No. First, there are several DNA secondary structures, and each of them has its own characteristics. Fo example, quadruplexes and Z-DNA are very different structures. Second, there are many enzymatic and chemical probing tools, each of them tailored to detect specific DNA structural features, such as single-stranded bases, Hoogsteen hydrogen bonded bases and so on. So, you may need to first guess what your structure(s) might be and then select your specific tools to check your hypothesis. Third ... long...if you mean hundreds of bases, the task of detecting specific unpaired or mispaired bases becomes very difficult for at least two reasons: a) resolution on sequencing gels is limited and b) there may be competing secondary structures.