturation, as expected, for the intra-molecular triplex DNA formation model in which single-stranded DNA coexists with triplexes. In addition, Thiazole Orange, previously described as capable of reproducing results obtained by antibodies to triple-helical DNA, binds to AAGAG repeats in situ thus validating both detection methods. Unusual phenotype and nuclear structure exhibited by Drosophila correlate with the non-canonical conformation of tandem satellite arrays. From the approaches that lead to the identification of triple-helical DNA in chromosomes, facilities particularly provided by Thiazole Orange use may broaden the investigation on the occurrence of triplex DNA in eukaryotic genomes.
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Chatain, Jean, Alain Blond, Anh Tuân Phan, Carole Saintomé, and Patrizia Alberti. "GGGCTA repeats can fold into hairpins poorly unfolded by replication protein A: a possible origin of the length-dependent instability of GGGCTA variant repeats in human telomeres." Nucleic Acids Research 49, no. 13 (July 2, 2021): 7588–601. http://dx.doi.org/10.1093/nar/gkab518.
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Abstract Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson–Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.
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Merritt, Kristen K., Kevin M. Bradley, Daniel Hutter, Mariko F. Matsuura, Diane J. Rowold, and Steven A. Benner. "Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance." Beilstein Journal of Organic Chemistry 10 (October 9, 2014): 2348–60. http://dx.doi.org/10.3762/bjoc.10.245.
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Background: Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide “letters”, the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson–Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so. Results: We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson–Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2’-deoxyisocytidine and 2’-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted. Conclusion: AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.
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Sharma, Sudha. "Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases." Journal of Nucleic Acids 2011 (2011): 1–15. http://dx.doi.org/10.4061/2011/724215.
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In addition to the canonical B-form structure first described by Watson and Crick, DNA can adopt a number of alternative structures. These non-B-form DNA secondary structures form spontaneously on tracts of repeat sequences that are abundant in genomes. In addition, structured forms of DNA with intrastrand pairing may arise on single-stranded DNA produced transiently during various cellular processes. Such secondary structures have a range of biological functions but also induce genetic instability. Increasing evidence suggests that genomic instabilities induced by non-B DNA secondary structures result in predisposition to diseases. Secondary DNA structures also represent a new class of molecular targets for DNA-interactive compounds that might be useful for targeting telomeres and transcriptional control. The equilibrium between the duplex DNA and formation of multistranded non-B-form structures is partly dependent upon the helicases that unwind (resolve) these alternate DNA structures. With special focus on tetraplex, triplex, and cruciform, this paper summarizes the incidence of non-B DNA structures and their association with genomic instability and emphasizes the roles of RecQ-like DNA helicases in genome maintenance by resolution of DNA secondary structures. In future, RecQ helicases are anticipated to be additional molecular targets for cancer chemotherapeutics.
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Teng, Ye, Hisae Tateishi-Karimata, Tatsuya Ohyama, and Naoki Sugimoto. "Effect of Potassium Concentration on Triplex Stability under Molecular Crowding Conditions." Molecules 25, no. 2 (January 17, 2020): 387. http://dx.doi.org/10.3390/molecules25020387.
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The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different C+*G-C triplet content (*: Hoogsteen base pair; - : Watson–Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K+ concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of C+*G-C triplets increased. Under molecular crowding conditions, Watson–Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (≤1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the C+*G-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K+ concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.
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Trajkovski, Marko, and Janez Plavec. "Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands." Molecules 25, no. 3 (January 21, 2020): 434. http://dx.doi.org/10.3390/molecules25030434.
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By substitution of natural nucleotides by their abasic analogs (i.e., 1′,2′-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson–Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
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Lopez, Jose J., Isaac Jardin, Jose Sanchez-Collado, Ginés M. Salido, Tarik Smani, and Juan A. Rosado. "TRPC Channels in the SOCE Scenario." Cells 9, no. 1 (January 5, 2020): 126. http://dx.doi.org/10.3390/cells9010126.
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Transient receptor potential (TRP) proteins form non-selective Ca2+ permeable channels that contribute to the modulation of a number of physiological functions in a variety of cell types. Since the identification of TRP proteins in Drosophila, it is well known that these channels are activated by stimuli that induce PIP2 hydrolysis. The canonical TRP (TRPC) channels have long been suggested to be constituents of the store-operated Ca2+ (SOC) channels; however, none of the TRPC channels generate Ca2+ currents that resemble ICRAC. STIM1 and Orai1 have been identified as the components of the Ca2+ release-activated Ca2+ (CRAC) channels and there is a body of evidence supporting that STIM1 is able to gate Orai1 and TRPC1 in order to mediate non-selective cation currents named ISOC. STIM1 has been found to interact to and activate Orai1 and TRPC1 by different mechanisms and the involvement of TRPC1 in store-operated Ca2+ entry requires both STIM1 and Orai1. In addition to the participation of TRPC1 in the ISOC currents, TRPC1 and other TRPC proteins might play a relevant role modulating Orai1 channel function. This review summarizes the functional role of TRPC channels in the STIM1–Orai1 scenario.
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Caulfield, Coban, Tek, and Flores. "Molecular Dynamics Simulations Suggest a Non-Doublet Decoding Model of –1 Frameshifting by tRNASer3." Biomolecules 9, no. 11 (November 18, 2019): 745. http://dx.doi.org/10.3390/biom9110745.
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In-frame decoding in the ribosome occurs through canonical or wobble Watson–Crick pairing of three mRNA codon bases (a triplet) with a triplet of anticodon bases in tRNA. Departures from the triplet–triplet interaction can result in frameshifting, meaning downstream mRNA codons are then read in a different register. There are many mechanisms to induce frameshifting, and most are insufficiently understood. One previously proposed mechanism is doublet decoding, in which only codon bases 1 and 2 are read by anticodon bases 34 and 35, which would lead to –1 frameshifting. In E. coli, tRNASer3GCU can induce –1 frameshifting at alanine (GCA) codons. The logic of the doublet decoding model is that the Ala codon’s GC could pair with the tRNASer3′s GC, leaving the third anticodon residue U36 making no interactions with mRNA. Under that model, a U36C mutation would still induce –1 frameshifting, but experiments refute this. We perform all-atom simulations of wild-type tRNASer3, as well as a U36C mutant. Our simulations revealed a hydrogen bond between U36 of the anticodon and G1 of the codon. The U36C mutant cannot make this interaction, as it lacks the hydrogen-bond-donating H3. The simulation thus suggests a novel, non-doublet decoding mechanism for −1 frameshifting by tRNASer3 at Ala codons.
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Wu, Jian, Cuiji Zhou, James Li, Chun Li, Xiaorong Tao, Neocles B. Leontis, Craig L. Zirbel, David M. Bisaro, and Biao Ding. "Functional analysis reveals G/U pairs critical for replication and trafficking of an infectious non-coding viroid RNA." Nucleic Acids Research 48, no. 6 (February 21, 2020): 3134–55. http://dx.doi.org/10.1093/nar/gkaa100.
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Abstract While G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson–Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system. This study identifies critical roles for G/U pairs in the survival of an infectious RNA, and increases understanding of structure-based regulation of replication and trafficking of pathogen and cellular RNAs.
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Kondo, Jiro, Tom Yamada, Chika Hirose, Itaru Okamoto, Yoshiyuki Tanaka, and Akira Ono. "Crystal structure of metallo-DNA duplex containing T-Hg(II)-T base pairs." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1375. http://dx.doi.org/10.1107/s2053273314086240.
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The DNA duplex containing mercury-mediated base pairs (T-Hg(II)-T) is an attractive biomacromolecular nanomaterials. In a recent study, it was confirmed that the Hg(II) ion significantly stabilizes a DNA duplex by binding selectively to a T-T mispair [1]. Based on the phenomenon observed, a DNA-based sensing system that selectively and sensitively detects Hg(II) ions in aqueous solution was developed [2]. In the present study, we have solved the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs [3]. The Hg(II) ion occupies the center between two T residues. The geometry of the T-Hg(II)-T base pair is very similar to that of the canonical Watson-Crick base pairs. The distance of N3-Hg(II) bond is 2.0 Å, suggesting that the N3 nitrogen releases an imino-proton even at neutral pH (pKa of N3 position of T is 9.8) and directly bonds to Hg(II). In the B-form DNA, the helical axis runs through the center of base pairs, and the Hg(II) ions are therefore aligned along the helical axis. The distance between the two neighboring Hg(II) ions is 3.3 Å. The relatively short Hg(II)-Hg(II) distance indicates that the metallophilic attraction could exit between them and may stabilize the B-form duplex. To support this, the DNA duplex is largely distorted and adopts an unusual non-helical conformation in the absence of Hg(II). In conclusion, the Hg(II) ion is essential for maintaining the B-form conformation of the DNA duplex containing T-T mispairs. The structure of the Hg(II)-DNA hybrid duplex itself and the Hg(II)-induced structural switching from the non-helical form to the B-form provide the basis for the structure-based design of metal-conjugated nucleic acid nanomaterials.
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Liberman, Joseph, Mohammad Salim, Ivan Belashov, and Joseph Wedekind. "Translational control by diverse RNA folds that recognize the metabolite preQ1." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1394. http://dx.doi.org/10.1107/s2053273314086057.
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Typical paradigms of translational regulation utilize proteins, whereas riboswitches are economical, RNA-based elements that govern gene expression without protein partners. Present in all domains of life, riboswitches are commonly located in the 5´-untranslated regions of bacterial mRNAs where they establish feedback loops that respond to cellular levels of a specific small-molecule effector. Here we present the novel crystal structure of the recently discovered preQ1-III (class 3) riboswitch at 2.85 Å resolution. The 101-nucleotide switch features an internal loop pseudoknot (iPK) that coaxially stacks upon flanking helices P2 and P3. PreQ1(7-aminomethyl-7-deazaguanine) – the last soluble intermediate in the biosynthesis of the hypermodified tRNA base queuosine (Scheme I) – binds to form a major groove base triple of the form U·preQ1·C that utilizes highly conserved pyrimidine bases that help define this riboswitch class. This mode of effector binding involves non-canonical Watson-Crick pairing reminiscent of the phylogenetically unrelated preQ1-II (class 2) riboswitch. Remarkably, both riboswitch classes utilize dual U·A-U base triples that stack against the ligand. The respective nine-nucleotide motifs and their preQ1ligands superimpose with an rmsd of 0.4 Å; the class 2 and 3 structures are otherwise unrelated. The class 3 preQ1binding pocket also includes contributions from junctions that connect the P2-iPK-P3 coaxial stack with perpendicularly positioned helix P4. Of special interest is the observation that P4 can form a hairpin-loop pseudoknot (hPK) with the ribosome binding site (RBS) of the mRNA, suggesting a mode of ligand-dependent RBS sequestration. Biochemical experiments describing the preQ1dependence of hPK formation will be presented, as well as a comparison to known, translational class 1 and 2 preQ1riboswitch structures [1-3]. Implications for bacterial translational control will be discussed based on this diverse riboswitch family.
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Infante-Rojas, Harvey, Leonardo Marino-Ramirez, and Javier Hernández-Fernández. "Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean." PeerJ 8 (June 18, 2020): e9204. http://dx.doi.org/10.7717/peerj.9204.
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The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4–5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson–Crick base pairing: adenine–adenine in stem D of tRNATrp, uracil–uracil and adenine–cytosine in the acceptor arm of the tRNALys and cytosine–cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4–5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop—variable region, and between spacer bases—variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.
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Hur, Jeong Hwan, Chan Young Kang, Sungjin Lee, Nazia Parveen, Jihyeon Yu, Amen Shamim, Wanki Yoo, et al. "AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation." Nucleic Acids Research, September 1, 2021. http://dx.doi.org/10.1093/nar/gkab728.
Full textAbstract:
Abstract I-motif or C4 is a four-stranded DNA structure with a protonated cytosine:cytosine base pair (C+:C) found in cytosine-rich sequences. We have found that oligodeoxynucleotides containing adenine and cytosine repeats form a stable secondary structure at a physiological pH with magnesium ion, which is similar to i-motif structure, and have named this structure ‘adenine:cytosine-motif (AC-motif)’. AC-motif contains C+:C base pairs intercalated with putative A+:C base pairs between protonated adenine and cytosine. By investigation of the AC-motif present in the CDKL3 promoter (AC-motifCDKL3), one of AC-motifs found in the genome, we confirmed that AC-motifCDKL3 has a key role in regulating CDKL3 gene expression in response to magnesium. This is further supported by confirming that genome-edited mutant cell lines, lacking the AC-motif formation, lost this regulation effect. Our results verify that adenine-cytosine repeats commonly present in the genome can form a stable non-canonical secondary structure with a non-Watson–Crick base pair and have regulatory roles in cells, which expand non-canonical DNA repertoires.
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Khisamutdinov, Emil F., Blake A. Sweeney, and Neocles B. Leontis. "Context-sensitivity of isosteric substitutions of non-Watson–Crick basepairs in recurrent RNA 3D motifs." Nucleic Acids Research, August 17, 2021. http://dx.doi.org/10.1093/nar/gkab703.
Full textAbstract:
Abstract Sequence variation in a widespread, recurrent, structured RNA 3D motif, the Sarcin/Ricin (S/R), was studied to address three related questions: First, how do the stabilities of structured RNA 3D motifs, composed of non-Watson–Crick (non-WC) basepairs, compare to WC-paired helices of similar length and sequence? Second, what are the effects on the stabilities of such motifs of isosteric and non-isosteric base substitutions in the non-WC pairs? And third, is there selection for particular base combinations in non-WC basepairs, depending on the temperature regime to which an organism adapts? A survey of large and small subunit rRNAs from organisms adapted to different temperatures revealed the presence of systematic sequence variations at many non-WC paired sites of S/R motifs. UV melting analysis and enzymatic digestion assays of oligonucleotides containing the motif suggest that more stable motifs tend to be more rigid. We further found that the base substitutions at non-Watson–Crick pairing sites can significantly affect the thermodynamic stabilities of S/R motifs and these effects are highly context specific indicating the importance of base-stacking and base-phosphate interactions on motif stability. This study highlights the significance of non-canonical base pairs and their contributions to modulating the stability and flexibility of RNA molecules.
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Chu, Betty, Daoning Zhang, and Paul J. Paukstelis. "A DNA G-quadruplex/i-motif hybrid." Nucleic Acids Research, November 14, 2019. http://dx.doi.org/10.1093/nar/gkz1008.
Full textAbstract:
Abstract DNA can form many structures beyond the canonical Watson–Crick double helix. It is now clear that noncanonical structures are present in genomic DNA and have biological functions. G-rich G-quadruplexes and C-rich i-motifs are the most well-characterized noncanonical DNA motifs that have been detected in vivo with either proscribed or postulated biological roles. Because of their independent sequence requirements, these structures have largely been considered distinct types of quadruplexes. Here, we describe the crystal structure of the DNA oligonucleotide, d(CCAGGCTGCAA), that self-associates to form a quadruplex structure containing two central antiparallel G-tetrads and six i-motif C–C+ base pairs. Solution studies suggest a robust structural motif capable of assembling as a tetramer of individual strands or as a dimer when composed of tandem repeats. This hybrid structure highlights the growing structural diversity of DNA and suggests that biological systems may harbor many functionally important non-duplex structures.