Sparky 3

Manufactured by Bruker

Sourced in United States

The Sparky 3.110 is a compact and versatile nuclear magnetic resonance (NMR) spectrometer designed for routine analysis and quality control. It offers reliable and consistent performance for a wide range of applications in various industries.

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Lab products found in correlation

Topspin 3, by Bruker (5 mentions) Avance 3 500, by Bruker (2 mentions) Nmrpipe, by Bruker (2 mentions) Topspin 2, by Bruker (2 mentions) Topspin, by Bruker (2 mentions) Avance 3, by Bruker (1 mentions) Topspin 1, by Bruker (1 mentions) Avance 2, by Bruker (1 mentions) Spectrometers, by Bruker (1 mentions) Avance 600 mhz spectrometer, by Bruker (1 mentions) Sparky, by Bruker (1 mentions) Avance 2 700 mhz spectrometer, by Bruker (1 mentions) Avance 800, by Bruker (1 mentions)

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Sparky (25 citations)

10 protocols using sparky 3

NMR Analysis of Biomolecular Structures

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The RNA concentration of the NMR samples ranged between 34 and 240 μM. NMR spectra were acquired on 600 MHz (cryoprobe-equipped) and 500 MHz Bruker Avance III spectrometers, and analysed using Topspin 1.3 (Bruker Biospin) and Sparky 3.110 (T.D. Goddard, D.G. Kneller, UCSF USA, 2004). The unlabeled systems were studied using 2D watergate-NOESY (with 150 ms mixing time) and watergate-TOCSY experiments (60 ms mixing time) recorded in 90% H₂O/10% D₂O at two temperatures (typically 16 and 27°C). TOCSY and NOESY (250 ms) experiments were also acquired in D₂O at 27°C. The recycle delays were 1.6 and 2 s for all homonuclear TOCSY and NOESY experiments, respectively.
The ¹⁵N-labeled and/or ¹³C/¹⁵N-labeled samples were analysed with two-dimensional ¹H-¹⁵N HSQC experiments recorded in H₂O at 16 and 27°C, as well as HNN COSY experiments allowing detection of hydrogen bonds between bases via two bond N–N couplings (33 ). For HSQC experiments we acquired 1024 and 256 complex points in the direct and indirect dimensions, respectively, and 64 scans for each indirect experiment. For HNN-COSY experiments, the delay for evolution of the ²J_NN coupling was set to 15 ms, and we collected 2048 and 128 complex points in the t₂ and t₁ dimensions, respectively, with 320 scans for each t₁ increment. The recycle delays ranged between 1.0 and 1.3 s for experiments with labeled samples.

Cantero-Camacho Á, & Gallego J. (2015). The conserved 3′X terminal domain of hepatitis C virus genomic RNA forms a two-stem structure that promotes viral RNA dimerization. Nucleic Acids Research, 43(17), 8529-8539.

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NMR Characterization of Nucleic Acid Structures

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All NMR experiments were carried out on Bruker Avance III 500 and 600
spectrometers equipped with 5 mm quadruple-resonance (QCI) and triple-resonance (TCI)
cryogenic probes, respectively. Exchangeable proton spectra were recorded using
H₂O samples at 283 K (10°C), and non-exchangeable proton spectra were
recorded on H₂O and D₂O samples at 303 K (30°C). NMR spectra
were processed and analyzed with TOPSPIN 3.2 (Bruker), NMRPipe^{48 (link)}, and Sparky 3.110. (University of California, San
Francisco, CA). As described previously^{49 (link)}, the assignments were obtained using 2D NOESY, 2D TOCSY,
¹H-¹⁵N HSQC, ¹H-¹³C HSQC, 2D HCCH-COSY, 3D
HCCH-TOCSY, HCCNH TOCSY, and HCN experiments on the unlabeled, uniformly labeled and
base-specifically ¹³C,¹⁵N-labeled RNA samples, and the
³¹P spin-echo difference CT-HSQC and spin-echo difference CH-HCCH correlation
experiments were used to determine the ε and β dihedral angles of the
backbone. The interactions between imino protons and phosphate oxygens were characterized
using ¹H-³¹P HSQC experiments^{50 (link)}.

Zhao B., Guffy S.L., Williams B, & Zhang Q. (2017). An excited state underlies gene regulation of a transcriptional riboswitch. Nature chemical biology, 13(9), 968-974.

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NMR Characterization of Nucleic Acid Structures

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Zhao B., Guffy S.L., Williams B, & Zhang Q. (2017). An excited state underlies gene regulation of a transcriptional riboswitch. Nature chemical biology, 13(9), 968-974.

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NMR Structural Characterization of DNA

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NMR experiments were performed at 25°C on Bruker Avance II and III spectrometers operating at 600 and 800 MHz respectively. The DNA concentration for NMR experiments was typically 0.1−1.5 mM in 70 mM KCl, 20 mM KPi (pH 7) at 25°C, unless otherwise specified. Assignment of the imino protons of guanine residues was obtained by ¹⁵N-filtered experiments using 2% site-specific labelled samples. Assignments of guanine aromatic protons were obtained via long-range through-bond correlation between imino and aromatic protons. Spectra analyses were performed using the Topspin 3.5 (Bruker) and SPARKY 3.1 (40 (link)) softwares.

Winnerdy F.R., Bakalar B., Maity A., Vandana J.J., Mechulam Y., Schmitt E, & Phan A.T. (2019). NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes. Nucleic Acids Research, 47(15), 8272-8281.

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NMR Characterization of DNA Structure

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NMR experiments were performed on a Bruker spectrometer operating at 600 MHz at 25°C. 0.1−1.5 mM DNA samples dissolved in 70 mM KCl, 20 mM KPi (pH 7), 10% D₂O, 20 μM DSS were used for NMR measurements. Assignments of the imino protons of guanine residues were obtained by ¹⁵N-filtered experiments using 2% site-specific labelled samples. Assignments of guanine aromatic protons was obtained via long-range through-bond correlation between imino and aromatic protons. Assignments of other protons were determined based on through-bond (TOCSY/COSY) and through-space correlation experiments. Spectra analyses were performed using the Topspin 3.5 (Bruker) and SPARKY 3.1 (59 (link)) software.

Das P., Ngo K.H., Winnerdy F.R., Maity A., Bakalar B., Mechulam Y., Schmitt E, & Phan A.T. (2021). Bulges in left-handed G-quadruplexes. Nucleic Acids Research, 49(3), 1724-1736.

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Structural Insights of G-Quadruplex Formation

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Experiments were performed on 600 and 700 MHz Bruker spectrometers at 10 and 25°C. DNA concentrations were 0.1–1.2 mM. Various salt concentrations (from 10 to ∼100 mM K⁺) were tested and similar NMR spectra were observed, indicating the formation of the same G-quadruplex structure. At every 20–30 min interval, NOESY experiment was suspended, and the sample was quenched before the experiment was resumed. All spectra were processed and analyzed using the TopSpin 2.1 (Bruker), Sparky 3.1 (41 ) and Spinworks 4.0 (http://home.cc.umanitoba.ca/∼wolowiec/spinworks) programs.

Heddi B., Martín-Pintado N., Serimbetov Z., Kari T.M, & Phan A.T. (2015). G-quadruplexes with (4n - 1) guanines in the G-tetrad core: formation of a G-triad·water complex and implication for small-molecule binding. Nucleic Acids Research, 44(2), 910-916.

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NMR Characterization of Heme Protein Mutants

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NMR spectra were acquired on a Bruker Avance 600 MHz spectrometer with a triple-resonance cryoprobe at 25°C. To assist the assignment of the backbone and side chain NH signals in each mutant, ¹⁵N-labeled samples were prepared in 45 mM sodium phosphate (pH 7) with 100 mM final ionic strength in 92% H₂O/8% ²H₂O. Natural abundance samples of the mutants were prepared in the same buffer to assist the assignment of the heme substituent signals. OmcF wild-type samples were also prepared in the same buffer (pH 6.1 and 9.4) in ²H₂O (99.9%) to study the pH dependence of the heme substituents’ signals.
Reduction of the proteins was achieved by adding an equimolar solution of sodium dithionite, after degassing the samples with a continuous flow of argon. The full reduction of the samples was confirmed by 1D ¹H NMR. 2D ¹H,¹⁵N-HSQC spectra were acquired for ¹⁵N-labeled samples, whereas 2D ¹H, ¹H-TOCSY (60 ms) and 2D ¹H, ¹H-NOESY (80 ms) were acquired for natural abundance samples.
The water signal was used to calibrate the ¹H chemical shifts. ¹⁵N chemical shifts were calibrated using indirect referencing (Wishart et al., 1995 (link)). The data were processed using TOPSPIN (Bruker Biospin, Karlsruhe, Germany) and analyzed with Sparky (TD Goddard and DG Kneller, Sparky 3, University of California, San Francisco, CA, United States).

Teixeira L.R., Cordas C.M., Fonseca M.P., Duke N.E., Pokkuluri P.R, & Salgueiro C.A. (2020). Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens. Frontiers in Microbiology, 10, 2941.

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Isotopic Labeling of VcDciA Protein

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Production of ¹⁵N and ¹³C labeled VcDciA^[1–111] was obtained using the same protocol as described above except that the cellular culture was performed in a minimal medium supplemented with ¹⁵N ammonium chloride and ¹³C glucose (Eurisotop) (30 (link)). NMR experiments were carried out on a Bruker AvanceII-700 MHz spectrometer. For assignment experiments, purified ¹⁵N–¹³C VcDciA^[1–111] was concentrated up to 0.9 mM, in the NMR buffer (20 mM phosphate buffer (NH₂PO₄) pH 5.8, NaCl 50 mM, 2 μM EDTA, 0.2 mM DSS, 0.1 mg/ml NaN₃, 10% D₂O). Data for assignment of the backbone resonances were collected at 293 K using standard ¹H-¹⁵N HSQC, ¹⁵N-edited NOESY-HSQC, TOCSY-HSQC, HBHA(CO)NH, HN(CA)N, HNCO, HNCA, HN(CO)CA, HN(CA)CO and CBCA(CO)NH experiments. Proton chemical shifts (in ppm) were referenced relative to internal DSS and ¹⁵N and ¹³C references were set indirectly relative to DSS using frequency ratios (31 (link)). NMR data were processed using Topspin (Bruker) and analyzed using SPARKY 3 (T.D. Goddard and D.G. Kneller, UCSF).

Marsin S., Adam Y., Cargemel C., Andreani J., Baconnais S., Legrand P., Li de la Sierra-Gallay I., Humbert A., Aumont-Nicaise M., Velours C., Ochsenbein F., Durand D., Le Cam E., Walbott H., Possoz C., Quevillon-Cheruel S, & Ferat J.L. (2021). Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Nucleic Acids Research, 49(11), 6569-6586.

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NMR Analysis of Nucleic Acid Structures

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NMR experiments were performed on 600-MHz and 700-MHz Bruker AVANCE spectrometers at 25ºC, unless stated otherwise. Samples were prepared in buffer containing 20 mM KPi (pH5.0–9.0), 70 mM KCl and 10% D₂O, with DNA strand concentration typically ranging from 0.1 to 0.7 mM. NMR spectra of HT at a lower salt condition (10 mM KPi and 10 mM KCl) were also recorded and no significant changes were observed. The chemical shifts were calibrated against DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid). Imino protons (H1) of guanines were unambiguously assigned via site-specific low enrichment (49 (link)), and through-bond correlation at natural abundance (50 (link),51 (link)). Spectral assignments were assisted by NOESY, TOCSY, COSY and {¹H-¹³C}-HSQC experiments. All spectra were processed by Topspin 2.1 (Bruker) and analyzed by SPARKY 3.115 (52 ).

Cheong V.V., Heddi B., Lech C.J, & Phan A.T. (2015). Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G·G·X·O tetrad. Nucleic Acids Research, 43(21), 10506-10514.

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Structure-Activity of HIV-1 RT-DNA Aptamers

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To determine the structure-activity relationship of HIV-1 RT complexed with DNA aptamers, an NMR experiment was performed following Thammaporn et al. [24 (link)]. NMR is an effective method for analyzing HIV-1 RT binding to drugs. The results show the ¹H-¹³C heteronuclear single-quantum coherence (HSQC) data of HIV-1 RT-NNRTIs. The ¹H-¹³C HSQC spectra of WT or KY HIV-1 RTs labeled at methyl-¹³C-methionine on the p66 subunit were measured in the presence and absence of DNA aptamers. The HIV-1 RT and DNA aptamers were prepared in 10 mM Tris-d11 buffer (pD 7.6) containing 200 mM KCl, 1.5 mM sodium azide, and 4 mM MgCl₂. Twenty-eight micromolar HIV-1 RT was complexed with 140 mM DNA aptamers (1:5 molar ratio). The reaction was measured by using an AVANCE800 (Bruker BioSpin; Karlsruhe, Germany) spectrometer supplied with a cryogenic probe. The spectra data were prepared and analyzed by the Topspin 3.2 (Bruker BioSpin; Karlsruhe, Germany) and SPARKY 3.115 programs (San Francisco, CA, USA).

Ratanabunyong S., Seetaha S., Hannongbua S., Yanaka S., Yagi-Utsumi M., Kato K., Paemanee A, & Choowongkomon K. (2022). Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase. Molecules, 27(1), 285.

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