Nuclease S1 reaction buffer is primarily used in molecular biology for the digestion of single-stranded DNA and RNA. It is essential in experiments involving the mapping of RNA transcripts, where it helps in identifying the start and end points of RNA molecules by selectively degrading single-stranded regions. The buffer is also employed in the removal of single-stranded overhangs from DNA fragments, which is crucial for creating blunt ends in cloning procedures. Additionally, it is utilized in the analysis of DNA-RNA hybrids, where it aids in distinguishing between single-stranded and double-stranded nucleic acids. The buffer's optimal pH and ionic conditions ensure efficient enzyme activity, making it a key component in various nucleic acid manipulation techniques.