Biology Reference
In-Depth Information
Folding of perylene units is signaled by a diagnostic optical
absorption change because both covalently bound perylene
cyclophanes [31] and folded oligomers (see Section 5.3) have an
inverse
intensity distributions among their vibronic states,
r
obs
0
0
0
1
= A
/A
= 0.7, whereas free perylene molecules have
normal
0
0
0
1
Franck
Condon progressions with
r
= A
/A
1.6. Hence, the
obs
absorption ratio of 0
1 transition can be used to quantify
the degree of folding in the DNA
0 to 0
perylene polymers.
κ
κ
B foldamers
form only loosely folded structures owing to steric limitations
imposed by their bulky DNA bases, as indicated by the diagnostic
optical absorption ratio of A
At room temperature, both NF-
B and mutated NF-
0
0
0
1
/A
= 1.10
1.15 for perylene
dimer (
) (Fig. 5.8).
This intensity ratio is intermediate between free monomers (
2B
), trimer (
3B
), tetramer (
4B
) and pentamer (
5B
1A
)
and closely packed perylene dimers (
). Upon heating, however, all
the foldable polymers become more ordered (Fig. 5.7a) as indicated
by the change in the absorption band intensity ratio, A
2B
0
0
0
1
/A
=
0.77
0.87 (Fig. 5.8). This abnormal behavior contrasts with thermal
denaturation in most proteins, but is supported by theoretical
calculations [25] and experimental observations [26,27] in the
hydrophobic collapse of elastin. Moreover, this inverse-temperature
behavior of folding is largely reversible as the samples were cycled
between 20 and 90
°
C up to 10 heating
cooling iterations (Fig. 5.9).
The DNA
perylene polymers clearly divulge that, unlike most other
molecular attractions, the strength of hydrophobic forces is more
pronounced at high temperatures.
-3
80x10
90 o C
0.14
0.12
0.12
0.10
0.15
60
0.10
0.08
0.08
0.10
40
0.06
0.06
20 o C
0.04
0.05
0.04
20
0.02
0.02
0.00
0.00
0.00
0
p entamer
t etramer
trime r
dime r
-0.02
-0.02
400
500
600
700
400
600
400 00
400 00
400
500
600
700
400 00
400 00
400
500
600
700
Wavelength (nm)
Figure 5.8
Electronic absorption of chromophoric dimer (
2B
), trimer
(
3B
), tetramer (
4B
), and pentamer (
5B
) linked by ssDNA
derived from mutated NF-
κ
B binding site at 20
°
C (blue) and
90
°
C (red). Note the intensity reversal between 0
0 and
0
1 transitions.
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