Prokaryotic argonautes are a unique class of nucleic acid-guided endonucleases putatively involved in cellular defense against foreign genetic elements. While their eukaryotic homologs and Cas protein counterparts require single-stranded RNAs as guides， some prokaryotic argonautes are able to utilize short single-stranded DNAs as guides for sequence-specific endonuclease activity. Many complications currently prevent the use of prokaryotic argonautes for in vivo gene-editing applications; however， they do exhibit potential as a new class of in vitro molecular tools if certain challenges can be overcome， specifically the limitations on substrate accessibility which leads to unequal levels of activity across a broad palate of substrates and the inability to act on double-stranded DNA substrates. Here we demonstrate the use of accessory factors， including thermostable single-stranded DNA binding proteins and UvrD-like helicase， in conjunction with prokaryotic argonautes to significantly improve enzymatic activity and enable functionality with a broader range of substrates， including linear double-stranded DNA substrates. We also demonstrate the use of Thermus thermophilus argonaute with accessory factors as a programmable restriction enzyme to generate long， unique single-stranded overhangs from linear double-stranded substrates compatible with downstream ligation.