Modified oligonucleotides were synthesized by solid phase on a Mermade 4 DNA synthesizer (Bioautomation). DNA templates for Pol II primer extension reactions were a 26-mer (5′-ACCTCAACTACTTGA A
Msd sl ion trap mass spectrometer
Manufactured by Agilent Technologies
Sourced in Germany
The Agilent MSD SL ion trap mass spectrometer is a high-performance analytical instrument designed for the identification and quantification of chemical compounds. It utilizes ion trap technology to capture, isolate, and analyze ions based on their mass-to-charge ratio. The MSD SL provides accurate mass measurements and versatile MS/MS capabilities for a wide range of applications.
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Lab products found in correlation
3 fluorescently labeled ssdna oligonucleotides, by Integrated DNA Technologies (2 mentions)
5 nitroindole containing, by Integrated DNA Technologies (2 mentions)
Cary 300, by Agilent Technologies (1 mentions)
Fluorolog 3 22, by Horiba (1 mentions)
Ltq orbitrap xl, by Thermo Fisher Scientific (1 mentions)
Avance 3 700 mhz spectrometer, by Bruker (1 mentions)
Avance 300 mhz spectrometer, by Bruker (1 mentions)
4 protocols using msd sl ion trap mass spectrometer
1
Synthesis and Purification of Oligonucleotides for Pol II Primer Extension
2
Probing APOBEC3 DNA interactions
3
Characterization of Spectroscopic Properties
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1H NMR and 13C NMR spectra were recorded with a Bruker Avance 300 MHz spectrometer, but in some cases, a Bruker Avance‐III 700 MHz spectrometer was used. Chemical shifts are given in parts per million according to the solvent signal. Electrospray (ES) mass spectra were obtained with an Agilent MSD SL ion‐trap mass spectrometer (Agilent, Waldbronn, Germany), and high‐resolution mass spectrometry (HRMS) was performed with a LTQ Orbitrap XL from Thermo Fisher Scientific (Waltham, MA, USA), operating in positive‐ion mode by using electrospray ionization. Absorption measurements were performed with a Hitachi U‐3010 or an Agilent Cary 300. Emission spectra were measured with a Hitachi F‐4500 or a Horiba Fluorolog‐3–22. The quantum yields were determined in aerated HBS 7.3 by the relative method41 by using rhodamine 6G (Φ=94 %)31 , 32 as a standard. The quantum yield determinations were performed with a Cary 300 UV/Vis spectrophotometer and a Fluorolog‐3–22 fluorimeter, whereby the data were corrected for changes in refractive indices. Excitation of reference standard and samples was performed at λ=335 nm, and the concentration was held below an absorbance value of 0.1. During all the measurements, the same quartz glass cuvette was used, and the orientation of the cuvette in the spectrometers was always identical.
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1H NMR and 13C NMR spectra were recorded with a Bruker Avance 300 MHz spectrometer, but in some cases, a Bruker Avance‐III 700 MHz spectrometer was used. Chemical shifts are given in parts per million according to the solvent signal. Electrospray (ES) mass spectra were obtained with an Agilent MSD SL ion‐trap mass spectrometer (Agilent, Waldbronn, Germany), and high‐resolution mass spectrometry (HRMS) was performed with a LTQ Orbitrap XL from Thermo Fisher Scientific (Waltham, MA, USA), operating in positive‐ion mode by using electrospray ionization. Absorption measurements were performed with a Hitachi U‐3010 or an Agilent Cary 300. Emission spectra were measured with a Hitachi F‐4500 or a Horiba Fluorolog‐3–22. The quantum yields were determined in aerated HBS 7.3 by the relative method
4
Probing APOBEC3 DNA interactions
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The ssDNA oligonucleotides for co-crystallization with A3A and A3Bctd* were 5′-AAAAAAATC GGGAAA and 5′-TTTTC AT, respectively (Integrated DNA Technologies). The unbiased experimental approach for identifying the former sequence is described below, and the latter is based on the fact that 5′-TC A is the most commonly mutated APOBEC signature motif in cancer13 (link)–15 (link). 3′-fluorescently labeled ssDNA oligonucleotides for in vitro DNA deamination experiments were obtained from Integrated DNA Technologies or Midland Certified Reagent Company. The ssDNA oligonucleotide substrates used in Fig. 3e are 5′-AAAAAAAAATC GGGAAAAAAA-3′-FAM, 5′-AAAAAAAAA[dU]C GGGAAAAAAA-3′-FAM, 5′-AAAAAAAAA[5-F-dU]C GGGAAAAAAA-3′-FAM, and 5′-AAAAAAAAA[iSuper-dT]C GGGAAAAAAA-3′-FAM (labeled dT, dU, Super T, and 5FdU, respectively). The ssDNA oligonucleotide substrate used in Fig. 5a is 5′-ATTATTATTATTC AAATGGATTTATTTATTTATTTATTTATTT-3′-FAM, the same except (A, C, G, or T)C A as trinucleotide targets in Fig. 5b . 5-Nitroindole containing ssDNA substrates were purchased from Integrated DNA Technologies (Coralville, IA) as desalted oligonucleotides and characterized by LC-MS on an Agilent 1100 series HPLC instrument equipped an Agilent MSD SL ion trap mass spectrometer. A full list of ssDNA oligonucleotides used in site-directed mutation is available upon request.
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