Self-Assemblies, Folding, and Properties of Perylene Monomers, Oligomers, and Polymers - Molecular Self-Assembly: Advances and Applications - page 145

increasingly red coloration. For the stacked oligomers, the red shift
of the emission maxima could come from a combination of localized
Franck

−

Condon emission or delocalized

π

-stack emission, both

shifting the emission spectra toward red.

Folding of Hybrid DNA − Perylene Polymers:
Gene Sensors

5.4

5.4.1 Thermophilic Foldamers

It is widely accepted that properly folded biopolymers will lose
their functions owing to unfolding at high temperatures. However,
proteins from thermophilic and hyperthermophilic microorganisms
have shown extraordinary thermal stability by properly optimizing
the delicate balance of weak molecular attractions. The critical issue,
namely which of these interactions establish the thermostability of
proteins, is still not clear [19]. Among the electrostatic interactions,
hydrogen bonding, and hydrophobic effects, there appears to be
no common determinant of thermostability [20 24]. Nonetheless,

hydrophobic effects in the folding of alternating hydrophobic
π

−

-conjugated chromophores and hydrophilic single-strand
deoxyribonucleic acid (ssDNA) strengthen as the temperature
increases, similar to the inverse-temperature transitions observed
in elastin [25 27]. Thus, better folding, albeit counter intuitively,

was observed at high temperatures.
DNA has been attached to nanoparticles [28], proteins [29],
and fluorescent dyes [30] as probes and nanowires. Using efficient
(

−

∼

100% yield) coupling, we have incorporated multiple optically
active chromophores into the backbone of DNA for folding studies.
The general strategy is to insert

π

-conjugated structures into DNA
using asymmetric building blocks with one end activated and the
other end protected. This coupling chemistry is compatible with
automated DNA syntheses. Using this strategy, we have constructed
foldable sequences of 5

′

-DNA-(-TEG-PDI-TEG-ssDNA) -TEG-PDI-

n

′

TEG-DNA-3 , where TEG is tetraethylene glycol. The foldamers

κ ′

2B , 3B , 4B , and 5B are based on mutated NF- B binding site (5 -

A-GTt-GAG- T G T - T CT-TtC-CCA-GGC-3

′

; Fig. 5.7a displays 3B for

n = 2). Foldamers 2C , 3C , 4C , and 5C are based on modified AP1

binding site (5

′

-ATC-CGG-AGT-CAG-CCG-GAT-3

′

; Fig. 5.7b). Using gel