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Structures in RNA
2
...
The information transformed
into functional proteins as a sequence of amino acids is encoded on the primary
sequence of RNA
...
2
...
1
Basic Structure Distinctions of RNA
As described in Chapter 1, by comparing natural RNA to DNA, there are two
difference in their chemical structures
...
Regarding structure formation, 2′-hydroxyl group of
ribose is the most important factor that confers unique conformational features
compared to the DNA
...
G
G
a
U
G
C
(a)
lines
...
AA
U
U
U
U
C
A
A U
A U
U A
U A
U A
U A
U A
C
A U
U A
G C
U
A
U A
A A
5′
U
3′
(b)
Flipped out
bulge
(C)
Intercalated
bulge
(A)
AG
G
A
C G
G C
G C
A U
U G
G C
U G
C G
A A
U A
A A
G A
C A
A U
G A
U G
G C
G C
G C
5′
(a)
3′
(b)
3′
5′
(c) 5′
3′
3′
5′
(d) 5′
3′
C G
C G
G CG
A
A
A
G
G
A
G
A
G C
G G
U A
G CA
C
A
A
A
G
A
G C
G C
structures
...
[24a]
...
3′
5′
5′
3′
3′
(a)
5′
(b)
5′
3′
RNA
C
U
GG
G
U AU
G CC
U A
5′
3′
(a)
3′
G
U
U
5′
(b)
right
...
1
2
4
3
5′
3′
(a)
2
1
3
4
(b)
(a)
...
The last three nucleobases in the GNRA tetraloop are exposed to solvent and
can interact with minor groove of other helices by forming hydrogen bonds
...
In the GAAA/
11nt interaction, a receptor helix has an internal loop with conserved sequence
neighboring to consecutive two G⋅C base pairs
...
Neighboring internal loop region
forms characteristic stacked adenine nucleobases that support the interaction by
forming hydrogen bonds with second adenine of the tetraloop (Figure 2
...
Pseudoknot Crosslinking Distant Stem Regions
Pseudoknot is one of the intramolecular tertiary structure motifs characterized
by base pairing between the single-stranded regions in a hairpin such as loop
and bulge with a region outside of the hairpin (Figure 2
...
Based on this
definition, irrespective of the distance of nucleobases, it can be regarded as a
pseudoknot when a region that is in the middle of the region forming particular
stem contributes to the formation of another stem with another RNA region
...
Since
the biological functions of pseudoknot are well studied during translation, the
detailed structures and their contributions are described in Chapter 7
...
6
...
6