Methoxyamine hydrochloride is widely used in organic synthesis as a reagent for the protection of carbonyl groups. It reacts with aldehydes and ketones to form oxime derivatives, which are stable under various reaction conditions, allowing further transformations without affecting the carbonyl functionality. This property makes it valuable in the synthesis of complex molecules, including pharmaceuticals and natural products. Additionally, it is employed in the modification of nucleic acids, particularly in the preparation of oligonucleotides for research and therapeutic applications. Its ability to form stable adducts with DNA bases also makes it useful in studies related to DNA damage and repair mechanisms.