-
1دورية أكاديمية
المؤلفون: Pramod M. Sabale, Uddhav B. Ambi, Seergazhi G. Srivatsan
المصدر: ACS Omega, Vol 3, Iss 11, Pp 15343-15352 (2018)
وصف الملف: electronic resource
Relation: https://doaj.org/toc/2470-1343
-
2دورية أكاديمية
المؤلفون: Liqing Ye, Uddhav B. Ambi, Marco Olguin-Nava, Anne-Sophie Gribling-Burrer, Shazeb Ahmad, Patrick Bohn, Melanie M. Weber, Redmond P. Smyth
المصدر: Viruses, Vol 13, Iss 9, p 1788 (2021)
مصطلحات موضوعية: RNA virus, RNA, RNA structure, genome packaging, viral assembly, evolution, Microbiology, QR1-502
الوصف: To generate infectious viral particles, viruses must specifically select their genomic RNA from milieu that contains a complex mixture of cellular or non-genomic viral RNAs. In this review, we focus on the role of viral encoded RNA structures in genome packaging. We first discuss how packaging signals are constructed from local and long-range base pairings within viral genomes, as well as inter-molecular interactions between viral and host RNAs. Then, how genome packaging is regulated by the biophysical properties of RNA. Finally, we examine the impact of RNA packaging signals on viral evolution.
وصف الملف: electronic resource
-
3
المصدر: Nature Methods.
مصطلحات موضوعية: Cell Biology, Molecular Biology, Biochemistry, Biotechnology
الوصف: Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on next-generation sequencing machines. One drawback of these experiments is that short sequencing reads can rarely be mapped to specific transcript isoforms. Consequently, information is acquired as a population average in regions that are shared between transcripts, thus blurring the underlying structural landscape. Here, we present nanopore dimethylsulfate mutational profiling (Nano-DMS-MaP)—a method that exploits long-read sequencing to provide isoform-resolved structural information of highly similar RNA molecules. We demonstrate the value of Nano-DMS-MaP by resolving the complex structural landscape of human immunodeficiency virus-1 transcripts in infected cells. We show that unspliced and spliced transcripts have distinct structures at the packaging site within the common 5′ untranslated region, likely explaining why spliced viral RNAs are excluded from viral particles. Thus, Nano-DMS-MaP is a straightforward method to resolve biologically important transcript-specific RNA structures that were previously hidden in short-read ensemble analyses.
-
4
المؤلفون: Liqing Ye, Anne-Sophie Gribling-Burrer, Patrick Bohn, Anuja Kibe, Charlene Börtlein, Uddhav B. Ambi, Shazeb Ahmad, Marco Olguin-Nava, Maureen Smith, Neva Caliskan, Max von Kleist, Redmond P. Smyth
المصدر: Nature Structural & Molecular Biology. 30:403-403
مصطلحات موضوعية: Structural Biology, Molecular Biology
-
5
المؤلفون: Liqing Ye, Anne-Sophie Gribling-Burrer, Patrick Bohn, Anuja Kibe, Charlene Börtlein, Uddhav B. Ambi, Shazeb Ahmad, Marco Olguin-Nava, Maureen Smith, Neva Caliskan, Max von Kleist, Redmond P. Smyth
مصطلحات موضوعية: Viral Proteins, Structural Biology, Riboswitches, Virology, HIV-1, Humans, Nucleic Acid Conformation, RNA, Viral, RNA, ddc:610, 5' Untranslated Regions, 610 Medizin und Gesundheit, Molecular Biology, Dimerization, Structure determination
الوصف: RNA dimerization is the noncovalent association of two human immunodeficiency virus-1 (HIV-1) genomes. It is a conserved step in the HIV-1 life cycle and assumed to be a prerequisite for binding to the viral structural protein Pr55Gag during genome packaging. Here, we developed functional analysis of RNA structure-sequencing (FARS-seq) to comprehensively identify sequences and structures within the HIV-1 5′ untranslated region (UTR) that regulate this critical step. Using FARS-seq, we found nucleotides important for dimerization throughout the HIV-1 5′ UTR and identified distinct structural conformations in monomeric and dimeric RNA. In the dimeric RNA, key functional domains, such as stem-loop 1 (SL1), polyadenylation signal (polyA) and primer binding site (PBS), folded into independent structural motifs. In the monomeric RNA, SL1 was reconfigured into long- and short-range base pairings with polyA and PBS, respectively. We show that these interactions disrupt genome packaging, and additionally show that the PBS–SL1 interaction unexpectedly couples the PBS with dimerization and Pr55Gag binding. Altogether, our data provide insights into late stages of HIV-1 life cycle and a mechanistic explanation for the link between RNA dimerization and packaging.
وصف الملف: application/pdf
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7b3baf4892f62e5286fd4d2e1b151eed
http://edoc.rki.de/176904/9792 -
6
المؤلفون: Jerrin Thomas George, Debojyoti Chakraborty, Souvik Maiti, Seergazhi G. Srivatsan, Meghali Aich, Dipanjali Sinha, Mohd Azhar, Uddhav B. Ambi
المصدر: J Am Chem Soc
مصطلحات موضوعية: Gene Editing, Models, Molecular, Chemistry, RNA, RNA Nucleotidyltransferases, Context (language use), General Chemistry, Computational biology, 010402 general chemistry, 01 natural sciences, Biochemistry, Article, Catalysis, 0104 chemical sciences, Chromatin, Colloid and Surface Chemistry, Genome editing, Click chemistry, CRISPR, Click Chemistry, Guide RNA, CRISPR-Cas Systems, Bioorthogonal chemistry, RNA, Guide, Kinetoplastida
الوصف: Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3' end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.
-
7
المؤلفون: Uddhav B. Ambi, Pramod M. Sabale, Seergazhi G. Srivatsan
المصدر: ACS Omega
ACS Omega, Vol 3, Iss 11, Pp 15343-15352 (2018)مصطلحات موضوعية: chemistry.chemical_classification, Peptide nucleic acid, 010405 organic chemistry, General Chemical Engineering, musculoskeletal, neural, and ocular physiology, General Chemistry, 010402 general chemistry, 01 natural sciences, Fluorescence, Cycloaddition, Article, 0104 chemical sciences, Amino acid, lcsh:Chemistry, chemistry.chemical_compound, Monomer, chemistry, Biotin, Biochemistry, lcsh:QD1-999, biological sciences, Nucleic acid, cardiovascular system, Bioorthogonal chemistry, tissues
الوصف: The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
-
8
المؤلفون: Jerrin Thomas George, Souvik Maiti, Dipanjali Sinha, Seergazhi G. Srivatsan, Meghali Aich, Debojyoti Chakraborty, Mohd. Azhar, Uddhav B. Ambi
مصطلحات موضوعية: 0303 health sciences, Computer science, Computational biology, 010402 general chemistry, 01 natural sciences, Genome, Small molecule, 0104 chemical sciences, Chromatin, 03 medical and health sciences, Click chemistry, Transferase, CRISPR, Molecule, Clickable, Bioorthogonal chemistry, Target gene, Gene, Function (biology), 030304 developmental biology, Subgenomic mRNA
الوصف: Locus-specific interrogation of the genome using programmable CRISPR-based technologies is tremendously useful in dissecting the molecular basis of target gene function and modulating its downstream output. Although these tools are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using this technique is not well developed due to inadequate labeling technologies. Here, we report the development of a modular technology, sgRNA-Click (sgR-CLK), which harnesses the power of bioorthogonal click chemistry for remodeling CRISPR to display synthetic molecules on target genes. A terminal uridylyl transferase (TUTase) was repurposed to construct an sgRNA containing multiple minimally invasive bioorthogonal clickable handles, which served as a Trojan horse on CRISPR-dCas9 system to guide synthetic tags site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Our results demonstrate that sgR-CLK could provide a simplified solution for site-directed display of small molecules to study as well as modulate the function of gene targets.
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::76b9558951b72f908abc101a39074957
https://doi.org/10.1101/846980 -
9
المؤلفون: Jyoti Singh, Uddhav B Ambi
المصدر: Journal of Insect Science
مصطلحات موضوعية: Computational biology, Molecular Entomological Genetics, conserved miRNA, Genome, Cell Line, Bombycidae, 03 medical and health sciences, 0302 clinical medicine, Bombyx mori, Drosophilidae, Animals, miRNA, 030304 developmental biology, Bombyx, repeat-associated miRNA, Regulation of gene expression, Whole genome sequencing, 0303 health sciences, Whole Genome Sequencing, biology, fungi, Chromosome Mapping, General Medicine, biology.organism_classification, MicroRNAs, Insect Science, Drosophila melanogaster, 030217 neurology & neurosurgery
الوصف: MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs, which play important regulatory roles in various biological processes. In this study, we have developed a computational approach for detecting conserved miRNAs based on comparison of whole genome sequences of closely related species by considering various key features of experimentally validated miRNAs. By applying this approach, we have identified 34 new miRNAs from Bombyx mori (L.), which are also conserved in Drosophila melanogaster (Diptera: Drosophilidae) and Anopheles gambiae (Diptera: Culicidae). Most of these miRNAs were associated with repeat region of the genome. We did an expression analysis of the 34 newly predicted miRNAs and found that 30 of these miRNAs are expressing in different tissues of B. mori. Besides, we have also predicted the putative targets of these miRNAs in B. mori based on several known characteristic features of miRNA::mRNA duplexes and found that these targets include diverse range of functions, suggesting multiple layers of gene regulation of various important biological processes.
URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bbfd8a3ad0cae5af00d3888bfd67bdde
https://doi.org/10.1093/jisesa/iez049 -
10
المؤلفون: Uddhav B. Ambi, Seergazhi G. Srivatsan, Pramod M. Sabale
المصدر: ChemBioChem. 19:767-767
مصطلحات موضوعية: biology, Chemistry, Organic Chemistry, RNA, biology.organism_classification, Biochemistry, Fluorescence, Feature (computer vision), Poly-A RNA, Biophysics, Molecular Medicine, Cover (algebra), Molecular Biology, Lucifer
Find this issue from the American Chemical Society 
Full Text Finder