Additional File 1:

DNA template constructs used in this study. The control template (top) contains annotations for the different oligonucleotides (Additional File 4) that make up the SMRTbell DNA template.

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Additional File 2:

Read termination induced by thymine glycol. The first instance of thymine glycol in the DNA template at which sequencing reads end is highlighted with a black bar and underlined sequence label.

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Additional File 3:

Animation of the DNA polymerase catalytic cycle during SMRT sequencing. The movie shows the binding of a phospholinked nucleotide, incorporation, and release of the pyrophosphate-linker-fluorophore reaction product. A hypothetical damaged DNA base is highlighted in red, and is moved into the active site following the phospholinked nucleotide incorporation and polymerase translocation. The animation highlights the close contact of the polymerase over an extended region with the nucleic acid: the incoming DNA template (positions -3 to zero) and nascent double-stranded DNA (positions +1 to approximately +7). The polymerization dynamics can be altered by the presence of DNA base modifications throughout this region. The animation is based on an in-house crystal structure and pdb structure 2PZS, followed by a brief energy minimization in PyMOL. The dye and linker are modeled solely for indicating their structures and do not reflect their real conformations and positions.

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Additional File 4:

Oligonucleotides and primers used to generate SMRTbell DNA templates. All sequences are listed 5' to 3'. All oligonucleotides contain 5' phosphate groups. The primer binding site in the "Hairpin-Right" sequence is underlined.

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