[en] An improved method for mapping RNA transcript boundaries by the nuclease protection technique is presented. This method exploits the large (> 20⁰C) difference in the thermal stability of RNA:DNA and DNA:DNA duplexes in concentrated chaotropic salt solutions. At 45⁰C in 3.0 M sodium trichloroacetate RNA:DNA hybridization is very efficient but DNA:DNA duplexes remain completely denatured. For many applications, this solvent system can eliminate the need to prepare probes that are free of completing or irrelevant DNA molecules. Fifty- to 100-fold more RNA:DNA hybridization is observed when reassociation is preformed in 3.0 M sodium tricholoroacetate than in solutions containing high concentrations of formamide. A comparison of the use of S1 nuclease or mung beam nuclease suggests than mung bean nuclease can produce more precise and less ambiguous nuclease protection patterns