By using the standard purine nucleosides, guanosine and adenosine, and the pyrimidine C-nucleosides, pseudoisocytidine and pseudouridine, as complements on a probe strand, it is possible to construct a regular Watson-Crick helix with a single-stranded target sequence having any arrangement of the four naturally-occurring bases found in nucleic acids. The major groove of this helix will have a unique configuration of hydrogen-bonding sites on the probe strand for each of these four base pairs. By using this duplex as a framework, an ensemble of recognition patterns composed of base triads may be constructed. In these patterns, either a homopyrimidine or homopurine third strand binds in the major groove of the duplex formed by the target and probe strands. Ten distinct geometries, or motifs, are shown, each one consisting of four isomorphic base triads built upon recognition of C, G, A, or U(T) residues in the target strand. Four motifs contain pyrimidines as residues on the third strand which base pair to the second strand through specific hydrogen-bonding interactions, four motifs involve purines which base-pair to the second strand through donor-acceptor sites located on their six-membered ring, and two motifs utilize purines binding to the second strand at sites located on both their five- and six-membered rings. For base triads or for base-pairing interactions which involve the common bases found in nucleic acids, most of the hydrogen-bonding patterns have been previously recognized. In order to maintain specific hydrogen bonding and to construct isomorphous triads, the use of several nonstandard bases is proposed. A subset of the base triads may also be used to design oligonucleotides which may bind as a third strand to naturally-occurring homopyrimidine-homopurine double-stranded target sites such as those found in DNA. In addition, another set of four bases which have Watson-Crick complementarity to the target-strand bases and which provide alternative patterns of donor-acceptor pairs for third-strand interactions can be proposed for use on the second strand. With the palette of eight second-strand bases, four possible permutations of (target strand)-(second strand) interactions are shown. For each of the four residues on the target strand, any single permutation presents unique hydrogen-bonding patterns for third-strand binding which may occur according to one of the ten triad motifs.