Biology Reference
In-Depth Information
1.1
1.0
0.9
0.8
1
2
3
4
5
6
7
8
9
10
11
Temperature Cycles
°
°
Figure 5.9
The cycles between 20
C (solid blue circles) and 90
C (solid
red squares) for chromophoric pentamer
, which has no
hybridization in the DNA loops, reveal oscillations. However,
the cycles between 20
5B
°
C (open blue circles) and 90
°
C (open
red squares) for chromophoric pentamer
, which has four
DNA stem loops, are nearly devoid of oscillations.
5C
The origin of the inverse-temperature behavior comes from
∆
H
0
±
an
endothermic
enthalpy
(Fig. 5.10a) of 2.72
0.09 kcal/mol,
4.44
±
0.09 kcal/mol, 4.78
±
0.09 kcal/mol, and 6.88
±
0.22 kcal/
mol for folding of perylene dimer (
2B
), trimer (
3B
), tetramer (
4B
),
and pentamer (
5B
), respectively. For an
endothermic
interaction, the
stability (
) of the folded polymers increases as the temperature
rises. The interactions between perylene
K
fold
π
-planes most likely
molecular interactions and
hydrophobic forces. To determine which of these two gives rise to
the inverse-temperature folding, we replaced the DNA sequences
with a phosphotriester to gain solubility in organic solvents
(
come from two contributions:
π−π
2A
−
5A
). In TCE, hydrophobic effects are eliminated. The difference
between the phenomena observed in water and TCE is attributed
to the hydrophobic effects. Consequently, we observed
exothermic
∆
H
0
−
±
processes (Fig. 5.10b) in TCE, with
=
3.01
0.06 kcal/mol,
−
6.62
±
0.43 kcal/mol,
−
5.09
±
0.09 kcal/mol, and
−
4.35
±
0.04 kcal/
mol for folding of perylene dimer (
2A
), trimer (
3A
), tetramer (
4A
),
and pentamer (
), respectively. Most intermolecular interactions,
including hydrogen bonds between DNA bases, are exothermic,
thereby generating instability at high temperatures. Consequently,
DNA loops cannot contribute to the inverse-temperature behavior.
Thus, it must be the hydrophobic effects that cause the thermophilic
folding—better and more organized folding at higher temperatures.
5A
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