Oligonucleotide synthesis and biophysical analyses

Oligonucleotides were purchased from Integrated DNA Technologies (Coralville, IA, USA), [γ-³²P]-ATP (6000 Ci/mmol) was purchased from Perkin-Elmer, uracil DNA glycosylase (UDG) and ϕ29 DNA polymerase were from New England Biolabs (Ipswich, MA, USA), C-18 Sep-Pak cartridges were purchased from Waters (Milford, MA, USA), and BS Poly-prep columns were obtained from BioRad (Hercules, CA, USA). Acrylamide/bis-acrylamide 19:1 (40% solution, electrophoresis grade) was purchased from Fisher Scientific (Waltham, MA, USA), spermine and all other chemical reagents were purchased from Sigma-Aldrich (St. Louis, MO, USA). A mixture of the four 2’-deoxynucleoside triphosphates (dNTPs) was purchased from Promega (Madison, WI, USA). Iron–EDTA–H₂O₂ footprinting (51 (link)–53 (link)), QTOF-MS (53 (link)–55 (link)), LC–MS/MS (53 (link),55 (link)) and phi-29 (ϕ29) DNA polymerase primer extension reactions (56 (link)) were conducted as described in published procedures, with minor modifications. Detailed experimental protocols for these experiments are provided in the Supplementary Data.