The blockage of transcription elongation by RNA polymerase II (pol II) at a DNA 
damage site on the transcribed strand triggers a transcription-coupled DNA 
repair (TCR), which rapidly removes DNA damage on the transcribed strand of the 
expressed gene and allows the resumption of transcription. To analyze the effect 
of UV-induced DNA damage on transcription elongation, an in vitro transcription 
elongation system using pol II and oligo(dC)-tailed templates containing a 
cyclobutane pyrimidine dimer (CPD) or 6-4 photoproduct (6-4PP) at a specific 
site was employed. The results showed that pol II incorporated nucleotides 
opposite the CPD and 6-4PP and then stalled. Pol II formed a stable ternary 
complex consisting of pol II, the DNA damage template, and the nascent 
transcript. Furthermore, atomic force microscopy imaging revealed that pol II 
stalled at the damaged region. These findings may provide the basis for analysis 
of the initiation step of TCR.