Final answer:
The best technique to identify the specific DNA sequence bound by a DNA-binding protein is the ChIP-Seq assay, which combines chromatin immunoprecipitation with high-throughput sequencing to map protein-DNA interactions across the genome.
Step-by-step explanation:
To define the identity of the specific DNA sequence to which a novel DNA-binding protein can bind, the best technique would be a ChIP-Seq assay. The ChIP-Seq assay (Chromatin Immunoprecipitation followed by Sequencing) enables researchers to isolate DNA sequences bound to a particular protein by immunoprecipitating the protein.
The isolated fragments are then subjected to high-throughput sequencing, which provides a readout of protein binding site occupancy across the entire genome. This method is highly sensitive and precise, offering a comprehensive profile of protein-DNA interactions.
Other techniques, such as Southern or northern blot hybridization, can also be used to identify specific sequences of interest. In these methods, DNA is fragmented, denatured, and then probed with a labeled oligonucleotide that is complementary to the sequence of interest. The DNA-probe hybrids can be visualized, indicating the position of the DNA sequence bound by the protein.
In summary, while the ChIP assay can also be used to determine DNA-protein interactions, it lacks the sequencing component that makes ChIP-Seq so powerful for the identification of specific DNA sequences bound by proteins.