1m magnesium chloride solution  (Millipore)

Journal: Cell Genomics

Article Title: Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3′ UTR of FAIM2

doi: 10.1016/j.xgen.2024.100556

Figure Lengend Snippet:

Article Snippet: 1M Magneisum Chloride Solution , Sigma , Cat# M1028-100ML.

Techniques: Recombinant, Saline, Modification, Transfection, Electron Microscopy, Membrane, Knock-Out, Gel Extraction, Plasmid Preparation, Mutagenesis, Reporter Assay, Sensitive Assay, Expressing, Purification, Software, Lysis, Cell Culture

Journal: Nucleic Acids Research

Article Title: Transient states during the annealing of mismatched and bulged oligonucleotides

doi: 10.1093/nar/gkae091

Figure Lengend Snippet: Kinetics for association and dissociation in short DNA oligonucleotides with defects. (A–C) Association rate constants and melting temperatures (for 1:1 mixtures containing 1 μM of each strand) for oligonucleotides with either single mismatches ( A ), double mismatches ( B ), or bulges ( C ) in 1 M NaCl, 10 mM Tris–HCl buffer pH 8.0. The grey shaded bands show k on for control oligonucleotides of lengths varying from 7 to 12 bp, yielding values varying by roughly a factor of two. Data are shown on a logarithmic scale to directly compare the relative contributions of k on and k off to K D . (D–F) Dissociation rate constants for short DNA oligonucleotides with either single mismatches ( D ), double mismatches ( E ), or bulges ( F ). Horizontal lines show k off for a series of perfectly paired control duplexes.

Article Snippet: Buffer mixtures were prepared using Tris (1M), sodium chloride (5 M) and magnesium chloride (1 M) stock solutions from Invitrogen and pH-adjusted using HCl from Sigma-Aldrich.

Techniques: Control

Journal: Nucleic Acids Research

Article Title: Transient states during the annealing of mismatched and bulged oligonucleotides

doi: 10.1093/nar/gkae091

Figure Lengend Snippet: Competition experiment for DNA probe hybridization. ( A ) Reaction scheme for the competition experiment between equimolar amounts of probe sequence (P), perfectly pairing target (T) and defected competitor (C). Target strands bear a fluorescent nucleotide (2Ap), sketched as a triangle, which allows tracking of the bound fraction over time. ( B ) Sketch of the time course of a typical competition experiment: the three strands are mixed and hybridize to produce a certain fraction of perfect and imperfect duplexes in ≈1 s, so that the system temporarily exhibits the initial binding accuracy θ in . After a certain amount of time depending on k on , k off and strand displacement rates, the metastable state converges to the energy minimum that is associated with its equilibrium binding accuracy θ eq . ( C ) Initial binding accuracy for competition experiments in case studies where θ in < θ eq . These values are expected to be equal to 1.0 for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $k_{on}^{C:P}$\end{document} << \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $k_{on}^{T:P}$\end{document} or 0.5 for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $k_{on}^{C:P}$\end{document} = \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $k_{on}^{T:P}$\end{document} . ( D ) Binding accuracy at equilibrium for competition experiments in case studies where θ in < θ eq . These values are expected to be equal to 1.0 for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $K_D^{C:P}$\end{document} >> \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $K_D^{T:P}$\end{document} or 0.5 for \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $K_D^{C:P}$\end{document} = \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $K_D^{T:P}$\end{document} . ( E ) Equilibration traces measured in competition experiments. The continuous lines were derived by interpolating/extrapolating the data. Vertical lines highlight half-lives for the shown samples. ( F ) Measured equilibration timescale, defined as the time required so that 50% of the transient state is equilibrated (see panel B). The transient low-accuracy state can last for a time ranging from a few seconds up to hours. All experiments were performed using 200 nM of each strand in 10 mM Tris–HCl pH 8.0 and 1 M NaCl.

Article Snippet: Buffer mixtures were prepared using Tris (1M), sodium chloride (5 M) and magnesium chloride (1 M) stock solutions from Invitrogen and pH-adjusted using HCl from Sigma-Aldrich.

Techniques: Hybridization, Sequencing, Binding Assay, Derivative Assay

Journal: Nucleic Acids Research

Article Title: Transient states during the annealing of mismatched and bulged oligonucleotides

doi: 10.1093/nar/gkae091

Figure Lengend Snippet: Predictions for competition experiments with DNA. ( A ) Initial binding accuracy ( θ in ) for the competitive mixtures compared to values computed from Eq. are in good agreement, showing that association rates can be used to predict the initial partition of duplexes. ( B ) Binding accuracy at equilibrium is well predicted by a simple binding model based on experimentally determined nucleic acids dissociation constants. Axes have been stretched to better visualize the cluster of points close to 1.0 ( C ) Partition at equilibrium and after initial mixing are not well-correlated, showing the importance of expanding our current models for complex mixtures of oligonucleotides. Red dashed line shows best fitting line. Axes have been stretched to better visualize the cluster of points close to 1.0. ( D ) Comparison of the measured equilibration timescale and the lifetime of the defect containing duplex as computed from the dissociation rate of the competitor oligonucleotide. All experiments were performed with 200 nM of each strand in 10 mM Tris–HCl pH 8.0 and 1 M NaCl.

Article Snippet: Buffer mixtures were prepared using Tris (1M), sodium chloride (5 M) and magnesium chloride (1 M) stock solutions from Invitrogen and pH-adjusted using HCl from Sigma-Aldrich.

Techniques: Binding Assay, Comparison