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Article ; Online: Biochemical and structural characterization of the flavodoxin-like domain of the

Sjekloća, Ljiljana / Ferré-D'Amaré, Adrian R

microPublication biology

2022 Volume 2022

Abstract: The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of ... ...

Abstract	The S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase TYW1 catalyzes biosynthesis of 4-demethylwyosine (imG-14), the precursor for wyosine, the hypermodified guanine-derived nucleotide present at position 37 of phenylalanine tRNAs of archaea and eukarya. Eukaryotic TYW1 enzymes contain N-terminal flavodoxin-like and C-terminal radical-SAM domains. We determined co-crystal structures of the flavodoxin-like domain of the putative Tyw1 from
Language	English
Publishing date	2022-06-08
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000570
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Article ; Online: The bacterial yjdF riboswitch regulates translation through its tRNA-like fold.

Trachman, Robert J / Passalacqua, Luiz F M / Ferré-D'Amaré, Adrian R

The Journal of biological chemistry

2022 Volume 298, Issue 6, Page(s) 101934

Abstract: Unlike most riboswitches, which have one cognate effector, the bacterial yjdF riboswitch binds to diverse azaaromatic compounds, only a subset of which cause it to activate translation. We examined the yjdF aptamer domain by small-angle X-ray scattering ... ...

Abstract	Unlike most riboswitches, which have one cognate effector, the bacterial yjdF riboswitch binds to diverse azaaromatic compounds, only a subset of which cause it to activate translation. We examined the yjdF aptamer domain by small-angle X-ray scattering and found that in the presence of activating ligands, the RNA adopts an overall shape similar to that of tRNA. Sequence analyses suggested that the yjdF aptamer is a homolog of tRNA
MeSH term(s)	Bacteria/genetics ; Bacteria/metabolism ; Gene Expression Regulation, Bacterial/genetics ; Ligands ; Nucleic Acid Conformation ; RNA Stability ; RNA, Bacterial/chemistry ; RNA, Bacterial/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/metabolism ; Riboswitch
Chemical Substances	Ligands ; RNA, Bacterial ; Riboswitch ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2022-04-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.101934
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Article ; Online: An uncommon [K

Trachman, Robert J / Ferré-D'Amaré, Adrian R

RNA (New York, N.Y.)

2021 Volume 27, Issue 10, Page(s) 1257–1264

Abstract: ... The ... ...

Abstract	The widespread
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Aptamers, Nucleotide/genetics ; Aptamers, Nucleotide/metabolism ; Base Pairing ; Base Sequence ; Biological Evolution ; Burkholderia/genetics ; Burkholderia/metabolism ; Chelating Agents/chemistry ; Chelating Agents/metabolism ; Clostridiales/genetics ; Clostridiales/metabolism ; Crystallography, X-Ray ; Dickeya/genetics ; Dickeya/metabolism ; Guanidines/chemistry ; Guanidines/metabolism ; Magnesium/chemistry ; Magnesium/metabolism ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Potassium/chemistry ; Potassium/metabolism ; Ribosomes/genetics ; Ribosomes/metabolism ; Riboswitch ; Water/chemistry ; Water/metabolism
Chemical Substances	Aptamers, Nucleotide ; Chelating Agents ; Guanidines ; Riboswitch ; Water (059QF0KO0R) ; Magnesium (I38ZP9992A) ; Potassium (RWP5GA015D)
Language	English
Publishing date	2021-07-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.078824.121
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Article ; Online: Improving RNA Crystal Diffraction Quality by Postcrystallization Treatment.

Zhang, Jinwei / Ferré-D'Amaré, Adrian R

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2323, Page(s) 25–37

Abstract: The crystallization and structural determination of large RNAs and their complexes remain major bottlenecks in the mechanistic analysis of cellular and viral RNAs. Here, we describe a protocol that combines postcrystallization dehydration and ion ... ...

Abstract	The crystallization and structural determination of large RNAs and their complexes remain major bottlenecks in the mechanistic analysis of cellular and viral RNAs. Here, we describe a protocol that combines postcrystallization dehydration and ion replacement that dramatically improved the diffraction quality of crystals of a large gene-regulatory tRNA-mRNA complex. Through this method, the resolution limit of X-ray data extended from 8.5 to 3.2 Å, enabling structure determination. Although this protocol was developed for a particular RNA complex, the general importance of solvent and counterions in nucleic acid structure may render it generally useful for crystallographic analysis of other RNAs.
MeSH term(s)	Crystallization/methods ; Crystallography, X-Ray/methods ; Desiccation ; Ions/chemistry ; Nucleic Acid Conformation ; RNA/chemistry ; RNA, Transfer/chemistry
Chemical Substances	Ions ; RNA (63231-63-0) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2021-06-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1499-0_3
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Article ; Online: Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.

Jones, Christopher P / Ferré-D'Amaré, Adrian R

RNA (New York, N.Y.)

2021 Volume 28, Issue 2, Page(s) 239–249

Abstract: SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially ... ...

Abstract	SARS-CoV-2 produces two long viral protein precursors from one open reading frame using a highly conserved RNA pseudoknot that enhances programmed -1 ribosomal frameshifting. The 1.3 Å-resolution X-ray structure of the pseudoknot reveals three coaxially stacked helices buttressed by idiosyncratic base triples from loop residues. This structure represents a frameshift-stimulating state that must be deformed by the ribosome and exhibits base-triple-adjacent pockets that could be targeted by future small-molecule therapeutics.
MeSH term(s)	Codon, Terminator ; Crystallography, X-Ray ; Frameshifting, Ribosomal ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; RNA, Viral/chemistry ; RNA, Viral/genetics ; SARS-CoV-2/genetics
Chemical Substances	Codon, Terminator ; RNA, Viral
Language	English
Publishing date	2021-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.078825.121
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Article ; Online: The emerging structural complexity of G-quadruplex RNAs.

Banco, Michael T / Ferré-D'Amaré, Adrian R

RNA (New York, N.Y.)

2021 Volume 27, Issue 4, Page(s) 390–402

Abstract: G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a ... ...

Abstract	G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2'-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Aptamers, Nucleotide/genetics ; Aptamers, Nucleotide/metabolism ; Base Pairing ; Base Sequence ; Binding Sites ; Complement C5a/chemistry ; Complement C5a/genetics ; Complement C5a/metabolism ; Fluorescent Dyes/chemistry ; Fragile X Mental Retardation Protein/chemistry ; Fragile X Mental Retardation Protein/genetics ; Fragile X Mental Retardation Protein/metabolism ; G-Quadruplexes ; Guanine/chemistry ; Guanine/metabolism ; Humans ; Protein Binding ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; Stereoisomerism
Chemical Substances	Aptamers, Nucleotide ; Fluorescent Dyes ; Fragile X Mental Retardation Protein (139135-51-6) ; Guanine (5Z93L87A1R) ; RNA (63231-63-0) ; Complement C5a (80295-54-1)
Language	English
Publishing date	2021-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.078238.120
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Article ; Online: Characterizing Fluorescence Properties of Turn-on RNA Aptamers.

Trachman, Robert J / Link, Katie A / Knutson, Jay R / Ferré-D'Amaré, Adrian R

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2568, Page(s) 25–36

Abstract: Fluorescent RNA aptamers are tools for studying RNA localization and interactions in vivo. The photophysical properties of these in vitro selected RNAs should be characterized prior to cellular imaging experiments. Here, we describe the process of ... ...

Abstract	Fluorescent RNA aptamers are tools for studying RNA localization and interactions in vivo. The photophysical properties of these in vitro selected RNAs should be characterized prior to cellular imaging experiments. Here, we describe the process of determining the fluorophore affinity, fluorescence enhancement, and fluorescence lifetime(s) of the Mango-III fluorescence turn-on aptamer. Parameters determined through these protocols will aid in establishing conditions for live-cell imaging.
MeSH term(s)	Aptamers, Nucleotide/genetics ; Fluorescence ; Fluorescent Dyes ; RNA
Chemical Substances	Aptamers, Nucleotide ; Fluorescent Dyes ; RNA (63231-63-0)
Language	English
Publishing date	2022-10-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2687-0_3
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Article ; Online: Intricate 3D architecture of a DNA mimic of GFP.

Passalacqua, Luiz F M / Banco, Michael T / Moon, Jared D / Li, Xing / Jaffrey, Samie R / Ferré-D'Amaré, Adrian R

Nature

2023 Volume 618, Issue 7967, Page(s) 1078–1084

Abstract: Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) ... ...

Abstract	Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures
MeSH term(s)	DNA/chemistry ; DNA/ultrastructure ; G-Quadruplexes ; Nucleic Acid Conformation ; RNA/chemistry ; Green Fluorescent Proteins/chemistry ; Green Fluorescent Proteins/ultrastructure ; Molecular Mimicry ; Crystallography, X-Ray ; Cryoelectron Microscopy ; Hydrogen Bonding ; Cations, Divalent/chemistry ; Cations, Monovalent/chemistry
Chemical Substances	DNA (9007-49-2) ; RNA (63231-63-0) ; Green Fluorescent Proteins (147336-22-9) ; Cations, Divalent ; Cations, Monovalent
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06229-8
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Article ; Online: Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence.

Sjekloća, Ljiljana / Ferré-D'Amaré, Adrian R

Cell chemical biology

2019 Volume 26, Issue 8, Page(s) 1159–1168.e4

Abstract: Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and ... ...

Abstract	Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Benzothiazoles/chemistry ; Binding Sites ; Fluorescence ; Fluorescent Dyes/chemistry ; G-Quadruplexes ; Models, Molecular ; Molecular Conformation ; Zea mays/chemistry
Chemical Substances	Aptamers, Nucleotide ; Benzothiazoles ; Fluorescent Dyes ; thioflavin T (2390-54-7)
Language	English
Publishing date	2019-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	2451-9448
ISSN (online)	2451-9448
DOI	10.1016/j.chembiol.2019.04.012
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Article ; Online: Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers.

Trachman, Robert J / Ferré-D'Amaré, Adrian R

Quarterly reviews of biophysics

2019 Volume 52, Page(s) e8

Abstract: Fluorescence turn-on aptamers, in vitro evolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse ... ...

Abstract	Fluorescence turn-on aptamers, in vitro evolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA-fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Aptamers, Nucleotide/metabolism ; Fluorescence ; Fluorescent Dyes/chemistry ; Fluorescent Dyes/metabolism ; Nucleic Acid Conformation ; RNA/chemistry ; RNA/metabolism
Chemical Substances	Aptamers, Nucleotide ; Fluorescent Dyes ; RNA (63231-63-0)
Language	English
Publishing date	2019-08-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Review
ZDB-ID	209912-3
ISSN	1469-8994 ; 0033-5835
ISSN (online)	1469-8994
ISSN	0033-5835
DOI	10.1017/S0033583519000064
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