Mikkel F. Jacobsen

Single-molecule chemical reactions on DNA origami

DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

Supramolecular Porous Network Formed by Molecular Recognition between Chemically Modified Nucleobases Guanine and Cytosine

The involvement of surfaces in the origin of the first genetic molecules on Earth has long been suggested. Prior to the emergence of nucleic acid polymerases in the prebiotic soup, the self-assembly of primitive nucleobase building blocks may have relied on surface-mediated recognition events which catalyzed the formation of a covalent backbone in prototype oligonucleotides that subsequently may have functioned as templates in a primitive copying mechanism. This initial replication process may have been catalyzed by surfaces or chemical substances in solution—including RNA itself, as postulated in the RNA world hypothesis. Today, the role and the relative importance of the basic, fundamental driving forces for nucleic acid replication such as base pairing, base stacking, and steric effects are still under intense debate. Watson–Crick hydrogen bonding has traditionally been thought to be a prerequisite for high-fidelity DNA replication. However, recent studies on nucleobase analogues with the same size and shape as the natural ones but without relevant hydrogen-bonding groups have revealed that these analogues can recognize each other with high fidelity when incorporated into DNA sequences in vivo. Watson–Crick hydrogen bonding thus seems not to be a requisite for the selectivity of base pairing in DNA replication. However, in the absence of polymerases in the prebiotic soup, Watson– Crick hydrogen bonding may have played a more crucial role in the molecular recognition between the nucleobase building blocks at surfaces and for further polymerization. In support of this postulation, molecular recognition between complementary bases, most likely driven by hydrogen bonding alone, has already been observed both at the liquid/solid (HOPG) interface and on the noble Au(111) surface under extreme ultrahigh vacuum (UHV) conditions. These previous experiments were, however, conducted with nucleobases alone, and hence did not take the presence of deoxyribose into account. It is therefore of utmost importance to explore the role that Watson–Crick hydrogen bonding plays at surfaces in chemical structures that mimic nucleotides so as to address the fundamental question of how the polymerization of nucleotides may have started in the prebiotic soup in the absence of enzymes. The development of the scanning tunneling microscopy (STM) technique has advanced our understanding of supramolecular self-assembly systems on surfaces and has allowed intermolecular interactions to be explored at the submolecular scale. Herein we show by using a combination of high-resolution STM imaging and density functional theory (DFT) that sequential co-deposition of N-aryl-modified nucleobases cytosine (C) and guanine (G) onto the Au(111) surface under UHV conditions results in the formation of highly ordered supramolecular porous networks, where Watson–Crick hydrogen bonding between chemically modified C and G molecules plays the primary role in their stabilization. As the N-arylation of the nucleobases has been performed on the nitrogen atom normally attached to the sugar moiety in DNA or RNA (Scheme 1), these N-aryl-modified nucleobases thus represent two-dimensional (2D) structural mimics of naturally occurring nucleotides. The current results outline a new route for directing the self-assembly of nucleobase-derived nanostructures at the surface. Furthermore, the observed [*] Prof. W. Xu, Dr. M. F. Jacobsen, Dr. M. Yu, Prof. E. Laegsgaard, Prof. I. Stensgaard, Prof. T. R. Linderoth, Prof. J. Kjems, Prof. K. V. Gothelf, Prof. F. Besenbacher Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Department of Physics and Astronomy, Department of Chemistry, and Department of Molecular Biology, Aarhus University 8000 Aarhus C (Denmark) E-mail: fbe@inano.au.dk

Model Systems for Activation of Nucleic Acid Encoded Prodrugs

The development of more selective chemotherapeutic agents for benign treatments of malicious diseases is highly desirable. In recent years model systems for the release of small molecule drugs from nucleic acid conjugates by templated chemical or photochemical reactions have been designed. Common for these systems is that the stoichiometric or catalytic drug release is controlled by the highly selective hybridization between complementary strands of nucleic acids. Herein, the concepts of the new field of nucleic acid templated release reactions are outlined.

Palladium-Catalyzed Carbonylative α-Arylation of tert-Butyl Cyanoacetate with (Hetero)aryl Bromides.

A three-component coupling protocol has been developed for the generation of 3-oxo-3-(hetero)arylpropanenitriles via a carbonylative palladium-catalyzed α-arylation of tert-butyl 2-cyanoacetates with (hetero)aryl bromides followed by an acid-mediated decarboxylation step. Through the combination of only a stoichiometric loading of carbon monoxide and mild basic reaction conditions such as MgCl2 and dicyclohexylmethylamine for the deprotonation step, an excellent functional group tolerance was ensured for the methodology. Through the use of (13)C-labeled carbon monoxide generated from (13)COgen, the corresponding (13)C-isotopically labeled β-ketonitriles were obtained, and these products could subsequently be converted into cyanoalkynes and 3-cyanobenzofurans with site specific (13)C-isotope labeling.

Self-assembly of artificial nucleobase 1H-benzimidazole-4,7-dione at the liquid/solid interface.

Self-assembly at the liquid/solid interface of an electrochemically active DNA nucleobase analogue, 1H-benzoimidazole-4,7-dione (Q), has been studied by means of scanning tunneling microscopy (STM). High-resolution STM images revealed the formation of well-ordered two-dimensional (2D) supramolecular nanostructures when the Q molecules are adsorbed onto the graphite surface from a 1-octanol solution. Detailed analysis shows that the observed 2D nanostructures are mainly dominated by hydrogen-bonded Q molecules. Since Q can be considered as a molecule mimicking the nucleobase guanine (G), which is known to form Watson-Crick base pairs with its complementary nucleobase cytosine (C), we have examined the binding ability of Q with C realized by available hydrogen-bonding sites on both Q and C molecules. Upon deposition of a mixture of Q and C molecules onto a graphite surface, one might expect that hydrogen-bonded QC dimers were observed in a new 2D self-assembled structure governed by inter- and intramolecular hydrogen-bonding interactions between Q and C molecules. However, our STM experiments showed that no well-ordered structures are formed and instead phase separation occurs where large-scale homodomains are formed consisting of the individual QQ and CC dimers. To gain further insight into the possible molecular arrangements of the Q and C nucleobases in the mixture phase, the high-resolution STM images are compared with the results from ab initio density functional theory (DFT) calculations.