  Far from being a passive information store, the genome is a mechanically
dynamic and diverse system in which torsion and tension fluctuate and combine
to determine structure and help regulate gene expression. Much of this
mechanical perturbation is due to molecular machines such as topoisomerases
which must stretch and twist DNA as part of various functions including DNA
repair and replication. While the broad-scale mechanical response of nucleic
acids to tension and torsion is well characterized, detail at the single base
pair level is beyond the limits of even super-resolution imaging. Here, we
present a straightforward, flexible, and extensible umbrella-sampling protocol
to twist and stretch nucleic acids in silico using the popular biomolecular
simulation package Amber -- though the principles we describe are applicable
also to other packages such as GROMACS. We discuss how to set up the simulation
system, decide forcefields and solvation models, and equilibrate. We then
introduce the torsionally-constrained stretching protocol, and finally we
present some analysis techniques we have used to characterize structural motif
formation. Rather than define forces or fictional pseudoatoms, we instead
define a fixed translation of specified atoms between each umbrella sampling
step, which allows comparison with experiment without needing to estimate
applied forces by simply using the fractional end-to-end displacement as a
comparison metric. We hope that this easy to implement solution will be
valuable for interrogating optical and magnetic tweezers data on nucleic acids
at base pair resolution.
