Keywords "kissing Complex" Or "kissing ...

"kissing Complex" Or "kissing loop"
Buyong Ma, Ganggang Bai, Ruth Nussinov, Jienyu Ding, Yun-Xing Wang
Cobalamin riboswitch is a cis-regulatory element widely found in the 5'-UTRs of the vitamin B12-associated genes in bacteria, resulting in modulation and production of a particular protein. Thermoanaerobacter tengcongensis ( Tte ) AdoCbl riboswitches are the largest of the known riboswitches with 210 nucleotides, partially due to its long peripheral P6-extension, which enable high affinity of AdoCbl. Two structural elements, T-loop/T-looplike motif and kissing loop are key to the global folding of the RNA. While the structure of the Tte AdoCbl riboswitch complex is known, we still do not understand the structure and conformation before AdoCbl ligand recognition...
March 8, 2021: Journal of Physical Chemistry. B
Lin Wu, Zhijun Liu, Yu Liu
Ligand binding and temperature play important roles in riboswitch RNAs' structures and functions. However, most studies focused on studying structural dynamics or gene-regulation function of riboswitches from the aspect of ligand, instead of temperature. Here we combined NMR, ITC, stopped-flow and in vivo assays to investigate the ligand-triggered switch of adenine riboswitch from 10 to 45 ºC. Our results demonstrated that at single-nucleotide resolution, structural regions sensed ligand and temperature diversely...
February 11, 2021: RNA Biology
Hongbo Li, Min Han, Xuan Weng, Yuye Zhang, Jing Li
In virtue of the inherent molecular recognition and programmability, DNA has recently become the most promising for high-performance biosensors. The rationally engineered nucleic acid architecture will be very advantageous to hybridization efficiency, specificity, and sensitivity. Herein, a robust and split-mode photoelectrochemical (PEC) biosensor for miRNA-196a was developed based on an entropy-driven tetrahedral DNA (EDTD) amplifier coupled with superparamagnetic nanostructures. The DNA tetrahedron structure features in rigidity and structural stability that contribute to obtain precise identification units and specific orientations, improving the hybridization efficiency, sensitivity, and selectivity of the as-designed PEC biosensor...
January 13, 2021: ACS Nano
Xin Ee Yong, Palur Venkata Raghuvamsi, Ganesh S Anand, Thorsten Wohland, Kamal K Sharma
The capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements using chaperone activity. However, the role of DENV2C during the interaction of RNA elements in the conserved 5' untranslated region (5'UTR) to the 3' untranslated region (3'UTR) is still unclear. Thus, we investigated the effect of DENV2C on the annealing mechanism of two RNA hairpin elements from the 5'UTR to their complementary sequences during (+)/(-) ds-RNAformation and (+) RNA circularization. DENV2C was found to switch the annealing pathway for RNA elements involved in (+)/(-) ds-RNA formation, but not for RNA elements related to (+) RNA circularization...
January 7, 2021: RNA Biology
Manuel Ramírez, Rocío Velázquez, Matilde Maqueda, Alberto Martínez
Wine killer yeasts such as killer strains of Torulaspora delbrueckii and Saccharomyces cerevisiae contain helper large-size (4.6 kb) dsRNA viruses (V-LA) required for the stable maintenance and replication of killer medium-size dsRNA viruses (V-M) which bear the genes that encode for the killer toxin. The genome of the new V-LA dsRNA from the T. delbrueckii Kbarr1 killer yeast (TdV-LAbarr1) was characterized by high-throughput sequencing (HTS). The canonical genome of TdV-LAbarr1 shares a high sequence identity and similar genome organization with its Saccharomyces counterparts...
2020: Frontiers in Microbiology
Joséphine Abi-Ghanem, Clémence Rabin, Massimiliano Porrini, Frédéric Rosu, Valérie Gabelica
When electrosprayed from typical native MS solution conditions, RNA hairpins and kissing complexes acquire charge states at which they get significantly more compact in the gas phase than their initial structure in solution. Here we also show the limits of using force field molecular dynamics to interpret the gas-phase structures of nucleic acid complexes in the gas phase, as the predicted CCS distributions do not fully match the experimental ones. We suggest that higher-level calculation levels should be used in the future...
August 19, 2020: Journal of the American Society for Mass Spectrometry
Hiromi Mutsuro-Aoki, Kokoro Hamachi, Ryodai Kurihara, Koji Tamura
The unique G3:U70 base pair in the acceptor stem of tRNAAla has been shown to be a critical recognition site by alanyl-tRNA synthetase (AlaRS). The base pair resides on one of the arms of the L-shaped structure of tRNA (minihelix) and the genetic code has likely evolved from a primordial tRNA-aaRS (aminoacyl-tRNA synthetase) system. In terms of the evolution of tRNA, incorporation of a G:U base pair in the structure would be important. Here, we found that two independent short hairpin RNAs change their conformation through kissing-loop interactions, finally forming a minihelix-like structure, in which the G3:U70 base pair, is incorporated...
July 5, 2020: Bio Systems
Charles Bou-Nader, Jinwei Zhang
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc...
June 23, 2020: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Arghya Sett, Lorena Zara, Eric Dausse, Jean-Jacques Toulme
Aptasensors are biosensors that include aptamers for detecting a target of interest. We engineered signaling aptasensors for the detection of RNA hairpins from the previously described malachite green (MG) RNA aptamer. The top part of this im-perfect hairpin aptamer was modified in such a way that it can engage loop-loop (so-called kissing) interactions with RNA hairpins displaying partly complementary apical loops. These newly derived oligonucleotides named malaswitches bind their cognate fluorogenic ligand (MG) exclusively when RNA-RNA kissing complexes are formed whereas MG does not bind to malaswitches alone...
June 4, 2020: Analytical Chemistry
Manindra Bera, Ramalingam Venkat Kalyana Sundaram
In eukaryotes, chromosomes often form a transcriptional kissing loop during interphase. We propose that these kissing loops facilitate the formation of protein complexes. mRNA transcripts from these loops could cluster together into phase-separated nuclear granules. Their export into the ER could be ensured by guided diffusion through the inter-chromatin space followed by association with nuclear baskets and export factors. Inside the ER, these mRNAs would form a translation hub. Juxtaposed translation of these mRNAs would increase the cis/trans protein complex assembly among the nascent protein chains...
September 2019: Yale Journal of Biology and Medicine
Julita Gumna, Katarzyna J Purzycka, Hyo Won Ahn, David J Garfinkel, Katarzyna Pachulska-Wieczorek
During replication of long terminal repeat (LTR)-retrotransposons, their proteins and genome (g) RNA assemble into virus-like particles (VLPs) that are not infectious but functionally related to retroviral virions. Both virions and VLPs contain gRNA in a dimeric form, but contrary to retroviruses, little is known about how gRNA dimerization and packaging occurs in LTR-retrotransposons. The LTR-retrotransposon Ty1 from Saccharomyces cerevisiae is an informative model for studying LTR-retrotransposon and retrovirus replication...
August 30, 2019: RNA Biology
Benoit Chovelon, Emmanuelle Fiore, Patrice Faure, Eric Peyrin, Corinne Ravelet
The development of enantioselective assays and sensors has received much attention for the determination of enantiomeric impurities. Herein, we demonstrated that the previously reported aptamer kissing complex (AKC) assay strategy can be implemented for designing a chiral tool that allows both the simultaneous enantiomer quantification and the enantiopurity analysis. D- and L-arginine vasopressin (AVP) were employed as model enantiomeric targets. The D- and L-AVP engineered aptamers (aptaswitch) were used as recognition units whereas the Fluorescein or Texas Red labelled D- and L-hairpin probes (aptakiss) served as probes of the enantiomer-dependent AKC formation...
December 1, 2019: Talanta
Tina Uroda, Eleni Anastasakou, Annalisa Rossi, Jean-Marie Teulon, Jean-Luc Pellequer, Paolo Annibale, Ombeline Pessey, Alberto Inga, Isabel Chillón, Marco Marcia
Long non-coding RNAs (lncRNAs) are key regulatory molecules, but unlike with other RNAs, the direct link between their tertiary structure motifs and their function has proven elusive. Here we report structural and functional studies of human maternally expressed gene 3 (MEG3), a tumor suppressor lncRNA that modulates the p53 response. We found that, in an evolutionary conserved region of MEG3, two distal motifs interact by base complementarity to form alternative, mutually exclusive pseudoknot structures ("kissing loops")...
September 5, 2019: Molecular Cell
Lei Jin, Ya-Lan Tan, Yao Wu, Xunxun Wang, Ya-Zhou Shi, Zhi-Jie Tan
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we employed our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict 3D structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations...
August 7, 2019: RNA
Michela Chiumenti, Beatriz Navarro, Pasquale Venerito, Francesco Civita, Angelantonio Minafra, Francesco Di Serio
In the absence of protein-coding ability, viroid RNAs rely on direct interactions with host factors for their infectivity. RNA structural elements are likely involved in these interactions. Therefore, preservation of a structural element, despite the sequence variability existing between the variants of a viroid population, is considered a solid evidence of its relevant role in vivo. In this study, apple hammerhead viroid (AHVd) was first identified in the two apple cultivars 'Mela Rosa Guadagno' (MRG) and 'Agostinella' (AG), which are cultivated since long in Southern Italy, thus providing the first solid evidence of its presence in this country...
June 27, 2019: Virus Research
Asmita Gupta, Manju Bansal
RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a variety of functions in biological processes. The location of these structures in the genomes of RNA viruses is often coordinated with specific processes in the viral life cycle, where the presence of the structure acts as a checkpoint for deciding the eventual fate of the process...
June 17, 2019: Briefings in Bioinformatics
Usha Bhardwaj, Paul Powell, Dixie J Goss
Barley Yellow Dwarf Virus (BYDV) is a positive strand RNA virus that lacks the canonical 5' 7-methylguanosine cap and a 3' poly-A tail. Instead, BYDV utilizes a cruciform cap independent translation element (CITE) in its 3'UTR RNA (BYDV-like CITE or BTE) that binds eukaryotic translation initiation factor (eIF) 4F and recruits 40S ribosomal subunits in the presence of active helicase factors (eIF4A, eIF4B, eIF4F and ATP). A long-range, 5-nucleotide, base-pairing kissing loop interaction between the 3'BTE and a 5'UTR stem-loop is necessary for translation to initiate...
May 22, 2019: Nucleic Acids Research
Shiqin Miao, Yufeng Liang, Ila Marathe, Jie Mao, Chris DeSantis, Dennis Bong
We report herein the synthesis and DNA/RNA binding properties of bPNA+, a new variant of bifacial peptide nucleic acid (bPNA) that binds oligo T/U nucleic acids to form triplex hybrids. By virtue of a new bivalent sidechain on bPNA+, similar DNA affinity and hybrid thermostability can be obtained with half the molecular footprint of previously reported bPNA. Lysine derivatives bearing two melamine bases (K2M) can be prepared on multigram scale by double reductive alkylation with melamine acetaldehyde, resulting in a tertiary amine sidechain that affords both peptide solubility and selective base-triple formation with 4 T/U bases; the Fmoc-K2M derivative can be used directly in solid phase peptide synthesis, rendering bPNA+ conveniently accessible...
May 16, 2019: Journal of the American Chemical Society
Benjamin S Brigham, Jonathan P Kitzrow, Joshua-Paolo C Reyes, Karin Musier-Forsyth, James B Munro
The highly conserved 5' untranslated region (5'UTR) of the HIV-1 RNA genome is central to the regulation of virus replication. NMR and biochemical experiments support a model in which the 5'UTR can transition between at least two conformational states. In one state the genome remains a monomer, as the palindromic dimerization initiation site (DIS) is sequestered via base pairing to upstream sequences. In the second state, the DIS is exposed, and the genome is competent for kissing loop dimerization and packaging into assembling virions where an extended dimer is formed...
May 8, 2019: Proceedings of the National Academy of Sciences of the United States of America
Nicolas Girard, Pierre Dagenais, Julie Lacroix-Labonté, Pascale Legault
Investigating the dynamics of structural elements in functional RNAs is important to better understand their mechanism and for engineering RNAs with novel functions. Previously, we performed rational engineering studies with the Varkud satellite (VS) ribozyme and switched its specificity toward non-natural hairpin substrates through modification of a critical kissing-loop interaction (KLI). We identified functional VS ribozyme variants with surrogate KLIs (ribosomal RNA L88/L22 and human immunodeficiency virus-1 TAR/TAR*), but they displayed ∼100-fold lower cleavage activity...
April 23, 2019: Nucleic Acids Research
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