Understanding protein-DNA complexes is one of the major challenges in structural biology ( 01PROG83 and 01METH343 ).

NMR Studies

It can be helpful to have the free protein and/or DNA structures before the assignment process of the complex is started. In principle, only the resonance frequencies of the interface will shift.

To form the complex, the protein is usually added to the DNA. The formation of the complex can be monitored by following the shifts of the imino protons of the DNA. Salt concentration must be as low as possible.

The DNA is usually unlabeled and the protein is 15N and/or 13C-labeled. This allows the application of the so-called multidimensional edited/filtered NMR experiments.

Some examples:

17kDa Antennapedia homeodomain / 14mer DNA complex (93JMB1084-234, 93JMB1070-234, 98JB25-12)

Three-amino-terminal zinc fingers of TFIIIA / 15 base pairs physiological DNA target (98JB51-12).

Transcription factor GATA-1 (93SCI438-261).

lac repressor headpiece (93JMB446-234).

trp repressor (94JMB592-238).

DNA binding domain of the protooncogene c-myb (94CELL639-79).

mal sex determining factor SRY (95CELL705-81).

architectural factor LEF-1 (95NAT791-376).

chromatin remodeling factor GAGA (97NAT122-4).

transcriptional coactivator HMG-I(Y) (97NAT657-4).

Assignment of intermolecular NOEs in large protein-DNA complexes remains difficult to obtain due to line broadening and overlapping. Recently, the use of doubly-labeled DNA and protein has been succesfully used to study a Protein-DNA complex ( 99JACS3547 )

DNA_binding domain of the Dead ringer protein (Gly262-Gly398) and its DNA binding site (26 kDa complex) ( 01JB231 )

Labeled Lac Operator-Lac Repressor complex ( 94MRC605 )

Two DNA-binding domains with Abp1 protein using dipolar couplings and diffusion anisotropiy restraints ( 02JB333-22 )