Structure and dynamics in molecular recognition: NMR studies of tfiiia zinc fingers 1-3 complexed to a 15 base pair dna recognition sequence

In order to understand the basis of sequence-specific recognition of DNA and RNA by zinc-finger proteins, we have undertaken an NMR study of a complex consisting of three zinc-finger domains from the Xf.nopus lac vis transcription factor IIIA. and a 15 basepair DNA oligonucleotide comprising its recognition sequence. We have used heteronuclear edited and filtered NMR experiments to obtain resonance assignments and structural restraints for the uniformly isotopically labeled (l '(', ' 'N ) protein, and unlabeled DNA. The resulting restraints have been used to calculate the solution structure of the complex. The /F1Ü/ DNA complex structure reveals interesting and unexpected insights into determinants of protein-DNA recognition. The complex differs in significant ways from published structures of zinc-finger protein/DNA complexes. Thr size of th1 DNA recognition site is larger, and the fingers do not pack identically. Finger-finger interactions and local sidechain motions appear to he important. These insights will have important consequences for understanding the nature of pi ot ein-D N'A specificity and stability, and for guiding efforts directed towards the dt novo design of proteins that bind to a predetermined ntjrlrotide sequence.