IDENTIFICATION OF 2 NOVEL ARGININE BINDING DNAS

RNA tertiary structure is known to play critical roles in RNA-protein recognition and RNA function, To examine how DNA tertiary structure mi ght relate to RNA structure, we performed in vitro selection experimen ts to identify single-stranded DNAs that specifically bind arginine, a nd compared the results with analogous experiments performed with RNA, In the case of RNA, a moth related to the arginine binding site in hu man immunodeficiency virus TAR RNA was commonly found, whereas in the case of DNA, two novel motifs and no TAR-like structures were found, O ne DNA motif, found in similar to 40% of the cloned sequences, forms a hairpin structure with a highly conserved 10 nucleotide loop, whereas the second moth is especially rich in G residues. Chemical interferen ce and mutagenesis experiments identified nucleotides in both moths th at form specific arginine binding sites, and dimethylsulfate footprint ing experiments identified single guanine residues in both that are pr otected from methylation in the presence of arginine, suggesting possi ble sites of arginine contact or conformational changes in the DNAs, C ircular dichroism experiments indicated that both DNAs undergo conform ational changes upon arginine binding and that the arginine guanidiniu m group alone is responsible for binding, A model for the G-rich motif is proposed in which mixed guanine and adenine quartets may form a no vel DNA structure, Arginine binding DNAs and RNAs should provide usefu l model systems for studying nucleic acid tertiary structure.