Scientific Report 2008

Chemistry

Design of Functional Synthetic Systems

M.R. Ghadiri, M. Amorin, J. Beierle, A. Chavochi, J. Chu, B. Frezza, N. Gianneschi, L. Leman, A. Loutchnikov, A. Montero, C. Olsen, J. Picuri, D. Radu, Y. Ura

We are engaged in multidisciplinary research to uncover new chemical and biochemical approaches for the design of functional molecular, supramolecular, and complex self-organized systems. Our efforts 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 catalysts, antimicrobial self-assembling peptide nanotubes, semisynthetic allosteric enzymes, self-replicating molecular systems and emergent networks, single-molecule DNA sensing, molecular computation, and prebiotic chemistry.

Antimicrobial Peptide Nanotubes

We have shown that appropriately designed cyclic peptide subunits can self-assemble through hydrogen bond—directed ring stacking into open-ended hollow tubular structures that have marked antibacterial and antiviral activities in vitro. The effectiveness of this novel supramolecular class of bioactive species as selective antibacterial agents was highlighted by the high efficacy of one of these antimicrobials against lethal methicillin-resistant Staphylococcus aureus infections in mice. Currently, we are exploring rational design of cyclic glycopeptides and selections from combinatorial libraries to discover novel antiviral supramolecular compounds (Fig. 1).

Fig. 1. Antiviral agents based on self-assembling cyclic peptide nanotubes. Cyclic D,L-α-peptides act on endosomal membranes to prevent the development of low pH in endocytic vesicles, arrest the escape of virions from the endosome, and abrogate adenovirus infection.

Design of Signal Self-Amplifying DNA Sensors

We constructed a novel sequence-specific DNA detection system based on rationally designed semisynthetic enzymes. The system is composed of covalently associated inhibitor-DNA-enzyme modules that function via DNA hybridization—triggered allosteric enzyme activation and signal amplification through substrate turnover (Fig. 2). 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, and 1-step detection of label-free DNA sequences that does not depend on polymerase chain reactions.

Fig. 2. Schematic representation of an intrasterically inactivated inhibitor-DNA-enzyme construct (left) and the DNA hybridization—triggered enzyme activation (right). The construct can be used to sense low concentrations of cDNA because of its built-in capacity for signal amplification via rapid substrate turnover.

Single-Molecule Dna Sequencing

We are interested in the study of matter at the level of single molecules. 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 the conductance levels produced in the ion channel in the native protein. Using this technique, we developed an approach by which a single-stranded DNA molecule can be trapped in a specific configuration inside an α-hemolysin channel, manipulated, and studied with high sensitivity at the single-molecule level. We have been able to detect up to 9 consecutive DNA polymerase—catalyzed single-nucleotide primer extensions (Fig. 3) with high sensitivity and spatial resolution (≤ 2.4 Å). The single-base resolution of this approach and the ability to control the passage of DNA in single-base steps satisfy the 2 minimal requirements of a nanopore-based sequencing device.

Fig. 3. Single-molecule monitoring of DNA polymerase—catalyzed single-nucleotide primer extensions with high sensitivity via an α-hemolysin—DNA—rotaxane device.

Complex Synthetic Networks

Living cells use complex networks of evolutionarily selected biomolecular interactions and chemical transformations to process multiple extracellular input signals rapidly and simultaneously. We are interested in understanding and experimentally modeling the organizational and functional properties of biological networks. We have developed a general strategy for the design and construction of self-organized synthetic peptide networks based on the sequence-selective autocatalytic and cross-catalytic template-directed coiled coil peptide fragment condensation reactions in aqueous solutions. The synthetic networks have some of the basic architectural and dynamic features of the living networks, reorganize in response to changes in environmental conditions and inputs (Fig. 4), and perform basic Boolean logic functions. We suggest that the ability to rationally construct predictable chemical circuitry might be useful in advancing the modeling and better understanding of some of the basic dynamic information-processing characteristics of the more complex cellular networks.

Fig. 4. Adaptive reorganization in a synthetic peptide network. The graph structure or wiring of a synthetic peptide network responds dramatically to changes in the environmental stimuli (pH or salt content).

Molecular Computation

A fundamental goal of computing is to reproduce in a molecular setting the familiar properties of microelectronics, such as digital logic, component modularity, and hierarchical design capacity. In this regard, significant advances have been made in the design of molecular logic gates by using small-molecule and rotaxane complexes, deoxyribozymes, enzymatic biochemical networks, peptide networks, and other systems. However, the molecular logic gates must be integrated into more complex networks in which outputs from each gate can serve as inputs to downstream gates.

We recently described the construction of a basis set of DNA-based logic gates (AND, OR, AND-NOT) capable of communicating with one another. These gates were rewired into a higher-order circuit that enforces a net XOR (Exclusive OR) Boolean behavior (Fig. 5), showing that the components can be modularly recombined to implement novel logic processing. Our results support the notion that with a basis set of only a few logic gates and within the limits imposed by the availability of uniquely addressable oligonucleotide sequences, design of molecular circuits capable of performing a large variety of digital logic operations might be within reach.

Fig. 5. A multilevel circuit built from OR, AND, and AND-NOT gates that performs a net XOR (Exclusive-OR) analysis on the inputs.

PREBIOTIC CHEMISTRY

The emergence of a polymer that could store genetic information, replicate, and exhibit phenotypic properties subject to selective environmental pressures marked a crucial stage in the transition from the prebiotic world to biology; however, the nature of such a polymer remains unresolved. We have discovered an oligomer family that quickly and efficiently self-assembles via reversible covalent anchoring of nucleobase recognition units onto simple peptide backbones. The resulting oligomers specifically self-pair and cross-pair with complementary strands of RNA and DNA in Watson-Crick fashion. Moreover, the oligomers undergo dynamic component exchange, template-directed assembly processes, and dynamic sequence modification in response to changing selective pressures. Such oligomers could therefore have participated in a number of processes that would be advantageous for primordial genetic systems, such as dynamic sequence repair and adaptation.

Publications

Cockroft, S.L., Chu, J., Amorin, M., Ghadiri, M.R. A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J. Am. Chem. Soc. 130:818, 2008.

Frezza, B.M., Cockroft, S.L., Ghadiri, M.R. Modular multi-level circuits from immobilized DNA-based logic gates. J. Am. Chem. Soc. 129:14875, 2007.

Gianneschi, N.C., Ghadiri, M.R. Design of molecular logic devices based on a programmable DNA-regulated semisynthetic enzyme. Angew. Chem. Int. Ed. 46:3955, 2007.

Leman, L.J., Weinberger, D.A., Huang, Z.-Z., Wilcoxen, K.M., Ghadiri, M.R. Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering. J. Am. Chem. Soc. 129:2959, 2007.