  For short DNA molecules in crowded environments, we evaluate macroscopic
parameters such as the average end-to-end distance and the twist conformation
by tuning the strength of the site specific confinement driven by the crowders.
The ds-DNA is modeled by a mesoscopic Hamiltonian which accounts for the three
dimensional helical structure and incorporates fluctuational effects at the
level of the base pair. The computational method assumes that the base pair
fluctuations are temperature dependent trajectories whose amplitudes can be
spatially modulated according to the crowders distribution. We show that the
molecule elongation, as measured by the end-to-end distance varies
non-monotonically with the strength of the confinement. Furthermore it is found
that, if the crowders mostly confine the DNA mid-chain, the helix over-twists
and its end-to-end distance grows in the strong confinement regime. Instead, if
the crowders mostly pin one chain end, the helix untwists while the molecule
stretches for large confinement strengths. Thus, our results put forward a
peculiar relation between stretching and twisting which significantly depends
on the crowders profile. The method could be applied to disegn specific DNA
shapes by controlling the environment which constrains the molecule.
