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Title: Unusual Base Pairs in a Duplex
Description: Anatomy and physiology course
Description: Anatomy and physiology course
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Unusual Base Pairs in a Duplex
2
...
1), which are almost identical in their
NH2
N
N
N
O
N
HN
N
O
N
H2N
NH
N
N
N
N
O
NH2
(a)
O
(b)
N
NH2
N
N
H2N
O
O
N
HN
N
N
N
H
N
H2N
H
N
N
N
O
O
(c)
(d)
(e)
(f)
as
+
mismatched base pairs, in which transient tautomeric and anionic species
form Watson–Crick-type hydrogen bonds [2]
...
2
...
1) is one of the major non-Watson–Crick base pairs
that can be seen in several crystal structures of duplexes containing A⋅T base
pairs
...
1) [3]
...
A unique
characteristic is that the adenine nucleobases in the duplex have syn conformation
in their glycosidic bond angles
...
Formation of Hoogsteen-type hydrogen bonding is also possible between
guanine (G) and cytosine (C+), in which N3 atom is protonated
...
1) [5]
...
2
...
2
Purine–Pyrimidine Mismatches
Mismatched base pairs between purine and pyrimidine nucleobases are known as
transition mismatches
...
2)
...
1 and
2
...
G⋅U base pair is frequently observed in natural RNAs
...
Thus, there is no significant worsening of base stacking and
littler perturbation of the duplex conformation
...
2)
...
Sequence
XY
−𝚫H ∘
−𝚫S ∘
o
−𝚫G37
Tm
(kcal
(cal mol−1 )
(kcal
(∘ C at
mol−1 )
K−1 )
mol−1 )
10−4 M)
5′ CAAA X AAAG
CG
64
...
7
42
...
8
179
7
...
8
AT
68
...
2
40
...
6
168
6
...
8
GG
53
...
5
25
...
6
165
4
...
7
GA
52
...
2
23
...
7
137
4
...
3
AG
39
...
9
18
...
9
107
3
...
0
CT
53
...
3
19
...
0
151
3
...
5
(120)b)
(3
...
3)b)
(54
...
8)b)
(17)b)
AC
(9)b)
(35
...
9)b)
CC
(55
...
3)b)
(171)b)
(15)b)
5′ CAACTTGATATTAATA
+
Mismatch
3′ GTTGAACTATAATTAT
–
102
...
4
55
...
6
266
10
...
4
3′ GTTGAACTATAGTTAT
TG
95
...
5
50
...
4
286
9
...
3
3′ GTTGAATTATAATTAT
GT
91
...
4
47
...
9
265
8
...
6
3′ GTTGAACAATAATTAT
AA
92
...
26
46
...
...
9 −4
...
6 −1
...
5
1
...
1
C/G
−4
...
1 −0
...
7 −0
...
8
1
...
4 1
...
7 2
...
3
U/A
−2
...
3
0
...
1
A/U
−1
...
2
0
...
6
3′ GCX′ ZYX
GC 5′
Closing base pair
X/X′ G/C
0
...
5
[1
...
2 2
...
8
2
...
5 2
...
O
N
N
NH
N
N
N
(a)
N
N
N
N
NH
N
N
N
G (anti)
A (anti)
HN
N
NH
O
N
NH
N
N
N
N
A (anti)
O
H
N
N
N
G (syn)
G (anti)
H
N
N
(b)
G (syn)
N
O
N
N
N
N
A (syn)
N
O
O
N
N
G (anti)
N
N
H
N
N
O
G (anti)
G (syn)
pairs
...
(b)
H
+
N
N
N
N
N
O
NH2
N
N
NH
+
N
O
O
N
T (anti)
O
H2N
C+ (anti)
Parallel strand orientation
(c)
Title: Unusual Base Pairs in a Duplex
Description: Anatomy and physiology course
Description: Anatomy and physiology course