  Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase
pair resolution) as an input to our model, we introduce cross-links between
monomers in a bead-spring model of a ring polymer at very specific points along
the chain. By suitable Monte Carlo Simulations, we show that the presence of
these cross-links leads to a particular architecture and organization of the
chain at large (micron) length scales of the DNA. We also investigate the
structure of a ring polymer with an equal number of cross-links at random
positions along the chain. We find that though the polymer does get organized
at the large length scales, the nature of the organization is quite different
from the organization observed with cross-links at specific biologically
determined positions. We used the contact map of $E. Coli$ bacteria which has
around $4.6$ million base pairs in a single circular chromosome. In our
coarse-grained flexible ring polymer model, we used $4642$ monomer beads and
observed that around $80$ cross-links are enough to induce the large-scale
organization of the molecule accounting for statistical fluctuations caused by
thermal energy. The length of a DNA chain of an even simple bacterial cell such
as $E. Coli$ is much longer than typical proteins, hence we avoided methods
used to tackle protein folding problems. We define new suitable quantities to
identify large scale structure of a polymer chain with a few cross-links.
