A comparison of adsorption property of homopolynucleotides poly(rA) and poly(rI) on the single-walled carbon nanotubes (SWCNTs) showed that adsorption of the poor base stacked poly(rI) onto the nanotube in aqueous suspension is less effective than the high stacked poly(rA) the chain of which is of higher rigidity. Molecular dynamics modeling demonstrated that oligomer r(I)25 has an essential weaker binding energy to the carbon nanotube surface than r(A)25 (250 kcal/mol versus 350 kcal/mol). Structural analysis of oligomers on the nanotube surface revealed that the more ordered oligomer is of tendency to the helical conformation around the nanotube and this provides higher binding energy. On the contrary, a more flexible r(I)25 forms a stable loop kept away from the nanotube surface, which is strengthened by hypoxanthine H-bonding between bases located in different loop places. As well, in comparison with poly(rA), less effective adsorption of poly(rI) is confirmed with a weaker hypochromic effect of nanotubes covered with poly(rI) than with poly(rA), which originates from π-π-stacking of nitrogen bases with the nanotube surface.