                  STEM and REGION STACKING

    To describe the concept of stem stacking it is useful to
first define some terminology. Thus, by a 'base-pair region'
or simply 'region' is meant a set of contiguous  base  pairs
configured  as  a  double  helix, and by a 'stem' is meant a
sequence of base-pair regions whose members are separated by
single strands in the form of 'inner loops' or bulges.  Four
numbers, b5,t5, b3 and t3 serve to delimit the extent  of  a
stem.  The numbers b5 and t5 stand for the bottom 5' and top
5' base numbers of  the  stem,  while  b3  and  t3  are  the
corresponding  3'  base  numbers.  Relative to the 5' end of
the parent RNA sequence  these  numbers  bear  the  relation
b5<t5<t3<b3.   Between  the  base positions t5 and t3, which
delimit the top of the stem, there may or  may  not  be  any
base  pairs.  In the absence of base pairs the corresponding
single strand is said to form a "hairpin loop" and the  stem
then  constitutes  the supporting part of the hairpin.  When
there are base pairs between positions t5 and t3,  the  stem
is  said  to  branch  or bifurcate into other stems which in
turn may or may not branch.  What would otherwise be  called
a hairpin is now called a "branching" or "bifurcation" loop.
A stem in the  branching  loop  of  a  stem  X  is  said  to
constitute a primary member of stem X's branching loop if it
is not a member of any other branching loop.  The  secondary
structure of an RNA molecule may thus be viewed as that of a
tree, the root of which is an imaginary stem of length  zero
whose loop is the entire sequence.

    With this kind of structuring and nomenclature in  mind,
the concept of stem-stacking is now easily described.  First
of all, stem-stacking is simply a means of forming a  larger
double  stranded  helix  out  of  two  stems by joining them
together in  a  coaxial  manner.  This  means  that  an  end
basepair of one of the stems is stacked with an end basepair
of the other stem. This may  occur  in  any  of  four  ways,
depending  on  which  ends are stacked.  Top-bottom stacking
occurs when a branching stem stacks with either the first or
last  primary  member  of its branching loop.  Bottom-bottom
stacking  occurs  when  successive  primary  members  of   a
branching   loop   are  stacked.   Top-top  stacking  occurs
relative to pseudoknots.  (Recall that two stems can form  a
pseudknot  when   a strand of each is part of the hairpin or
branching loop of the other stem in such a manner  that  one
stem  can be regarded as a coaxial extension of the other by
stacking their tops together).  It should also be noted that
pseudoknots  can  bottom stack with each other or with stems
that are not one of the two members of  a  pseudoknot,  thus
extending the variety of bottom stacking which can occur.

    The concept of region-stacking is also  straightforward.
It  applies  to  a  pair of successive regions from the same
stem, and is a means of increasing stacking  interaction  of
successive basepairs.

    It will be appreciated that stacking or not stacking can
markedly  affect  the  3D structure of an RNA molecule.  But
because there is no definitve experimental evidence of  when
the  stacking  of  two  stems or regions is to be favored or
disfavored, we leave it to the user to  invoke  his  or  her
criteria   in  an  interactive  manner  subject  to  certain
constraints relative to pseudoknots which reflect  a  policy
adopted  in  generating the 2D-template of a structure which
contains pseudoknots.  This policy is described in the  help
topic  PSEUDOKNOTS  and  rules out interactive 2D editing of
the stacking of two stems when either  is  one  of  the  two
stems forming a pseudoknot.  However, the degree of stacking
of two such stems can be edited at the 3D level as described
in  the  help topic PSEUDOKNOT STACKING/EDITING.  Top-bottom
and bottom-bottom stacking is otherwise unrestricted and  is
invoked  by  simply  pointing  to  the  two  stems  to be so
stacked.  A user-stacked stem pair can be unstacked.

    The stacking of a stem pair may sometimes result  in  an
overlapping  of  the  stacked  pair  with other stems of the
structure. Such a violation  can  someimes  be  relieved  by
deleting  one  or more of the pseudo basepairs introduced by
the compactification procedure.  The deletion is  done  with
the  built-in basepair editor.  Also available is a means of
rotating the stacked pair about a designated axis formed  by
a line joining two bases.

                          THE END


