Spontaneous
pairing
of
homologous
DNA
sequences
–
a challenging subject in molecular biophysics,
often
referred to as
‘homology recognition’
–
ha
s
been observed
in
vitro
for several
DNA
system
s
a
. One of th
e
se
experiments
involved
liquid crystalline quasi
-
columnar phases formed by
a mixture of
two
kinds
of
oligo
mer
of double stranded
DNA
. Both
oligomer types
were
of
the same length and
identical
stoichiometric
base
-
pair
composition
,
but
the
base
-
pairs
followed a different order
. Phase segregation of
the two DNA types was observed
in the experiments
, wit
h the formation of
boundaries
between
domai
ns
rich in
molecules of one
type (order) of
base pair sequence
.
We formulate here
a
modified
‘
X
-
Y model
’
for phase segregation in
such
assemblies
, obtain approximate solutions of the model
,
compare analytical
results to
Monte Carlo
simulations, and rationalize past
experimental observations
. This study,
furthermore
,
reveals the factors
that affect the degree of segregat
ion
. Such information c
ould be
used
in
planning
new versions of
similar
segregation
experiments
, needed
for
deepen
i
ng
our understanding of
forces that might be involved
, e.g.,
in
gene
-
gene recognition
.