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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 signatures of CD spectra (Figure 4
...
The typical CD
spectrum of a parallel G4 topology shows a positive Cotton effect at around the

30

3

θ (104 deg cm–2 dmol–1)

θ (104 deg cm–2 dmol–1)

4

2
1
0
–1
–2
200

(a)

250

300

350

10
5

(b)

250

300

350

Wavelength (nm)
15

6

θ (104 deg cm–2 dmol–1)

θ (104 deg cm–2 dmol–1)

15

–5
200

8

(c)

20

0

Wavelength (nm)

4
2
0
–2
–4
200

25

250

300

Wavelength (nm)

10
5
0
–5
–10
200

350

(d)

250

300

350

Wavelength (nm)

Figure 4
...
Source: The data was obtained from Ref
...


wavelength of 260 nm and a negative Cotton effect at 240 nm (Figure 4
...
In
the case of a mixed G4 topology, negative and positive bands are assigned at
240 and 260 nm like the parallel G4 topology and an additional positive band at
290 nm (Figure 4
...
On the other hand, the antiparallel G4 topology indicates
positive and negative bands at 240 and 265 nm, respectively, and shows a
positive band at 295 nm (Figure 4
...

The structure of i-motif also shows a unique CD spectrum [5]
...
3d)
...
However, the
difference of the topology cannot be solved by CD analysis because the polarity
of the stacking of C⋅C+ base pair does not change
...
For example,
G4 formation, which requires metal ions such as K+ and Na+, can be detected
by the titration of metal cations
...
In addition to UV, the CD measurement with increasing
temperature provides information about the melting of the non-canonical
structures to analyze the thermal stability

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