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1.
Nat Commun ; 12(1): 5201, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34465779

RESUMO

N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20°C-65°C) NMR relaxation dispersion, we show that m6A pairs with uridine with the methylamino group in the anti conformation to form a Watson-Crick base pair that transiently exchanges on the millisecond timescale with a singly hydrogen-bonded low-populated (1%) mismatch-like conformation in which the methylamino group is syn. This ability to rapidly interchange between Watson-Crick or mismatch-like forms, combined with different syn:anti isomer preferences when paired (~1:100) versus unpaired (~10:1), explains how m6A robustly slows duplex annealing without affecting melting at elevated temperatures via two pathways in which isomerization occurs before or after duplex annealing. Our model quantitatively predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions, and provides an explanation for why the modification robustly slows diverse cellular processes.


Assuntos
Adenosina/análogos & derivados , DNA/química , DNA/metabolismo , Adenosina/química , Adenosina/genética , Adenosina/metabolismo , Pareamento de Bases , DNA/genética , Ligação de Hidrogênio , Cinética , Modelos Moleculares , Conformação de Ácido Nucleico , Hibridização de Ácido Nucleico , Processamento Pós-Transcricional do RNA , Uridina/química , Uridina/genética , Uridina/metabolismo
2.
J Phys Chem B ; 125(28): 7613-7627, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34236202

RESUMO

Measuring the strength of the hydrogen bonds between DNA base pairs is of vital importance for understanding how our genetic code is physically accessed and recognized in cells, particularly during replication and transcription. Therefore, it is important to develop probes for these key hydrogen bonds (H-bonds) that dictate events critical to cellular function, such as the localized melting of DNA. The vibrations of carbonyl bonds are well-known probes of their H-bonding environment, and their signals can be observed with infrared (IR) spectroscopy. Yet, pinpointing a single bond of interest in the complex IR spectrum of DNA is challenging due to the large number of carbonyl signals that overlap with each other. Here, we develop a method using isotope editing and infrared (IR) spectroscopy to isolate IR signals from the thymine (T) C2═O carbonyl. We use solvatochromatic studies to show that the TC2═O signal's position in the IR spectrum is sensitive to the H-bonding capacity of the solvent. Our results indicate that C2═O of a single T base within DNA duplexes experiences weak H-bonding interactions. This finding is consistent with the existence of a third, noncanonical CH···O H-bond between adenine and thymine in both Watson-Crick and Hoogsteen base pairs in DNA.


Assuntos
DNA , Isótopos , Hidrogênio , Ligação de Hidrogênio , Análise Espectral
3.
Angew Chem Int Ed Engl ; 59(39): 17062-17069, 2020 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-32558232

RESUMO

We present the access to [5-19 F, 5-13 C]-uridine and -cytidine phosphoramidites for the production of site-specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5-19 F, 5-13 C]-pyrimidine labels into five RNAs-the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ϵ (hHBV ϵ) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre-microRNA (miRNA) 21 and the 59 nt full length pre-miRNA 21. The main stimulus to introduce the aromatic 19 F-13 C-spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole-dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic 13 C-19 F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5-19 F, 5-13 C]/[5-19 F] pyrimidine labeling. For the 61 nt hHBV ϵ we find a beneficial 19 F-13 C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [19 F, 13 C]-labeling of the SAM VI aptamer domain and the pre-miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Pirimidinas/química , RNA Viral/química , Isótopos de Carbono , Flúor
4.
J Am Chem Soc ; 141(51): 19988-19993, 2019 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-31826614

RESUMO

N6-Methyladenosine (m6A) is an abundant epitranscriptomic modification that plays important roles in many aspects of RNA metabolism. While m6A is thought to mainly function by recruiting reader proteins to specific RNA sites, the modification can also reshape RNA-protein and RNA-RNA interactions by altering RNA structure mainly by destabilizing base pairing. Little is known about how m6A and other epitranscriptomic modifications might affect the kinetic rates of RNA folding and other conformational transitions that are also important for cellular activity. Here, we used NMR R1ρ relaxation dispersion and chemical exchange saturation transfer to noninvasively and site-specifically measure nucleic acid hybridization kinetics. The methodology was validated on two DNA duplexes and then applied to examine how a single m6A alters the hybridization kinetics in two RNA duplexes. The results show that m6A minimally impacts the rate constant for duplex dissociation, changing koff by ∼1-fold but significantly slows the rate of duplex annealing, decreasing kon by ∼7-fold. A reduction in the annealing rate was observed robustly for two different sequence contexts at different temperatures, both in the presence and absence of Mg2+. We propose that rotation of the N6-methyl group from the preferred syn conformation in the unpaired nucleotide to the energetically disfavored anti conformation required for Watson-Crick pairing is responsible for the reduced annealing rate. The results help explain why in mRNA m6A slows down tRNA selection and more generally suggest that m6A may exert cellular functions by reshaping the kinetics of RNA conformational transitions.


Assuntos
Adenosina/análogos & derivados , Ressonância Magnética Nuclear Biomolecular , RNA/química , Adenosina/análise , Adenosina/metabolismo , RNA/metabolismo
5.
Nucleic Acids Res ; 47(21): 11430-11440, 2019 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-31665419

RESUMO

Although group II intron ribozymes are intensively studied the question how structural dynamics affects splicing catalysis has remained elusive. We report for the first time that the group II intron domain 6 exists in a secondary structure equilibrium between a single- and a two-nucleotide bulge conformation, which is directly linked to a switch between sugar puckers of the branch site adenosine. Our study determined a functional sugar pucker equilibrium between the transesterification active C2'-endo conformation of the branch site adenosine in the 1nt bulge and an inactive C3'-endo state in the 2nt bulge fold, allowing the group II intron to switch its activity from the branching to the exon ligation step. Our detailed NMR spectroscopic investigation identified magnesium (II) ions and the branching reaction as regulators of the equilibrium populations. The tuneable secondary structure/sugar pucker equilibrium supports a conformational selection mechanism to up- and downregulate catalytically active and inactive states of the branch site adenosine to orchestrate the multi-step splicing process. The conformational dynamics of group II intron domain 6 is also proposed to be a key aspect for the directionality selection in reversible splicing.


Assuntos
Íntrons/genética , Conformação de Ácido Nucleico , Splicing de RNA/fisiologia , RNA/química , Açúcares/química , Sítios de Ligação , Carboidratos/química , Magnésio/química , Espectroscopia de Ressonância Magnética , RNA/metabolismo , Açúcares/metabolismo
6.
Acta Crystallogr E Crystallogr Commun ; 75(Pt 1): 75-80, 2019 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-30713738

RESUMO

The structure of [Ir{(4-Cl-C6H4N3)C(dppm)-κ3 P,C,N}(dppm-κ2 P,P')]Cl·1.5CH2Cl2·0.5C7H8 (C57H48Cl2IrN3P4·1.5CH2Cl2·0.5C7H8) (2), dppm = bis-(di-phenyl-phosphino)methane {systematic name: [7-(4-chloro-phen-yl)-1,1,3,3-tetra-phenyl-5,6,7-tri-aza-κN 7-1,3λ4-diphospha-κP 1-hepta-4,6-dien-4-yl][methyl-ene-bis(di-phenyl-phosphine)-κ2 P,P']iridium(I) chloride-di-chloro-methane-toluene (2/3/1)}, resulting from the reaction of [IrClH{C(dppm)2-κ3 P,C,P)(MeCN)]Cl (1a) with 1-azido-4-chloro-benzene, shows a monocationic five-coordinate IrI complex with a distorted trigonal-bipyramidal geometry. In 2, the iridium centre is coordinated by the neutral triazeneyl-idene-phospho-rane (4-Cl-C6H4N3)C(dppm) acting as a PCN pincer ligand, and a chelating dppm unit. The structure of the coordination compound [IrCl(CN)H(C(dppm)2-κ3 P,C,P)]·CH3CN, (C52H45ClIrNP4·CH3CN) (1b) [systematic name: chlorido-cyanidohydrido(1,1,3,3,5,5,7,7-octa-phenyl-1,3λ5,5λ4,7-tetra-phospha-κ2 P 1,P 7-hept-3-en-4-yl)iridium(III) aceto-nitrile monosolvate], prepared from 1a and KCN, reveals an octa-hedral IrIII central atom with a meridional PCP pincer carbodi-phospho-rane (CDP) ligand; the chloride ligand is located trans to the central carbon of the CDP functionality while the hydrido and cyanido ligands are situated trans to each other. The chiral coordination compound [Ir(CN)((4-Cl-C6H4N3)CH(CH(P(Ph)2)2)-κ3 P,C,N)(dppm-κ2 P,P')]·2CH3OH, (C58H48ClIrN4P4·2CH3OH) (3) (systematic name: {4-[3-(4-chloro-phen-yl)triazenido-κN 3]-1,1,3,3-tetra-phenyl-1,3λ5-diphospha-κP 1-but-2-en-4-yl}cyanido[methyl-enebis(di-phenyl-phosphine)-κ2 P,P']iridium(III) methanol disolvate), formed via prolonged reaction of 1-azido-4-chloro-benzene with 1b, features a six-coordinate IrIII central atom. The iridium centre is coordinated by the dianionic facial PCN pincer ligand [(4-Cl-C6H4N3)CH(CH(P(Ph2)2)2)], a cyanido ligand trans to the central carbon of the PCN pincer ligand and a chelating dppm unit. Complex 2 exhibits a 2:1 positional disorder of the Cl- anion. The CH2Cl2 and C7H8 solvent mol-ecules show occupational disorder, with the toluene mol-ecule exhibiting additional 1:1 positional disorder with some nearly overlying carbon atoms.

7.
Genes (Basel) ; 10(2)2019 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-30691071

RESUMO

RNA modifications are crucial factors for efficient protein synthesis. All classes of RNAs that are involved in translation are modified to different extents. Recently, mRNA modifications and their impact on gene regulation became a focus of interest because they can exert a variety of effects on the fate of mRNAs. mRNA modifications within coding sequences can either directly or indirectly interfere with protein synthesis. In order to investigate the roles of various natural occurring modified nucleotides, we site-specifically introduced them into the coding sequence of reporter mRNAs and subsequently translated them in HEK293T cells. The analysis of the respective protein products revealed a strong position-dependent impact of RNA modifications on translation efficiency and accuracy. Whereas a single 5-methylcytosine (m5C) or pseudouridine () did not reduce product yields, N¹-methyladenosine (m¹A) generally impeded the translation of the respective modified mRNA. An inhibitory effect of 2'O-methlyated nucleotides (Nm) and N6-methyladenosine (m6A) was strongly dependent on their position within the codon. Finally, we could not attribute any miscoding potential to the set of mRNA modifications tested in HEK293T cells.


Assuntos
Elongação Traducional da Cadeia Peptídica , Processamento Pós-Transcricional do RNA , RNA Mensageiro/genética , 5-Metilcitosina/metabolismo , Adenosina/análogos & derivados , Adenosina/metabolismo , Animais , Linhagem Celular Tumoral , Células HEK293 , Humanos , Camundongos , Pseudouridina/metabolismo , RNA Mensageiro/metabolismo
8.
Acta Crystallogr E Crystallogr Commun ; 74(Pt 6): 846-852, 2018 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-29951243

RESUMO

Compound [Ir(C8H12)(C51H45P4)]Cl2 or [Ir(cod)(CH(dppm)2-κ3P,C,P)]Cl2 (1a), was obtained from [IrCl(cod)]2 and the carbodi-phospho-rane (CDP) salt [CH(dppm)2]Cl [where cod = cyclo-octa-1,5-diene and dppm = bis-(di-phenyl-phosphino)methane]. Treatment of 1a with thallium(I) tri-fluoro-methane-sulfonate [Tl(OTf)] and subsequent crystallization gave complex [Ir(C8H12)(C51H45P4)](OTf)2·CH3CO2C2H5·CH2Cl2 or [Ir(cod)(CH(dppm)2-κ3P,C,P)](OTf)2·CH3CO2C2H5·CH2Cl2 (1b) [systematic name: (cyclo-octa-1,5-diene)(1,1,3,3,5,5,7,7-octa-phenyl-1,7-diphospha-3,5-di-phospho-niaheptan-4-yl)iridium(I) bis-(tri-fluoro-methane-sulfonate)-ethyl acetate-di-chloro-methane (1/1/1)]. This five-coordinate iridium(I) complex cation adopts a trigonal-bipyramidal geometry with the CDP carbon and one cod double bond in axial sites. Compound 1b represents the first example of a non-meridional coordination of the PCP pincer ligand [CH(dppm)2]+ with a P-Ir-P angle of 98.08 (2)°. Compound 2, [IrCl2H(C51H44P4)]·(CH3)2CO or [IrCl2H(C(dppm)2-κ3P,C,P)]·(CH3)2CO [systematic name: di-chlorido-hydrido(1,1,3,3,5,5,7,7-octa-phenyl-1,5λ5,7-triphospha-3-phospho-niahept-4-en-4-yl)iridium(III) acetone monosolvate], crystallizes as an acetone monosolvate. It is a six-coordinate IrIII coordination compound. Here, the PCP pincer ligand is coordinated in a meridional manner; one chlorido ligand is positioned trans to the carbon donor, the remaining two coordination sites being occupied by the second chlorido and a hydrido ligand trans to each other. Complex 3, [IrCl2H(C51H45P4)]Cl·5H2O or [IrCl2H(CH(dppm)2-κ3P,C,P)]Cl·5H2O [systematic name: di-chlorido-hydrido(1,1,3,3,5,5,7,7-octa-phenyl-1,7-diphospha-3,5-di-phospho-niaheptan-4-yl)iridium(III) chloride penta-hydrate], represents the conjugate CH acid of 2. The ligand [CH(dppm)2]+ is coordinated in a meridional manner. In the cationic six-coordinate IrIII complex 4, [IrClH(CO)(C51H44P4)]Cl·2CH3OH·H2O or [IrClH(CO)(C(dppm)2-κ3P,C,P)]Cl·2CH3OH·H2O [systematic name: carbonyl-chlorido-hydrido(1,1,3,3,5,5,7,7-octa-phenyl-1,5λ5,7-triphospha-3-phos-pho-niahept-4-en-4-yl)iridium(III) chloride-methanol-water (1/2/1)], the chlorido ligand is found in the plane defined by the Ir center and the meridional PCP ligand; the H and CO ligands are positioned axially to this plane and trans to each other.

9.
Methods ; 148: 39-47, 2018 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-29753787

RESUMO

Using chemical synthesis and solution NMR spectroscopy, RNA structural ensembles including a major ground state and minor populated excited states can be studied at atomic resolution. In this work, atom-specific 13C labeled RNA building blocks - a 5-13C-uridine and a 2,8-13C2-adenosine building block - are used to introduce isolated 13C-1H-spin topologies into a target RNA to probe such structural ensembles via NMR spectroscopy. First, the 5-13C-uridine 2'-O-TBDMS-phosphoramidite building block was introduced into a 21 nucleotide (nt) tP5c stem construct of the tP5abc subdomain of the Tetrahymena group I ribozyme. Then, the 2,8-13C2-adenosine 2'-O-TBDMS-phosphoramidite building block was incorporated into a 9 kDa and a 15 kD construct derived from the epsilon (ε) RNA element of the duck Hepatitis B virus. The 2,8-13C2-adenosine resonances of the 9 kDa 28 nt sequence could be mapped to the full-length 53 nt construct. The isolated NMR active nuclei pairs were used to probe for low populated excited states (<10%) via 13C-Carr-Purcell-Meiboom-Gill (CPMG)-relaxation dispersion NMR spectroscopy. The 13C-CPMG relaxation dispersion experiment recapitulated a secondary structure switching event in the P5c hairpin of the group I intron construct previously revealed by 15N relaxation dispersion experiments. In the ε-HBV RNA an unfolding event occurring on the millisecond time scale was found in the upper stem in-line with earlier observations. This unpaired conformational state is presumed to be important for the binding of the epsilon reverse transcriptase (RT) enzyme. Thus, a full description of an RNA's folding landscape helps to obtain a deeper understanding of its function, as these high energy conformational states often represent functionally important intermediates involved in (un)folding or ribozyme catalysis.


Assuntos
Ressonância Magnética Nuclear Biomolecular/métodos , RNA/análise , RNA/genética , Radioisótopos de Carbono/análise , Radioisótopos de Carbono/química , Conformação Proteica , RNA/síntese química
10.
Chemistry ; 24(21): 5462-5468, 2018 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-29412477

RESUMO

Conformational dynamics of RNA molecules play a critical role in governing their biological functions. Measurements of RNA dynamic behavior sheds important light on sites that interact with their binding partners or cellular stimulators. However, such measurements using solution-state NMR are difficult for large RNA molecules (>70 nt; nt=nucleotides) owing to severe spectral overlap, homonuclear 13 C scalar couplings, and line broadening. Herein, a strategic combination of solid-phase synthesis, site-specific isotopic labeled phosphoramidites, and enzymatic ligation is introduced. This approach allowed the position-specific insertion of isotopic probes into a 96 nt CCR5 RNA fragment. Accurate measurements of functional dynamics using the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments enabled extraction of the exchange rates and populations of this RNA. NMR chemical shift perturbation analysis of the RNA/microRNA-1224 complex indicated that A90-C1' of the pseudoknot exhibits similar changes in chemical shift observed in the excited state. This work demonstrates the general applicability of a NMR-labeling strategy to probe functional RNA structural dynamics.


Assuntos
MicroRNAs/química , Modelos Moleculares , Receptores CCR5/genética , MicroRNAs/metabolismo , Ressonância Magnética Nuclear Biomolecular , Técnicas de Síntese em Fase Sólida
11.
Nucleic Acids Res ; 45(15): 9178-9192, 2017 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-28911104

RESUMO

We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations on structural and dynamic features via NMR spectroscopy. In detail, 6-13C-modified pyrimidine and 8-13C purine DNA phosphoramidites were synthesized and incorporated into a polypurine tract DNA/RNA hybrid duplex to showcase the facile resonance assignment using site-specific labeling. We also addressed micro- to millisecond dynamics in the mini-cTAR DNA. This DNA is involved in the HIV replication cycle and our data points toward an exchange process in the lower stem of the hairpin that is up-regulated in the presence of the HIV-1 nucleocapsid protein 7. As another example, we picked a G-quadruplex that was earlier shown to exist in two folds. Using site-specific 8-13C-2'deoxyguanosine labeling we were able to verify the slow exchange between the two forms on the chemical shift time scale. In a real-time NMR experiment the re-equilibration of the fold distribution after a T-jump could be monitored yielding a rate of 0.012 min-1. Finally, we used 13C-ZZ-exchange spectroscopy to characterize the kinetics between two stacked X-conformers of a Holliday junction mimic. At 25°C, the refolding process was found to occur at a forward rate constant of 3.1 s-1 and with a backward rate constant of 10.6 s-1.


Assuntos
DNA Cruciforme/química , DNA/química , Repetição Terminal Longa de HIV , Proteínas do Nucleocapsídeo/química , Compostos Organofosforados/química , RNA/química , Pareamento de Bases , Isótopos de Carbono , Quadruplex G , HIV-1/química , Marcação por Isótopo , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Mimetismo Molecular , Conformação de Ácido Nucleico , Compostos Organofosforados/síntese química , Técnicas de Síntese em Fase Sólida
12.
Angew Chem Int Ed Engl ; 55(39): 12008-12, 2016 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-27533469

RESUMO

In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear (13) C and (1) H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific (2) H and (13) C labeling, spin topologies are introduced into DNA and RNA that make (1) H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for (1) H RD experiments of nucleic acids.


Assuntos
DNA/química , Marcação por Isótopo/métodos , Ressonância Magnética Nuclear Biomolecular/métodos , RNA/química , Sequência de Bases , Conformação de Ácido Nucleico , Prótons
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