Numerous compounds are known as base-specific probes, including DMS, a small molecule probe that was first used for RNA structural analysis, CMCT, and Kethoxal. For obtaining structural information for all nucleotides using base-specific probes, multiple reagents are required.
Table. Example of base-specific probes Probe | Primary Modification Sites | Product Number |
DMS | Guanine N7, Adenine N1, Cytosine N3 | D0797 |
DEPC | Adenine N7 | O0103 |
CMCT | Guanine N1, Uracil N3 | C0793 |
Kethoxal | Guanine N1 and N4 | - |
DMAS-Cl | Guanine N2 | - |
Naz | Guanine C8, Adenine C8 | N1268 |
[Abbreviations]
DMS: Dimethyl Sulfate; DEPC: Diethyl Pyrocarbonate, CMCT: 1-Cyclohexyl-3-(2-morpholinoethyl)carbodiimide Metho-p-toluenesulfonate; DMAS-Cl: N,N-(Dimethylamino)dimethylchlorosilane; Naz: Nicotinoyl Azide
Naz (Nicotinoyl Azide) is used to study the solvent accessibility of purine nucleobases in RNA with the RNA structural analysis method LASER (Light Ativated Structural Examination of RNA).
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References
- Probing the structure of RNAs in solution
- Chemical probes for higher-order structure in RNA
- DMS footprinting of structured RNAs and RNA–protein complexes
- Light-activated chemical probing of nucleobase solvent accessibility inside cells
- C. Feng, D. Chan, J. Joseph, M. Muuronen, W. H. Coldren, N. Dai, I. R. Corrêa, F. Furche, C. M. Hadad, R. C. Spitale, Nat. Chem. Biol. 2018, 14, 276.
- In Vitro Methods to Decipher the Structure of Viral RNA Genomes
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