The present invention relates to peptide-based nucleic acid surrogates (PNAs) having a repeating structure of (AA.sup.B-aa.sub.n).sub.m and a particular secondary structure that can bind to particular single-stranded nucleic acid targets. Preferably the peptide-based nucleic acid surrogate has an alpha-helical secondary structure (.alpha.PNA). Also, the present invention relates to the method of forming peptide-based nucleic acid surrogates having a particular secondary structure. The nucleic acid surrogates may be utilized for therapeutic (antisense, antigene), diagnostic (genetic), and molecular switching (.alpha.PNA chips) applications.