Assessment and comparison of thermal stability of phosphorothioate-DNA, DNA, RNA, 2′-F RNA, and LNA in the context of Phi29 pRNA 3WJ

Thermal stability and stability against 50% serum of selected 3WJs. (A) Resistance to heat denaturation for homogeneous 3WJ_LNA. (B) Resistance to heat denaturation for hybrid 2/3 3WJ_LNA (For A and B, lane 1: monomer, ³²P-labeled 3WJ-c_LNA; lane 2: dimer, ³²P-labeled 3WJ-c_LNA + 3WJ-a_LNA; lane 3: ³²P-labeled 3WJ without heat denaturation; lanes 4–10: heat-denaturated 3WJ samples in the presence of increasing nonradiolabeled competitor up to 50-fold). (C) Resistance to 8 M urea denaturation for homogeneous LNA 3WJ and 2/3 LNA hybrid 3WJ (all samples were incubated with 8 M urea, lane 1: monomer, ³²P-labeled 3WJ-c_LNA; lane 2: dimer, ³²P-labeled 3WJ-c_LNA + 3WJ-a_LNA; lanes 3–6: 3WJ_LNA in the presence of increasing nonradiolabeled competitor up to 100-fold; lanes 7–10: 2/3 3WJ_LNA in the presence of increasing nonradiolabeled competitor up to 100-fold). (D) Stability of 3WJs in 50% serum (green: homogeneous 3WJ_LNA, 3WJ-a_LNA + 3WJ-b_LNA + 3WJ-c_LNA; blue: hybrid 2/3 3WJ_LNA, 3WJ-a_2′-F + 3WJ-b_LNA + 3WJ-c_LNA; red: hybrid 1/3 3WJ_LNA, 3WJ-a_2′-F + 3WJ-b_2′-F + 3WJ-c_LNA; black: homogeneous 3WJ_2′-F, 3WJ-a_2′-F + 3WJ-b_2′-F + 3WJ-c_2′-F).