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Chemical probing for examining the structure of modified RNAs and ligand binding to RNA.

Methods. 2019; 
WadugePrabuddha,SakakibaraYogo,ChowChristi
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Biochemicals The following are from New England Biolabs: RNase-free DNaseI and proof ethanol (Decon Labs), glacial acetic acid (EMD), ethylene diammine tetracetic acid (EMD), [γ-32P]-ATP (Perkin Elmer), Improm II reverse transcriptase and 10× buffer (Promega), deoxynucleotide triphosphates (GenScript), and dideoxynucleotide triphosphates (ddATP, ddGTP, ddCTP, and ddTTP) (Roche Diagnostics). Get A Quote

摘要

Among different RNA modifications, the helix 69 (H69) region of the bacterial ribosomal RNA (rRNA) contains three pseudouridines (Ψs). H69 is functionally important due to its location in the heart of the ribosome. Several structural and functional studies have shown the importance of Ψ modifications in influencing the H69 conformation as well as maintaining key interactions in the ribosome during protein synthesis. Therefore, a need exists to understand the influence of modified nucleosides on conformational dynamics of the ribosome under solution conditions that mimic the cellular environment. In this review on chemical probing, we provide detailed protocols for the use of dimethyl sulfate (DMS) to ex... More

关键词

Aminoglycosides,Dimethyl sulfate,Footprinting,Helix 69,Pseudouri