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In the guanine functionalization reaction, single-wall carbon nanotubes (SWCNTs) coated with physisorbed single-stranded DNA become covalently bonded to guanine bases in the DNA. The resulting perturbations to SWCNT electronic and optical properties depend on the spacings between the sites of covalent bonding. To model those spacings, we have used advanced molecular dynamics simulations (replica exchange with solute tempering) to study adsorbed conformations of (GT)10 ssDNA strands and the corresponding distributions of guanine locations prior to reaction. The simulations explored the effects of interstrand interactions, nanotube end effects, solution ionic strength, DNA/SWCNT mass ratio, and SWCNT diameter on conformations and guanine spacings. We analyzed the impacts of such simulation conditions on the spatial distribution of guanine nucleobases along the nanotube axis. Irregularities in those spacings are suggested to cause inhomogeneities in exciton energy landscapes and be a source of spectral broadening in SWCNTs modified by guanine functionalization.