In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS [1].

During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such 'backtracking' involved extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS [2]. TFIIS is a protein of about 300 amino acids. It contains two conserved regions, a central domain which is required for Pol II binding and a C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a 'zinc ribbon' (see <PDB:1TFI>) [3] characterized by a three-stranded antiparallel β-sheet and two β-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a β hairpin protrudes from the zinc finger and complements the pol II active site [4].

The TFIIS zinc finger is also found in the following proteins:

• Eukaryotic and archebacterial RNA polymerase subunits of the 15 Kd / M family (see <PDOC00790>).
• Vaccinia virus RNA polymerase 30 Kd subunit (rpo30) [5].
• African swine fever virus protein I243L [6].

The pattern we developed starts at the first cysteine of the zinc finger and ends at the last one. We also developed a profile which spans the whole structural domain.