Search for Clipped Motifs

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Search for Clipped Motifs Stacking
Classification Eli Hershkovits, Loren Dean
William Georgia Institute of Technology
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Rings local coordinate system
The ring coordinates are defined by Carter and
Pople method (Cramer, D. and Pople, A J. Am .
Chem. Soc. 1975, 97 1354 ). The center of the
ring is chosen to be the origin. The plane of the
ring is defined by two vectors R1 S rj
cos2p(j-1)/N R2 S rj sin2p(j-1)/N Where
rj is the position vector of each atom on the
ring (six for pyrimidines and five for imidazoles
rings). The numbering is taken to be clockwise
around the ring. The set of the three
orthogonal directions (X, Y and Z) is calculated
from these two planar vectors where X is the unit
vector in the R1 direction, Y is orthogonal to
the ring plan and Z is orthogonal to both and in
the ring plan.
3
Z2
Y2
Z1
Y1
r12
X2
X1
Local coordinate system for the ring
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Spherical coordinate system
Z
r
j
Y
q
X
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Euler angles
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Bases doublets with horizontal interaction
j
q
r
g
a
b
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Watson-Crick / Watson-Crick (1) Pyr/Pyr,
50ltrlt60, 26ltqlt37, 45ltjlt60, 70ltalt81, 61ltblt88,
15ltglt45 Watson-Crick / Watson-Crick (2) Pyr/Pyr,
54ltrlt65, 26ltqlt40, 34ltjlt55, 81ltalt99, 50ltblt88,
15ltglt100 Watson-Crick / Hoogsteen (3,4) Im/Pyr,
50ltrlt65, 30ltqlt40, 34ltjlt58, 21ltalt41, 60ltblt77,
15ltglt40 Or 50ltrlt65, 30ltqlt40, 34ltjlt58, 38ltalt68,
19ltblt25, 15ltglt40 Watson-Crick / Sugar Edge (5,6)
Pyr/Pyr, 50ltrlt70, 20ltqlt90, 34ltjlt58, 0ltalt40,
0ltblt40, 0ltglt40 Or 50ltrlt65, 20ltqlt90, 34ltjlt58,
0ltalt40, 50gtb, glt40 Hoogsteen / Hoogsteen (7,8)
Im/Im, 55ltrlt62, 45ltqlt52, 38ltjlt58, 80ltalt100,
22ltblt85, 5ltglt95 Hoogsteen / Sugar Edge (9,10)
Im/Pyr, 55ltrlt65, 45ltqlt52 or qlt10, 38ltjlt58,
75ltalt92, 60ltblt95, glt40 Sugar Edge / Sugar Edge
(11,12) Pyr/Pyr, 50ltrlt70, qlt15 or qgt94,
34ltjlt58,
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Bases doublets without horizontal interaction
j
r
q
a
b
g
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Major cluster of base stacking
1) Pyrimidine ring/Pyrimidine ring
intrastrand rlt43 q all, jgt80 or jlt20, alt30,
blt35, glt45 2) Imidazole ring/Pyrimidine ring
intrastrand AA,AG,GA,GG rlt38 q all, jlt15,
alt27, blt30, glt30 AU, GU, GC 38ltrlt47 qgt50,
19ltjlt36, 27ltalt36, blt30, glt30 AA, AG, GC rlt35
qgt50, jlt13, agt30, blt30, glt30 3) Imidazole ring
/Imidazole ring interstrand and
intrastrand rlt45, qlt50, jlt20, alt30, blt30,
glt30 4) Pyrimidine ring /Pyrimidine ring
interstrand AG, GA, AA, GG 30ltrlt42, qlt41, jlt25,
85ltalt97, 15ltblt42, 62ltglt90 Other
40ltrlt45, qlt43, jlt28, 85ltalt97, 65ltblt92, 10ltglt40
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Summary
1) We have shown that these doublet geometries
are distributed among clusters. We have
identified the clusters of the base pairs. 2) We
classified four major stacking geometries. 3)
The list of stacking clusters is still
incomplete. 4) Other geometries have not been
classified yet.