Dimethyl Sulfate Sequencing
Dimethyl Sulfate Sequencing - Related Videos
10:34
Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Cited by 4 •
2022
The protocol provides instruction for modifying RNA with dimethyl sulfate for mutational profiling experiments. It includes in vitro and in vivo probing with two alternative library preparation methods.
03:15
Silver Staining of Sulfated Glycosaminoglycans: A Staining Method for Visualization of Sulfated Glycosaminoglycans in Polyacrylamide Gels
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2025
In this video, we demonstrate a procedure for combined Alcian blue and silver staining of sulfated glycosaminoglycan oligosaccharide fragments. This combined staining technique significantly amplifies the bands of glycosaminoglycan polymers of different lengths in polyacrylamide gels.
02:35
Long-Term Cryopreservation of Cyanobacterial Strains Using Glycerol or Dimethyl Sulfoxide
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2025
Source: Lea-Smith, D. J., et al. Generation of Marked and Markerless Mutants in Model Cyanobacterial Species. J. Vis. Exp. (2016)This video demonstrates the cryopreservation of cyanobacterial strains by combining concentrated cell suspensions with glycerol or DMSO and storing them at low temperatures, enabling long-term maintenance of viable cultures for photosynthesis and genetic studies.
01:29
Sulfate Attack on Concrete
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2024
Sulfate attack on concrete is a deterioration process characterized by a whitish discoloration beginning at the edges and corners, accompanied by cracking and spalling. This phenomenon occurs when sulfates react with the components of hardened concrete, forming compounds like calcium sulfate and calcium sulfoaluminate which occupy more space than the substances they replace, causing the concrete to expand and disrupt. Sulfates from sources like soil, groundwater, or industrial effluents...
08:01
Sulfate Separation by Selective Crystallization with a Bis-iminoguanidinium Ligand
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2016
A protocol for in situ aqueous synthesis of a bis(iminoguanidinium) ligand and its utilization in selective separation of sulfate is presented.
FAQs
Chemical reactivity is concentrated at exposed N1 positions of adenine and N3 positions of cytosine. When those sites participate in base pairing or become shielded by protein binding, methylation can decrease. Comparing modification patterns therefore distinguishes accessible nucleotides from protected regions, providing biochemical constraints for interpreting RNA folding rather than treating every base as equally informative.
Reduced reactivity can indicate either base pairing or protein-associated protection, so it represents restricted accessibility rather than a unique structural assignment. Regions with contrasting reactivity across conditions can reveal rearrangements, while localized protection can support analysis of RNA-protein contacts. This distinction helps connect chemical probing data with biochemical models of RNA architecture.
During reverse transcription, a methylated nucleotide can cause the reaction to stop or introduce a mutation. Sequencing captures these events, and their positions are converted into reactivity profiles. The profiles provide a nucleotide-resolved record of accessibility, allowing investigators to identify patterns associated with unpaired segments and other structural features.
Condition-to-condition comparison reveals structural changes that a single measurement may not show. If cellular conditions or ligand binding alter nucleotide accessibility, corresponding profile changes indicate that RNA architecture has been remodeled. This makes the method useful for examining conformational regulation, including how biochemical environments or bound molecules influence structural elements linked to RNA function.
An experiment applies dimethyl sulfate to RNA, performs reverse transcription, sequences the resulting products, and maps stops or mutations back to nucleotide positions. The resulting accessibility pattern is analyzed as a reactivity profile. This workflow connects chemical treatment to a sequence-aligned readout that can be compared across samples or experimental conditions.
Reactivity profiles provide experimental constraints for distinguishing exposed, likely unpaired nucleotides from regions with reduced accessibility. These constraints can be incorporated into secondary-structure analysis to evaluate folding patterns against biochemical observations. The approach complements sequence-based interpretation by adding measurements of the RNA accessibility state, helping identify structural elements that may regulate function.
At the scale of an individual RNA, the method can resolve local accessibility patterns and structural elements. Applied across transcriptomes, it extends the same information to many RNA molecules, enabling broader comparisons of folding behavior. This range supports focused mechanistic studies as well as larger surveys of RNA architecture and structural variation.