Sequence-specific binding polymers for duplex nucleic acids

A polymer composition effective to bind in a sequence-specific manner to a target sequence of a duplex polynucleotide containing different Watson-Crick basepair orientations at selected target sequence positions, comprising a selected sequence of subunits having the form:

• ##STR8## where Y is a 2- or 3-atom length, uncharged subunit linkage group;
• R is H, OH, or O-alkyl;
• the 5'-methylene has a .beta. stereochemical orientation in the 5-membered ring and a uniform steroeochemical orientation in the 6-membered ring;
• R.sub.i has a .beta. sterochemical orientation;
• and at least about 70% of R.sub.i groups in the polymer have the following target basepair-orientation specificities:
• (a) for a T:A or U:A orientation, R.sub.i is diaminopurine;
• (b) for a C:G orientation, R.sub.i is guanine or 6-thioguanine;
• (c) for a G:C orientation, R.sub.i is selected from the group consisting of planar bases having the following ring structures and hydrogen bonding arrays, where B indicates the polymer backbone:
• ##STR9## where the * ring position may carry a hydrogen-bond acceptor group;
• and (d) for an A:T orientation, R.sub.i is selected from the group consisting of planar bases having the following ring structures and hydrogen bonding arrays, where B indicates the polymer backbone:
• ##STR10## where the * ring position may carry a hydrogen-bond donating group.