# Leptomonas colosoma spliced leader RNA - as reported
by LeCuyer and Crothers, Biochemistry 1993,32,5301-5311.
In this paper it is proposed that there are two stable
secondary structures, referred to as form1 and form2,
between which transitions occur.  It is speculated that
that the transition form1->form2 occurs by first nucleating
a pseudoknot according to the potential tertiary interactions
shown in "form1_tertiary".  The structure "form1_pseudoknot"
shows this pseudoknot.  One is to imagine that the yellow
stem of this pseudoknot grows at the expense of the red one
to eventually yield the structure of form2.  Other researchers
(private communication), have suggested a pathway for the
opposite transition form2->form1 by the nucleation of a
pseudoknot according to the potential tertiary interactions
shown in "form2_tertiary".  The structure "form2_pseudoknot"
shows this pseudoknot.

The last basepair list, called "myform_tertiary" (proposed by HMM)
is that of a structure which contains the hairpin loops of
both form1 and form2 and shows the potential tertiary interactions
that would give simultaneous nucleation for going in either
direction of form1 or form2 while maintaining the nucleation
for the reverse transition.  A refined 3D structure for
this basepair list (with stacking of the two hairpin stems) 
is shown in the PDB files "myform.amber_pdb" and "myform.biosym_pdb"
of the Sample/PDBfiles/amber and Sample/PDBfiles/biosym directories,
respectively.


> spliced_leader
AACUAAAACA AUUUUUGAAG AACAGUUUCU GUACUUCAUU GGUAUGUAGA GACUUC
$ form1
2	43
3	42
4	41
5	40
6	39
16	38
17	37
18	36
19	35
20	34
22	32
23	31
24	30
25	29
$ form1_tertiary
2	43
3	42
4	41
5	40
6	39
16	38
17	37
18	36
19	35
20	34
22	32
23	31
24	30
25	29

-26	-52
-27	-51
-28	-50
$ form1_pseudoknot
2	43
3	42
4	41
5	40
6	39
16	38
17	37
18	36
19	35
20	34
22	32
23	31
24	30
25	29

26	52
27	51
28	50
$ form2
24	54
25	53
26	52
27	51
28	50
29	49
30	48

31	45
32	44
33	43
34	42
35	41
$ form2_tertiary
24	54
25	53
26	52
27	51
28	50
29	49
30	48

31	45
32	44
33	43
34	42
35	41

-16	-38
-17	-37
-18	-36
$ form2_pseudoknot
24	54
25	53
26	52
27	51
28	50
29	49
30	48

31	45
32	44
33	43
34	42
35	41

16	38
17	37
18	36
$ myform_tertiary
23	31
24	30
25	29

32	44
33	43
34	42

-16	-38
-17 	-37
-18	-36

-19	-35
-20	-34
-22	-32

-2	-43
-3	-42
-4	-41
-5	-40
-6	-39

-24	-54
-25	-53
-26	-52
-27	-51
-28	-50

-29	-49
-30	-48
-31	-45


