The present invention relates to ligation and/or assembly of nucleic acid molecules. Particularly, a double-stranded target nucleic acid having overhangs of at least one nucleotide is ligated with another nucleic acid molecule capable of forming a stem-loop structure with an overhang of at least one nucleotide. The invention is suitable for tagging nucleic acid molecules. In specific embodiments, the overhangs can be produced by chemical cleavage of phosphorothioate-modified nucleic acid molecules. The invention further relates to the amplification of the ligated product, and using the resultant amplicon for assembly of multiple nucleic acid fragments.