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Catherine Tran

Bio: Catherine Tran is an academic researcher from University of California, Irvine. The author has contributed to research in topics: RNA & Dopaminergic. The author has an hindex of 3, co-authored 3 publications receiving 106 citations.

Papers
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Journal ArticleDOI
TL;DR: The design and utility of chemical reagents used in RNA structure probing are detailed, and how these reagents have been used to gain a deeper understanding of RNA structure in vivo are outlined.
Abstract: Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges.

80 citations

Journal ArticleDOI
TL;DR: In this paper, the first cellular application of a photoclick SPAAC reagent to label azide-functionalized RNA 350 nm irradiation of a cyclopropenone caged oxo-dibenzocyclooctyne (photo-ODIBO) biotin yields formation of the sPAAC reactive species, which rapidly forms adducts with RNA containing 2′-azidoadenosine (2′N3-A).
Abstract: We report the first cellular application of a photoclick SPAAC reagent to label azide-functionalized RNA 350 nm irradiation of a cyclopropenone caged oxo-dibenzocyclooctyne (photo-ODIBO) biotin yields formation of the SPAAC reactive species, which rapidly forms adducts with RNA containing 2′-azidoadenosine (2′N3-A) Photo-ODIBO was found to be highly stable in the presence of thiols, conferring greater stability relative to ODIBO Light activated photo-ODIBO enabled tagging of cellular RNA, in addition to fluorescent imaging as well as enrichment of RNA in cell subpopulations via selective irradiation

38 citations

Journal ArticleDOI
TL;DR: Using combined pharmacological, chemogenetic, and cell-specific ablation approaches, it is revealed that the D2R-dependent inhibition of acetylcholine (ACh) signaling is fundamental to cocaine-induced changes in behavior and the striatal genomic response.

16 citations

Proceedings ArticleDOI
27 Mar 2023
TL;DR: Germanium sulfide (GeS) is a 2D semiconductor with high carrier mobility, a moderate band gap of about 1.6 eV, and highly anisotropic optical properties as discussed by the authors .
Abstract: Germanium sulfide (GeS) is a 2D semiconductor with high carrier mobility, a moderate band gap of about 1.6 eV, and highly anisotropic optical properties. In-plane anisotropy and a large in-plane spontaneous electric polarization in GeS monolayers have been predicted to result in significant second order nonlinear effects in response to above-the-gap excitation with photon energy < 2.5 eV1. We have further confirmed it experimentally by demonstrating surface shift current generation in GeS using THz emission spectroscopy with 3.1 eV excitation.3 Here, we use time-resolved THz spectroscopy to investigate the dynamics and lifetimes of photoexcited carriers in GeS single crystals and nanoribbons in response to excitations with energies ranging from 1.5 eV, resonant with the bulk gap, to 3.1 eV. We find that resulting dynamics vary considerably. Lower energy (1.5 eV) excitation injects carriers directly into three low-lying valleys in the conduction band. Those carriers have long, which photoconductivity persisting for over 500 ps, as it can be seen in Fig. 1(a). On the other hand, injecting carriers high into the conduction band results in THz emission due to the shift current as well as into transient photoconductivity that recovers over <100 ps. Pronounced changes in the transient photoconductivity in response to optical excitation with photon energy across the visible-NIR range open intriguing possibilities for applications in ultrafast spectrally-sensitive photodetectors and solar energy conversion.
Proceedings ArticleDOI
28 Aug 2022
TL;DR: In this article , the authors used time-resolved THz spectroscopy to investigate ultrafast carrier dynamics in Germanium sulfide (GeS) single crystals as well as in GeS nanoribbons.
Abstract: Germanium sulfide (GeS) is a 2D semiconductor with high carrier mobility and a moderate band gap of about 1.5 eV, which holds promise for high-speed optoelectronics and photovoltaics. We use time-resolved THz spectroscopy to investigate ultrafast carrier dynamics in in GeS single crystals as well as in GeS nanoribbons. In both bulk and nanostructured GeS, we find that near gap excitation at 1.55 eV results in much longer lived photocarriers compared to 3.1 eV excitation. We also explore how intercalation of small molecules influences the photoexcited carrier dynamics in GeS. We find that presence of edge states in nanoribbons results in decreased carrier lifetime. Organic molecules such as octylamine, which do not form chemical bonds with the host GeS layers, increase photoexcited carrier lifetime. These findings demonstrate the possibility of engineering the properties of 2D materials by intercalation.

Cited by
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Journal ArticleDOI
TL;DR: This Review discusses known 5′ UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.
Abstract: RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways. We discuss known 5' UTR RNA structures and how new structure probing technologies coupled with prospective validation, particularly compensatory mutagenesis, are likely to identify classes of structured RNA elements that shape post-transcriptional control of gene expression and the development of multicellular organisms.

499 citations

Journal ArticleDOI
23 Sep 2016-Science
TL;DR: In mammals, thousands of endogenous RNA sequences have regions that can fold into RG4s in vitro, but these regions are globally unfolded in eukaryotic cells, presumably by robust and effective machinery that remains to be fully characterized.
Abstract: INTRODUCTION Many cellular RNAs contain regions that fold into stable structures required for function. Both Watson−Crick and noncanonical interactions can play important roles in forming these structures. An intriguing noncanonical structure is the RNA G-quadruplex (RG4), a four-stranded structure containing two or more layers of G-quartets, in which the Watson–Crick face of each of four G residues pairs to the Hoogsteen face of the neighboring G residues. RG4 regions can be very stable in vitro, particularly in the presence of K + , and thus they are generally assumed to be predominantly folded within cells, which have ample K + . Indeed, these structures have been implicated in mRNA processing and translation, with recently proposed roles in cancer and other human diseases. However, the number of cellular RNAs that can fold into RG4 structures has been unclear, as has been the extent to which these RG4 regions are folded in cells. RATIONALE Enzymes and chemicals that act on RNA with structure-dependent preferences provide valuable tools for detecting and monitoring RNA folding. For example, dimethyl sulfate (DMS) treatment of RNA, either in vitro or in cells, coupled with high-throughput sequencing of abortive primer-extension products can monitor the folding states of many RNAs in one experiment. Analogous high-throughput methods use cell-permeable variants of SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) reagents. These methods reveal important differences between RNA structures formed in vivo and those formed in vitro. However, they are designed to detect Watson−Crick pairing and thus do not identify RG4 structures or provide information on their folding states. After recognizing that RG4 regions can block reverse transcriptase, we reasoned that this property, together with the known ability of RG4s to protect the N7 of participating G nucleotides from DMS modification, could be used to develop a suite of high-throughput methods to both identify endogenous RNAs that can fold into RG4s in vitro and determine whether these regions also fold in cells. RESULTS We first developed a high-throughput method that identifies RG4 regions on the basis of their propensity to stall reverse transcriptase in a K + -dependent manner. Applying this method to RNA from mammalian cell lines and yeast, we identified >10,000 endogenous regions that form RG4s in vitro, thereby expanding by a factor of >100 the catalog of endogenous regions with experimentally supported propensity to fold into RG4 structures. To infer the folding state of these RG4 regions in vitro and in cells, DMS treatment was performed before profiling of reverse-transcriptase stops. These analyses showed that, in contrast to previous assumptions, regions that folded into RG4 structures in vitro were overwhelmingly unfolded in vivo, as indicated by their accessibility to DMS modification in cells. A complementary probing strategy using a SHAPE reagent confirmed the unfolded state of most RG4 regions in eukaryotic cells. Moreover, RG4 regions remained unfolded both in cells depleted of adenosine 5′-triphosphate and in cells lacking a helicase known to unfold RG4 regions in vitro. Applying our probing methods to bacteria revealed a different behavior, in that model RG4 regions that were unfolded in eukaryotic cells were folded when expressed in Escherichia coli . However, these ectopically expressed quadruplexes impaired mRNA translation and cell growth, which helps explain why very few endogenous sequences that could fold into RG4s were detected in the transcriptomes of E. coli and the two other eubacteria analyzed. CONCLUSION In mammals, thousands of endogenous RNA sequences have regions that can fold into RG4s in vitro, but these regions are globally unfolded in eukaryotic cells, presumably by robust and effective machinery that remains to be fully characterized. In contrast, RG4 regions are permitted to fold in E. coli cells, but E. coli and other bacteria have undergone evolutionary depletion of endogenous RG4-forming sequences.

356 citations

Journal ArticleDOI
TL;DR: It is proposed that symmetrical triplex-forming motifs, especially those in cis-acting lncRNAs, favor triplex formation, and the effects of lncRNA structures, protein or ligand binding, and chromatin structures on the lnc RNAs triPlex formation are considered.

175 citations

Journal ArticleDOI
TL;DR: This work hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure and describes the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA3D structure prediction programs to determine the capabilities and bottlenecks of current predictions.
Abstract: Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson–Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction.

150 citations

Journal ArticleDOI
TL;DR: This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science and places a particular emphasis on the historical contexts and mechanistic insights into each of the selected reactions.
Abstract: The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.

128 citations