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Title: Circular Dichroism of Non-canonical Nucleic Acids
Description: Anatomy and physiology course
Description: Anatomy and physiology course
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Circular Dichroism of
Non-canonical Nucleic
Acids
4
...
2
Circular Dichroism of Non-canonical Nucleic Acids
Circular dichroism (CD) is a phenomenon of the difference in absorption of left-or
right-circular polarization through a chiral compound
...
In the canonical structure of DNA
duplex, Watson–Crick base pairs planarly stack with twisted configuration
...
The canonical DNA duplex forms B-type in physiological condition
but forms different types of duplex such as A-, C-, and Z-types
...
Because these CD spectra are different, CD analysis has been
used for the determination of helical configuration of the DNA and RNA duplexes of
interest
...
Therefore, CD analysis is quite useful to analyze the structures of non-canonical
nucleic acids
...
1b) [1]
...
As the nucleotide can adopt either
type of glycosidic bond angle (GBA), an anti or a syn form, various configurations
of the backbone of the nucleic acids can be available (see Chapter 2)
...
Resulting orientation of loop direction
categorizes the G4 structures such as parallel, (3 + 1) mixed (hybrid), and
antiparallel topology (Figure 4
...
In the parallel topology
of G4s, all arrangements of GBA consist of anti forms
...
The other category of antiparallel G4 contains
quadruplexes with
O
O
N
N
H2N
NH2
N
O
O
O
O
O
A
N
anti
S
Parallel
A
A
A
syn
(3+1) Mixed
Anti-parallel
5′
5′
3′
S
S
A
S
S
A
A
S
A
A
S
A
A
S
S
A
A
S
A
A
A
A
A
A
A
A
A
A
A
A
A
A
S
A
S
5′
A
O
NH
Tail
A
N
Head
N
HN
3′
3′
(a)
(b)
Homopolarity stacking
Heteropolarity stacking
Head to tail
Head to head
Figure 4
...
(a) Images for the conformation of bases and stacking arrangement depending on the
topology of G4
...
S and A refer to the syn and anti conformation around the glycosyl bond
...
The arrows represent
the transition moments corresponding to the absorption band at around 250 nm
...
g
...
Because an anti form and a syn form have opposite polarity, the nearest-neighbor
G-tetrads connected with different GBA stack in a heteropolarity manner referred to
as head to head or tail to tail
...
2b)
...
The antiparallel type is
formed with heteropolarity stacking of G-tetrads (Figure 4
...
These different
polarities of stackings reflect the different effects on the exciton coupling of guanine
bases, resulting in different sig
Title: Circular Dichroism of Non-canonical Nucleic Acids
Description: Anatomy and physiology course
Description: Anatomy and physiology course