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

Xu, Wei; Wang, Jianguo; Jacobsen, Mikkel F.; Mura, Manuela; Wang, Yuanlin; Kelly, Ross E. A.; Meng, Qiangqiang; Lægsgaard, Erik; Stensgaard, I.; Linderoth, Trolle R.; Kjems, Jørgen; Kantorovich, Lev; Gothelf, Kurt V.; Besenbacher, Flemming

doi:10.1002/anie.201003390

Cited by 47 publications

(37 citation statements)

References 27 publications

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“…As demonstrated in our previous work, the deposition of 9eG molecules on Au(111)l eads to the formation of zigzag ribbon structures (Scheme 1a nd Figure S1) [16,26] rather than G-quartet structures, and besides the intra-quartet hydrogen bonding, am etal center (i.e. Fe in that study) is mandatory for the formation of an isolated G-quartet-Fe complex.…”

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confidence: 63%

Solventless Formation of G‐Quartet Complexes Based on Alkali and Alkaline Earth Salts on Au(111)

et al. 2015

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Template cations have been extensively employed in the formation, stabilization and regulation of structural polymorphism of G-quadruplex structures in vitro. However, the direct addition of salts onto solid surfaces, especially under ultra-high-vacuum (UHV) conditions, to explore the feasibility and universality of the formation of G-quartet complexes in a solventless environment has not been reported. By combining UHV-STM imaging and DFT calculations, we have shown that three different G-quartet-M (M: Na/K/Ca) complexes can be obtained on Au(111) using alkali and alkaline earth salts as reactants. We have also identified the driving forces (intra-quartet hydrogen bonding and electrostatic ionic bonding) for the formation of these complexes and quantified the interactions involved. Our results demonstrate a novel route to fabricate G-quartet-related complexes on solid surfaces, providing an alternative feasible way to bring metal elements to surfaces for constructing metal-organic systems.

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confidence: 63%

Solventless Formation of G‐Quartet Complexes Based on Alkali and Alkaline Earth Salts on Au(111)

et al. 2015

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“…[62][63][64][65] In a parallel effort, supramolecular networks of nucleobases have been achieved by using complementary Watson-Crick-type H-bonding, as well as non-complementary pairing patterns. 66,67 The documented variations in network structures consisting of peptides and nucleobases manifest the interaction specificity and diversity among the elemental assembly units that are prevalent in the recognition process of biological systems.…”

Section: Probing Biomolecular Self-assembly Via Scanning Tunneling Microscopymentioning

confidence: 99%

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

et al. 2018

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Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

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“…In this work we only modified dU residues, but there are other examples in the literature in which polymerizable moieties have been introduced on other nucleotides as well. 17 Dynamic light scattering (DLS) analysis reported hydrodynamic diameter values ranging from 10 nm to 33 nm (Table 1). These data are consistent with the transmission electron microscopy (TEM) analysis (taking into account the swelling in aqueous medium), which showed that OligoMIP NPs appeared spheroidal in shape with their size ranging between 5-15 nm ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Improvement of DNA recognition through molecular imprinting: hybrid oligomer imprinted polymeric nanoparticles (oligoMIP NPs)

et al. 2016

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High affinity and specific binding are cardinal properties of nucleic acids in relation to their biological function and their role in biotechnology. To this end, structural preorganization of oligonucleotides can significantly improve their binding performance, and numerous examples of this can be found in Nature as well as in artificial systems. Here we describe the production and characterization of hybrid DNA-polymer nanoparticles (oligoMIP NPs) as a system in which we have preorganized the oligonucleotide binding by molecular imprinting technology. Molecularly imprinted polymers (MIPs) are cost-effective "smart" polymeric materials capable of antibody-like detection, but characterized by superior robustness and the ability to work in extreme environmental conditions. Especially in the nanoparticle format, MIPs are dubbed as one of the most suitable alternatives to biological antibodies due to their selective molecular recognition properties, improved binding kinetics as well as size and dispersibility. Nonetheless, there have been very few attempts at DNA imprinting in the past due to structural complexity associated with these templates. By introducing modified thymine bases into the oligonucleotide sequences, which allow establishing covalent bonds between the DNA and the polymer, we demonstrate that such hybrid oligoMIP NPs specifically recognize their target DNA, and that the unique strategy of incorporating the complementary DNA strands as "preorganized selective monomers" improves the recognition properties without affecting the NPs physical properties such as size, shape or dispersibility.

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

Cited by 47 publications

References 27 publications

Solventless Formation of G‐Quartet Complexes Based on Alkali and Alkaline Earth Salts on Au(111)

Solventless Formation of G‐Quartet Complexes Based on Alkali and Alkaline Earth Salts on Au(111)

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Improvement of DNA recognition through molecular imprinting: hybrid oligomer imprinted polymeric nanoparticles (oligoMIP NPs)

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