Exploring the DNA binding interactions of the Kaposi's sarcoma-associated herpesvirus lytic switch protein by selective amplification of bound sequences in vitro.

ABSTRACT: The lytic switch protein RTA of Kaposi's sarcoma-associated herpesvirus (KSHV) can be targeted to DNA by either direct sequence-specific recognition or via protein-protein interactions with host transcription factors. We have searched for sequences capable of direct RTA binding by screening synthetic oligonucleotide pools and KSHV genomic libraries for RTA-interacting elements, using repeated cycles of in vitro binding followed by amplification of the bound sequences. Multiple low-affinity sequences were recovered from the random pools, with generation of only a weak consensus sequence. The genomic library, by contrast, yielded many biologically relevant fragments, most of which could be shown to interact with RTA in vitro and some of which likely play important regulatory roles in vivo. S

SUBMITTER: Ziegelbauer J 

PROVIDER: S-EPMC1395432 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature