Synthetic oligonucleotides

All candidate ligands and synthetic oligonucleotides were purchased from Sigma-Aldrich. [γ-³²P] ATP (specific activity: 6,000 Ci/mmol) was purchased from PerkinElmer.

3-Aminopropyltriethoxysilane (APTS, 98%), glutaric acid (GA), 1-(2-chloroethyl)piperidine hydrochloride, 2,4-dihydroxybenzaldehyde and synthetic oligonucleotides 100 μM (Table 1) were supplied by Sigma-Aldrich. Dimethyl sulfoxide, nickel(II) acetate tetrahydrate [Ni(OAc)₂•4H₂O], N,N′-dimethylformamide (DMF), ethyl acetate, chloroform and n-hexane were obtained from ChemAR. 1,2-diamino benzene, diethyl ether and potassium carbonate were purchased from Merck. Tetraethyl orthosilicate (TEOS, 98%) and Tween 20 surfactant were procured from Fluka. Sodium fluoride (NaF, 98.5%) and methanol (99.8%) were obtained from R & M Chemicals and JT Baker, respectively. Stock solution of DNA probe was prepared in 0.05 M K-phosphate buffer (pH 7.0), whilst complementary DNA (cDNA) solution was prepared in 0.05 M K-phosphate buffer containing 0.1 M KCl at pH 7.0. Milli-Q water was used for all aqueous solutions preparation.

Holliday junctions with mobile (HJ-X26)^{55 (link)} and immobile (HJ-Y2Ap, modified from Y2A^{17 (link)}) cores were prepared by annealing synthetic oligonucleotides (Sigma Aldrich) provided in Supplementary information Table 3, following a previously published protocol^{56 (link)}. In brief, the oligonucleotides were purified by native 6% PAGE (TAE buffer) and mixed in appropriate ratios in annealing buffer (buffer 4) (25 mM NaCl, 10 mM Tris-HCl pH 8). The annealing reaction was performed in a 0.2 ml tube and covered with a thin layer of mineral oil to prevent water evaporation. The mixture was heated to 95 °C for 10 min, and the temperature was subsequently decrease in 10 °C temperature steps every 10 min. To obtain homogenous four-way Holliday junction preparations, the annealing reaction was supplemented with a DNA sample buffer (New England Biolabs) and separated by native 6% PAGE (TAE buffer). Bands corresponding to four-way Holliday junctions were cut out from the gel and eluted by incubation in 5 mM Tris-HCl pH 8. For DNA-binding assays (electro mobility shift assay (EMSA)), one oligonucleotide strand was labelled with radioactive ³²P (3,000 Ci mmol⁻¹) at the 5′ end prior to annealing. For the branch migration activity assays, one oligonucleotide strand was fluorescently labelled with ATTO 647N.

Synthetic oligonucleotides used as primers in polymerase chain reactions (PCR) and sequencing reactions were purchased from Sigma-Aldrich (St. Louis, MO, USA), while assays for ddPCR, containing differently labeled normal and mutated probes for each mutation under investigation, were purchased from Thermo Fisher Scientific and Bio-Rad.

Stock solutions (100 mM) of dNTPs were obtained from GE Healthcare. [γ−³²P] ATP (10 mCi/mL; 3000 Ci/mmol) was provided by Perkin Elmer. Synthetic oligonucleotides were obtained from Sigma and Integrated DNA Technologies. Nevirapine, efavirenz, etravirine and Rilpivirine were obtained from the AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH. Rilpivirine and etravirine were supplied to the Program by Tibotec Pharmaceuticals, Inc. Doravirine, raltegravir (potassium salt) and dolutegravir were purchased from MedChem Express LLC (Monmouth Junction, NJ, USA).

Biochemicals and media were purchased from Thermo Fisher Scientific (EDTA), VWR (glycerol, NaPi, NaCl), BD (peptone, yeast extract), Euromedex (isopropyl β-D-1-thiogalactopyranoside; IPTG), and Sigma-Aldrich (imidazole). The enzymes for genetic manipulation were purchased from Thermo Fisher Scientific and NADH peroxidase from NZYTech. DNA isolation and manipulation were performed using standard methods^{34 (link),35 (link)}. Isolation of DNA fragments from agarose gel and purification of PCR products were carried out using the NucleoSpin Extract II kit (Macherey Nagel, Hoerdt, France). Standard PCR reactions were performed with Phusion high-fidelity DNA polymerase (Thermo Fisher Scientific); reactions were carried out on a Mastercycler Pro (Eppendorf). Synthetic oligonucleotides were purchased from Sigma-Aldrich, and DNA sequencing was carried out by GATC Biotech (Mulhouse, France). All organic solvents used were HPLC grade and purchased from Sigma-Aldrich.

Synthetic oligonucleotides were purchased from Sigma-Aldrich and diluted in water. Oligonucleotides were heated at 85 °C for 3 min in 1 mM sodium phosphate buffer pH 7 or 1 mM sodium phosphate pH 7, 10 mM potassium phosphate pH 7 and 90 mM KCl buffer and slowly cooled down to room temperature. CD measurements were carried out with a Jasco 815 (Jasco International Co., Ltd.,Tokyo, Japan) dichrograph in 1 cm path-length microcells at 23 °C. A set of four scans with a data pitch of 0.5 nm and 200 nm/min scan speed was averaged for each sample. CD signal is expressed as the difference in molar absorption, Δε, of the left- and right-handed circularly polarized light [31 (link)].