The Experts below are selected from a list of 270 Experts worldwide ranked by ideXlab platform
Robert C Spitale - One of the best experts on this subject based on the ideXlab platform.
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Assaying rna structure with laser seq
Nucleic Acids Research, 2019Co-Authors: Boris Zinshteyn, Dalen Chan, Whitney England, Chao Feng, Rachel Green, Robert C SpitaleAbstract:Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson-Crick pairing, but tertiary structure parameters such as solvent accessibility can provide an additional layer of structural information, particularly in RNA-protein complexes. Herein we report the development of Light Activated Structural Examination of RNA by high-throughput sequencing, or LASER-Seq, for measuring RNA structure in cells with deep sequencing. LASER relies on a light-generated nicotinoyl nitrenium ion to form covalent adducts with the C8 position of adenosine and guanosine. Reactivity is governed by the accessibility of C8 to the light-generated probe. We compare structure probing by RT-stop and mutational profiling (MaP), demonstrating that LASER can be integrated with both platforms for RNA structure analyses. We find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and that LASER can be used to rapidly survey for ligand binding sites in an unbiased fashion. LASER has a particular advantage in this last application, as it readily modifies paired nucleotides, enabling the identification of binding sites and conformational changes in highly structured RNA.
Mark D Shriver - One of the best experts on this subject based on the ideXlab platform.
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melting curve analysis of snps mcsnp a gel free and inexpensive approach for snp genotyping
BioTechniques, 2001Co-Authors: Joshua M Akey, D Sosnoski, E Parra, S Dios, K Hiester, Carolina Bonilla, Li Jin, Mark D ShriverAbstract:High-throughput methods for Assaying DNA variation require two important steps: (i) discriminating the variation and (ii) de-tecting the signal. In this report, we describe a novel SNP genotyping m...
Rachel Green - One of the best experts on this subject based on the ideXlab platform.
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Assaying rna structure with laser seq
Nucleic Acids Research, 2019Co-Authors: Boris Zinshteyn, Dalen Chan, Whitney England, Chao Feng, Rachel Green, Robert C SpitaleAbstract:Chemical probing methods are crucial to our understanding of the structure and function of RNA molecules. The majority of chemical methods used to probe RNA structure report on Watson-Crick pairing, but tertiary structure parameters such as solvent accessibility can provide an additional layer of structural information, particularly in RNA-protein complexes. Herein we report the development of Light Activated Structural Examination of RNA by high-throughput sequencing, or LASER-Seq, for measuring RNA structure in cells with deep sequencing. LASER relies on a light-generated nicotinoyl nitrenium ion to form covalent adducts with the C8 position of adenosine and guanosine. Reactivity is governed by the accessibility of C8 to the light-generated probe. We compare structure probing by RT-stop and mutational profiling (MaP), demonstrating that LASER can be integrated with both platforms for RNA structure analyses. We find that LASER reactivity correlates with solvent accessibility across the entire ribosome, and that LASER can be used to rapidly survey for ligand binding sites in an unbiased fashion. LASER has a particular advantage in this last application, as it readily modifies paired nucleotides, enabling the identification of binding sites and conformational changes in highly structured RNA.
Richard H. Griffey - One of the best experts on this subject based on the ideXlab platform.
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SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets.
Journal of Medicinal Chemistry, 2002Co-Authors: Eric E. Swayze, Elizabeth A. Jefferson, Kristin A. Sannes-lowery, Lawrence B. Blyn, Lisa M. Risen, Satoshi Arakawa, Stephen A. Osgood, Steven A. Hofstadler, Richard H. GriffeyAbstract:A technique for lead discovery vs RNA targets utilizing mass spectrometry (MS) screening methods is described. The structure−activity relationships (SAR) derived from Assaying weak binding motifs a...
Matthew E. Hurles - One of the best experts on this subject based on the ideXlab platform.
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Assaying chromosomal inversions by single-molecule haplotyping
Nature Methods, 2006Co-Authors: Daniel J. Turner, Jay Shendure, Greg Porreca, Chris Tyler-smith, Matthew E. Hurles, George Church, Peter GreenAbstract:Inversions are an important form of structural variation, but they are difficult to characterize, as their breakpoints often fall within inverted repeats. We have developed a method called 'haplotype fusion' in which an inversion breakpoint is genotyped by performing fusion PCR on single molecules of human genomic DNA. Fusing single-copy sequences bracketing an inversion breakpoint generates orientation-specific PCR products, exemplified by a genotyping assay for the int22 hemophilia A inversion on Xq28. Furthermore, we demonstrated that inversion events with breakpoints embedded within long (>100 kb) inverted repeats can be genotyped by haplotype-fusion PCR followed by bead-based single-molecule haplotyping on repeat-specific markers bracketing the inversion breakpoint. We illustrate this method by genotyping a Yp paracentric inversion sponsored by >300-kb-long inverted repeats. The generality of our methods to survey for, and genotype chromosomal inversions should help our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer.
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Assaying chromosomal inversions by single-molecule haplotyping
Nature Methods, 2006Co-Authors: Daniel J. Turner, Jay Shendure, Greg Porreca, George M. Church, Peter M. Green, Chris Tyler-smith, Matthew E. HurlesAbstract:Inversions are an important form of structural variation, but are difficult to characterize as their breakpoints often fall within inverted repeats. We have developed a novel method, called ‘Haplotype Fusion’, in which an inversion breakpoint is genotyped by performing Fusion-PCR on single molecules of DNA. Fusing single copy sequences bracketing an inversion breakpoint generates orientation-specific PCR products, as exemplified by a genotyping assay for the int22 hemophilia A inversion on Xq28. This method is suitable for surveying inversion polymorphism at most inverted repeats in the human genome. Furthermore, we demonstrate that inversion events with breakpoints embedded within long (>100kb) inverted repeats can be genotyped by Haplotype Fusion PCR followed by bead-based single molecule haplotyping on repeat-specific markers bracketing the inversion breakpoint. We illustrate this method by genotyping a Yp paracentric inversion sponsored by >300kb long inverted repeats. The generality of our methods for genotyping chromosomal inversions should catalyse our understanding of the contribution of inversions to genomic variation, inherited diseases and cancer.
