Table 3. Protocol for nucleic acid‒target simulations.

Process	Time interval (ns)
Structure minimization	2500 NAMD steps
DNA side chains, water molecules and ions released; rest fixed	0.1
DNA backbone except phosphorous atoms released but with some artificial bonds between complementary nucleobases; protein harmonic restrained	0.5
Harmonic constraints applied to DNA with some artificial bonds between complementary nucleobases	2
All atoms released	5
NVT ensemble, production simulation	100

The simulations were carried out in the present study for each of the DNA and LNA/DNA sequences summarized in Table 1 and antibody ED-10.