Peptide nucleic acid (PNA) is a DNA mimic with valuable properties and a rapidly growing scope of applications. Binding of PNAs to target sites located inside linear double-stranded (ds) DNAs is essentially restricted to homopurine-homopyrimidine motifs, which hampers some of PNA's applications. We report a set of different approaches to overcome these sequence limitations. The highly selective PNA-directed recognition of designated random-sequence sites within dsDNA featuring considerable practical potential for variety of molecular-biological applications. To demonstrate this, we perform efficient and sequence-specific targeting of dsDNA sites with mixed-base composition that makes it possible to perform capturing of designated DNA fragments from complex mixtures. We also perform multiple labeling of random-sequence dsDNA sites with fluorophores via the primer-extension reaction by DNA polymerases with strand displacement potential. We conclude that the using PNA with mixed base composition for strand invasion offer great potential for lifting sequence limitations in some of applications of PNA targeting of duplex DNA. Other possible biotechnological and diagnostic applications of mixed-base PNAs will be discussed.