Beruflich Dokumente
Kultur Dokumente
Secondary Structures
Institute for Mathematics and Its
Applications: RNA in Biology,
Bioengineering and Nanotechnology,
University of Minnesota
October 29 November 2, 2007
Asamoah Nkwanta, Morgan State University
Nkwanta@jewel.morgan.edu
This
Secondary
Tertiary
RNA Molecule
Ribonucleic acid (RNA) molecule: Three main
categories
CAGCAUCACAUCCGCGGGGUAAACGCU
Geometric Representation
Secondary
structure is a graph
defined on a set of n labeled points
(M.S. Waterman, 1978)
Biological
Combinatorial/Graph
Random
Theoretic
Walk
Other Representations
RNA Structure
3-D structure of
Haloarcula marismortui
5S ribosomal RNA in
large ribosomal subunit
RNA NUMBERS
1,1,1,2,4,8,17,37,82,185,423,978,
These
RNA Combinatorics
Recurrence Relation:
s 0 s1 s 2 1
n 1
s n 1 s n s j 1 s n j , n 2
j 1
The
N.J.A.
s z 1 z z 2 z 4 z 8 z 17 z 37 z L
2
s z 1 z z 2 2 z 3 4 z 4 8 z 5 17 z 6 37 z 7 L
Based
27
s z
1 z z 2 1 2z z 2 2z3 z 4
2z
s z 1 z z 2 2 z 3 4 z 4 8z 5 17 z 6 L 1,392, 251,012 z 27 L
1 nk
s n
k 1 n k k 1
s n ~
15 7 5
n
nk
3 5
1 n k n k 1
s n, k
k k 1 k 1
s 6,1 10 and s 6, 2 6
a b 2
a 1
k a,b
k 0
a b 4
a 2
K a,b
k 0
Random Walk
NSE*
No
2
4
17
0
1
0
0
0
0
0
0
0
0
0
0
2
3
6
1
3
6
0
1
4
0
0
1
0
0
0
0
0
0
13
28
13
30
10
24
5
15
1
6
0
1
0
1
2
0
0
1
0
0
0
0
0
0
0
0
0
2
4
3
6
3
6
1
4
0
1
0
0
13
13
10
17
28
30
24
15
1
1
1
0
0
0
m n 1,0 m n j , j
j 0
m n 1, k m n, k 1 m n j , k j
m n 1, k 0, k n 1
j 0
0
0
1 1
1 2 1
0
3
1
2 3
4 6
6
4
8 13 13 10
0
0
0
0
1
5
0
0
0
0
0
1
1
2
3
4
5
6
3
8
21
55
144
NSE**
1
2
4
8
1
2
4
9
0
1
3
7
0
0
1
4
0
0
0
1
0
0
0
0
17
20
17
11
37
45
41 29 16 6
Examples
Type
I:
ENNESNESSE
Type
II: NEEENSEEES
Source:
Main Theorem
Theorem:
Source:
Proof
i,
N, S
GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCU
GGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUU
GCCUUGAGUGCUUCAAGUAGUGUGUGCCCGUCUGUUGUGUG
ACUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUG
UGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAA
GCGAAAGGGAAACCAGAGGAGCUCUCUCGACGCAGGACUCG
GCUUGCUGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGA
CUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAA
GGAGAGAGAUGGGUGCGAGAGCGUCAGUAUUAAGCG
Color key:
SL2 yellow
SL3 - red
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