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. Author manuscript; available in PMC: 2020 Apr 15.
Published in final edited form as: Methods. 2019 Feb 22;159-160:29–34. doi: 10.1016/j.ymeth.2019.02.019

Figure 2. Transcription assay results using mini-scaffold or full-bubble scaffold.

Figure 2.

(A) An example of transcription assay is performed by using mini-scaffold harboring non-damaged G (upper panel) or 8-oxoguanine (8OG, bottom panel) in its template strand DNA. Reaction is initiated by adding 50 μM of NTPs, ATP, GTP, CTP, or UTP. Time points are: 0 (without NTPs), 10 sec, 3 min, 30 min, and 2 hr. Note that 8OG can be bypassed by adding A or C, producing full-length transcripts after 3 min, as described in previous paper [13]. (B) Example of full-bubble transcription assay, using the same scaffold in our previous paper [24]. Time points are: 0, 1, 3, 10, 30, and 60 min, respectively. In this experiment, cyclobutane pyrimidine dimer (CPD) is tested to see whether presence of Rad26 can rescue arrested elongation complex (EC). As previously reported [24], Rad26 fails to rescue CPD induced EC arrest. Gel image was processed by Image Lab (Bio-rad). DNA and RNA oligos used in this study are summarized in Table S1.