Title Design and Synthesis of DNA Binding Organofullerene
Adviser Eiichi Nakamura
Thesis Committee Eiichi Nakamura (Professor, The University
of Tokyo); Koichi Narasaka (Professor, The University of Tokyo); Kazuo
Tachibana (Professor, The University of Tokyo); Yoshio Umezawa (Professor,
The University of Tokyo); Kaoru Yamanouchi (Professor, The University
My thesis entitled "Design and Synthesis of DNA Binding
Organofullerene" describes design and synthesis of functional
DNA binding molecules with fullerene scaffold. The binding to and
recognition of DNA by synthetic organic compounds is important and
challenging subjects, and the present study shed the light on the
new synthetic route to DNA binding molecules. Development of symmetry-defined
multiple addition reactions to fullerene has led to the rational
design of functional DNA binding molecule.
Fullerene was discovered as the third carbon allotrope
by a group led by three scientists, Kroto, Curl and Smalley in 1985.
After the development of an arc vaporization method for the production
of  and fullerenes in a large quantity, application of a wide
range of reactions revealed its basic chemical reactivities and led
to the synthesis of "organo-functionalized" fullerenes (organofullerenes).
This work in my thesis started when such studies on the organofunctionalization
of fullerene were started by chemists in the world. I started with
the fundamental studies on the reactivities of fullerene toward vinylcarbene
species and silyl ketene acetals. The work on the thermal and photochemical
reactions with fullerene gave an important information of inherent
reactivity of fullerenes. With such fundamental method in hand, I
started to investigate a new route to the structurally unique organofullerenes.
Controlled multiple addition reactions to spherical
fullerene can provide a useful scaffold for construction of structurally
unique functional molecules. From synthetic point of view, challenging
problems of regio- and stereochemical issue are inherent to the multiple
addition reactions to fullerene, which possesses thirty equivalent
double bonds on its spherical surface. With the aim of synthesizing
DNA binding fullerene, two symmetry-defined multiple functionalizations
of fullerene have been developed, and synthesis of structurally
unique organofullerenes has been achieved. At the time this work was
started, there were no preceding work on the multiple addition reaction
to fullerene, and I have decided to develop multiple addition
reactions that can be utilized for the rational design of organofullerenes
with a wide range of structures.
In my thesis work, by utilizing inherent reactivities
of fullerene, a cage compound with fullerene end caps has been
synthesized. Four-fold photochemical addition reaction was utilized
for the construction of cage compound with fullerene end caps. The
new cage compound showed hypochromic effect that is induced by dipolar
coupling between fullerene chromophores. This is the first interesting
example of physical communication between far-separated fullerenes,
which may lead to the development of optical devices based on the
fullerenes. The presented route to the cage compounds is also applicable
to the other reagents and varieties of the cage compounds may be synthesized.
The tether-directed method in double addition to fullerene,
on the other hand, provided a symmetry-defined functionalization route
to a series of organofullerenes (two-handed fullerenes) with spatially
defined orientation of organic residues. I synthesized various tris-annulating
reagents that enabled double-cycloaddition reaction to fullerene,
and the thus obtained double functionalized fullerenes led to the
basic design of "two-handed fullerenes". In my work, systematic computational
studies also led to the development of a "double differential" procedure,
which is useful for estimating the directing effects of the tether.
The regio- and stereo-controlled formation of C2 chiral derivatives
opened a new possibility for the asymmetric synthesis of optically
active chiral polyfunctionalized fullerenes.
After development of multiple addition reactions to
fullerene, I started investigating the synthesis and binding properties
of DNA binding fullerene. Interaction of organofullerenes with DNA
continues to attract the interest of chemists since the discovery
that a photo-excited water-soluble fullerene oxidatively cuts DNA
duplex. In the following years, a number of studies on structural
variations of the reagent, the mechanism of the photo cleavage, and
the applications to photodynamic therapy have been reported. Further
detailed studies on the fullerene-DNA interactions have been required
for the development of fullerene-based functional DNA binding molecules.
Tailor-made organofullerene was designed based on the
tether-directed double cycloaddition reaction and synthesis of DNA
binding molecule with fullerene has been carried out in this study.
Two-handed fullerene tetramine as well as the reference fullerenes
have been synthesized for the study of DNA binding abilities. Structure/activity
relationship of the DNA binding properties of organofullerenes showed
that the structural synergy of hydrophobic core and hydrophilic residues
plays important roles in binding. The new tight binding fullerene
was found to be inert in the photo cleavage, which suggest that the
interactions of fullerenes with nucleobases changes the energy transfer
path after photo-excitation. Detailed study on the photo-induced damage
on the DNA suggested that covalent bond formation may occur with the
DNA binding fullerenes. This observation calls recently proposed mechanisms
of photo cleavage in question, and further detailed mechanistic study
on this subject is awaited.
The DNA-binding fullerene has also been found to induce
formation of higher order structure of DNA. Microscopic studies with
AFM on the DNA/fullerene complex revealed that tight binding as well
as the hydrophobic nature of fullerene led to highly efficient condensation
of DNA. This study also showed that the size and morphology of the
condensed materials is dependent on the fullerene to DNA ratio. Recent
studies on the gene transfer technology suggested that the size and
morphology of DNA condensates plays an important role in the gene
transfer, which suggest the development of transfection agents based
on the DNA binding fullerenes. Extension of the thesis work now led
to the development of organofullerene as a new artificial vector for
gene transfer. The fullerene-based design does not rely on lipid-mimicry
generally used for "lipofection", but on the strong hydrophobicity
of the fullerene core that is not "lipo"philic. Success of this new
gene transfer vector will lead to the development of future gene transfer
reagent that will be metabolized to inorganic soot.
In this thesis was described the development of new
synthetic methods for new organofullerenes and the design and synthesis
of functional DNA binding fullerenes. Through this study, I, as a
young chemist, learned that powerful synthetic methods and thus synthesized
new organic architectures are the new source of imagination.