Design of Functional Synthetic Systems
M.R. Ghadiri, M. Al-Sayah,
G. Ashkenasy, N. Ashkenasy, A. Chavochi, J. Fletcher, V. Haridas, W.S. Horne, Z.-Z. Huang, P. Imming,
L. Leman, A. Loutchnikov, L. Motiei, Y. Norikane, N. Rahe, S. Rahimipour, J. Shin, J. van Maarseveen,
D. Vodak, M. Yadav, R. Yamasaki
engaged in a multidisciplinary research effort to uncover new chemical and biochemical approaches
for the design of functional molecular, supramolecular, and complex self-organized systems.
Our endeavors span disciplines ranging from synthetic organic, bioorganic, and physical organic
chemistry to nanotechnology, biophysics, enzymology, and molecular biology. Current research
includes the design of synthetic peptide receptors and catalysts, antimicrobial self-assembling
peptide nanotubes, semisynthetic allosteric enzymes, self-replicating molecular systems
and emergent networks, single-molecule stochastic DNA sensing, and DNA-based logic gates and
Synthetic Peptide Catalysts
Rational design of biomolecular catalysts
based on first principles is fundamentally valuable for assessing and advancing basic understanding
of factors that contribute to the functioning of natural enzymes. Such endeavors also provide
blueprints for fabrication of novel synthetic catalysts with tailored functional properties.
In particular, we are interested in the aminoacyl transfer class of reactions because of their
prominent roles in a number of chemical and biological processes. Our aim is to mimic the sequential
aminoacyl transferase activity of nonribosomal peptide synthetases. Recently, we designed
a modular peptide construct capable of catalyzing stoichiometric and site-specific aminoacyl
transfer between noncovalently associated α-helical
peptides with catalytic efficiencies on the order of 105 in neutral aqueous solutions
|Fig. 1. Aminoacyl transferase reaction cycle of an engineered
peptide catalyst. The process consists of the aminoacyl loading, rapid intersubunit acyl transfer,
and aminoacyl reloading at the active site.
Antimicrobial Peptide Nanotubes
We showed that appropriately designed
cyclic peptide subunits can self-assemble through hydrogen bonddirected ring stacking
into open-ended hollow tubular structures (Fig. 2) that have marked antibacterial and antiviral
activities in vitro. The effectiveness of this novel supramolecular class of bioactive species
as selective antibacterial agents was recently highlighted by the high efficacy of one of these
antimicrobials against lethal methicillin-resistant Staphylococcus aureus infections
in mice. Currently, we are using rational design and selections from combinatorial cyclic peptide
libraries to discover cell-specific targeting sequences and anticancer compounds.
|Fig. 2. Self-assembling cyclic peptide nanotubes constitute a new class of a supramolecular approach to drug design. The illustration represents selective
insertion of cyclic D,L-α-peptide nanotubes into the cell membranes of pathogens.
Design of Signal Self-Amplifying DNA Sensors
We constructed a novel sequence-specific
DNA detection system (Fig. 3) based on rationally designed semisynthetic enzymes. The system
is composed of covalently associated inhibitor-DNA-enzyme modules that function via DNA hybridizationtriggered
allosteric enzyme activation and signal amplification through substrate turnover. The functional
capacity of the system is highlighted by the sequence-specific detection of approximately 10
fmol of DNA in less than 3 minutes under physiologic conditions. Our studies suggest that rationally
designed intrasterically regulated enzymes may be a promising new class of reagents for highly
sensitive, rapid 1-step detection of label-free DNA sequences that does not depend on polymerase
|Fig. 3. Schematic representation of an intrasterically inactivated
inhibitor-DNA-enzyme construct (left) and the DNA hybridizationtriggered enzyme activation
(right). The construct can be used to sense low concentrations of complementary DNA because of
its built-in capacity for signal amplification via rapid substrate turnover.
Stochastic Analysis of Single-Molecule DNA Rotaxanes
We have a growing interest in the study of matter at the single-molecule level. For these studies,
we use the transmembrane protein α-hemolysin
as a rapid and highly sensitive sensor element for stochastic analysis of the molecules lodged
or trapped inside the protein pore; the analysis relies on detecting the perturbations in conductance
levels produced in the ion channel in the native protein. Using this technique, we recently developed
an approach by which a single-stranded DNA molecule can be trapped in a specific configuration
inside an α-hemolysin
channel (Fig. 4), manipulated, and studied with high sensitivity at the single-molecule level.
We are extending this approach to the design of rapid single-molecule DNA sensing and sequencing.
|Fig. 4. Trapping a single DNA strand inside the pore of the transmembrane
protein α-hemolysin in the form of a rotaxane. The identity of the nucleobase residing in the channel can be sensed by
analyzing the interactions of the DNA with the protein channel residues near the constriction
Dna-based Logic Gates and Molecular Computation
Semiconductor-based logic gates provide
the fundamental computing devices of all microprocessors in use today. A logic gate functions
by providing a specific output that depends on the inputs it receives. Various logic gates (or logic
operations) can be coupled (wired) in a network to provide the higher order functions of a computer.
Similarly, molecular analogs of logic gates may provide miniaturized and highly efficient parallel
computing at the level of single molecules. However, to date, mimicking electronic computational
processes by using purely molecular systems has been limited in most instances by the lack of design
generality and/or potential addressability of the molecular logic gates.
We use the universal recognition properties
of DNA to create addressable logic gates that are capable of AND, OR, XOR, NOR, NAND, and INHIBIT
logic operations (Fig. 5). We used DNA-based logic gates to design computational circuits capable
of performing simple arithmetic operations. Together these recent findings suggest the usefulness
of DNA-based logic gates as a novel and effective supramolecular platform for the fabrication
of molecular computational devices.
|Fig. 5. Arithmetic operations can be conducted with molecules
in solution. A half adder is shown using a network of AND and XOR DNA-based logic gates.
Horne, W.S., Stout, C.D., Ghadiri, M.R. A heterocyclic peptide
nanotube. J. Am. Chem. Soc. 125:9372, 2003.