1
|
Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
Collapse
Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| |
Collapse
|
2
|
H H, Mallajosyula SS. Unveiling DNA Translocation in Pristine Graphene Nanopores: Understanding Pore Clogging via Polarizable Simulations. ACS APPLIED MATERIALS & INTERFACES 2023; 15:55095-55108. [PMID: 37965826 DOI: 10.1021/acsami.3c12262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Graphene has garnered remarkable attention in recent years as an attractive nanopore membrane for rapid and accurate sequencing of DNA. The inherent characteristics of graphene offer exquisite experimental control over pore dimensions, encompassing both the width (pore diameter) and height. Despite these promising prospects, the practical deployment of pristine graphene nanopores for DNA sequencing has encountered a formidable challenge in the form of pore clogging, which is primarily attributed to hydrophobic interactions. However, a comprehensive understanding of the atomistic origins underpinning this clogging phenomenon and the nuanced impact of individual nucleobase identities on clogging dynamics remain an underexplored domain. Elucidating the atomistic intricacies governing pore clogging is pivotal to devising strategies for its mitigation and advancing our understanding of graphene nanopore behavior. We harness Drude polarizable simulations to systematically dissect the nucleobase-dependent mechanisms that play a pivotal role in nanopore clogging. We unveil nucleobase-specific interactions that illuminate the multifaceted roles played by both hydrophobic and electrostatic forces in driving nanopore clogging events. Notably, the Drude simulations also unveil the bias-dependent translocation dynamics and its pivotal role in alleviating pore clogging─a facet that remains significantly underestimated in conventional additive (nonpolarizable) simulations. Our findings underscore the indispensability of incorporating polarizability to faithfully capture the intricate dynamics governing graphene nanopore translocation phenomena, thus deepening our insights into this crucial field.
Collapse
Affiliation(s)
- Hemanth H
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| | - Sairam S Mallajosyula
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat 382355, India
| |
Collapse
|
3
|
Demir Gİ, Demir S, Tekin A. 2D‐FFCASP—A New Approach for 2D Structure Prediction Applied to Self‐Assemblies of DNA Bases. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Gözde İniş Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
| | - Samet Demir
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| | - Adem Tekin
- Informatics Institute Istanbul Technical University Maslak Istanbul 34469 Turkey
- TÜBİTAK Research Institute for Fundamental Sciences Gebze Kocaeli 41470 Turkey
| |
Collapse
|
4
|
Non-G Base Tetrads. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165287. [PMID: 36014524 PMCID: PMC9414646 DOI: 10.3390/molecules27165287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Tetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.
Collapse
|
5
|
Xu X, Li Y, Xu S, Leng X, Chen X, Li W. Directional observations of guanine and cytosine pairing structures on HOPG. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
6
|
Jin J, Li S, Wang Z, Lu Y, Liu X, Wang L. Polymorphic Pairing Configurations of Guanine and Cytosine at the Water-HOPG Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3761-3765. [PMID: 33724026 DOI: 10.1021/acs.langmuir.1c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A series of nucleobases guanine (G) and cytosine (C) pairing configurations have been fabricated on highly oriented pyrolytic graphite (HOPG) surface by controlling the molar ratio of G and C in water solution. Watson-Crick (WC) base pairing governs the association of C and G nucleobases when the molar ratio of C/G is adjusted to 1:1. Nucleobase-rich is preferentially hydrogen-bonded to the sites exposed around WC motifs with the adjustment of the C/G molar ratio. At a higher C/G molar ratio imbalance, the pairing configurations depend on the combination of interspace and sites of hydrogen binding between G and C bases. The systematic analysis of the high-resolution STM images and DFT calculations reveal that hydrogen bonding plays a dominant role in the formation of these pairing configurations and that the competition between the priority and diversity of hydrogen-bonded configurations bonding between G and C is the key for the pairing structural polymorphism.
Collapse
Affiliation(s)
- Jing Jin
- Department of Physics, Nanchang University, Nanchang 330031, China
| | - Sihao Li
- Department of Physics, Nanchang University, Nanchang 330031, China
| | - Zhongping Wang
- Department of Physics, Nanchang University, Nanchang 330031, China
| | - Yan Lu
- Department of Physics, Nanchang University, Nanchang 330031, China
| | - Xiaoqing Liu
- Department of Physics, Nanchang University, Nanchang 330031, China
| | - Li Wang
- Department of Physics, Nanchang University, Nanchang 330031, China
| |
Collapse
|
7
|
H H, Mallajosyula SS. Polarization influences the evolution of nucleobase-graphene interactions. NANOSCALE 2021; 13:4060-4072. [PMID: 33595570 DOI: 10.1039/d0nr08796c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In recent years, graphene has attracted attention from researchers as an atomistically thin solid state material for the study on the self-assembly of nucleobases. Non-covalent interactions between nucleobases and graphene sheets play a fundamental role in understanding the self-assembly of nucleobases on the graphene sheet. A fundamental understanding of the effect of molecular polarizability on these non-covalent interactions between the nucleobases and the underlying graphene sheet is absent in the literature. In this paper, we present the results from polarizable molecular dynamics simulation studies to understand the effect of polarization on the strength of non-covalent interactions. To this end, we report the development of Drude parameters for describing the polarizable graphene sheet. The developed parameters were used to study the self-aggregation phenomenon of nucleobases on a graphene support. We observe a significant change in the interaction patterns upon the inclusion of polarization into the system, with polarizable simulations yielding results that closely resemble the experimental studies. Two of the key observations were the probability of the formation of stacks in guanine-rich systems, and the spontaneous formation of H-bonded structures over the graphene sheet, which allude to the importance of the DNA sequence and composition. Both these effects were not observed in the additive simulations. The present study sheds light on the effect of polarization on the adsorption of DNA nucleobases on a graphene sheet, but the methodology can be extended to include a variety of small molecules and complete DNA strands.
Collapse
Affiliation(s)
- Hemanth H
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
| | - Sairam S Mallajosyula
- Discipline of Chemistry, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India-382355.
| |
Collapse
|
8
|
Wei Li, Xu S, Cai Y, Wu S, He H. Direct Observation of Guanine and Water Supramolecular Assemblies. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2020. [DOI: 10.1134/s0036024420130129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
9
|
De Marchi F, Galeotti G, Simenas M, Ji P, Chi L, Tornau EE, Pezzella A, MacLeod J, Ebrahimi M, Rosei F. Self-assembly of 5,6-dihydroxyindole-2-carboxylic acid: polymorphism of a eumelanin building block on Au(111). NANOSCALE 2019; 11:5422-5428. [PMID: 30855042 DOI: 10.1039/c8nr09810g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Investigating two-dimensional (2D) self-assembled structures of biological monomers governed by intermolecular interactions is a prerequisite to understand the self-assembly of more complex biomolecular systems. 5,6-Dihydroxyindole carboxylic acid (DHICA) is one of the building blocks of eumelanin - an irregular heteropolymer and the most common form of melanin which has potential applications in organic electronics and bioelectronics. By means of scanning tunneling microscopy, density functional theory and Monte Carlo calculations, we investigate DHICA molecular configurations and interactions underlying the multiple 2D patterns formed on Au(111). While DHICA self-assembled molecular networks (SAMNs) are dominated by the hydrogen bonding of carboxylic acid dimers, a variety of 2D architectures are formed due to the multiple weak interactions of the catechol group. The hydroxyl group also allows for redox reactions, caused by oxidation via O2 exposure, resulting in molecular rearrangement. The susceptibility of the molecules to oxidation is affected by their SAMNs architectures, giving insights on the reactivity of indoles as well as highlighting non-covalent assembly as an approach to guide selective oxidation reactions.
Collapse
Affiliation(s)
- F De Marchi
- Centre Energie, Materiaux et Telecommunications, Institut National de la Recherche Scientifique, 1650 Boulevard Lionel-Boulet, Varennes, QC, Canada J3X 1S2.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Saikia N, Johnson F, Waters K, Pandey R. Dynamics of self-assembled cytosine nucleobases on graphene. NANOTECHNOLOGY 2018; 29:195601. [PMID: 29461252 DOI: 10.1088/1361-6528/aab0ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.
Collapse
|
11
|
Saravanan RK, Avasthi I, Prajapati RK, Verma S. Surface modification and pattern formation by nucleobases and their coordination complexes. RSC Adv 2018; 8:24541-24560. [PMID: 35539208 PMCID: PMC9082088 DOI: 10.1039/c8ra03903h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
This review presents recent progress concerning the organization of nucleobases on highly ordered pyrolytic graphite (HOPG), mica, Cu(110) and Au(111) surfaces, followed by their studies using microscopy methods such as atomic force microscopy (AFM), scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). Interesting research prospects related to surface patterning by nucleobases, nucleobase-functionalized carbon nanotubes (CNTs) and metal–nucleobase coordination polymers are also discussed, which offer a wide array of functional molecules for advanced applications. Nucleobases and their analogs are able to invoke non-covalent interactions such as π–π stacking and hydrogen bonding, and possess the required framework to coordinate metal ions, giving rise to fascinating supramolecular architectures. The latter could be transferred to conductive substrates, such as HOPG and gold, for assessment by high-end tunneling microscopy under various conditions. Clear understanding of the principles governing nucleobase self-assembly and metal ion complexation, and precise control over generation of functional architectures, might lead to custom assemblies for targeted nanotechnological and nanomaterial applications. This review highlights recent advancements in surface patterning of nucleobases, their analogs including nucleobase-CNT hybrids and metal complexes, using various microscopy techniques for nanotechnological applications.![]()
Collapse
Affiliation(s)
- R. Kamal Saravanan
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur, 208016
- India
| | - Ilesha Avasthi
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur, 208016
- India
| | - Rajneesh Kumar Prajapati
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur, 208016
- India
- Centre for Nanoscience
| | - Sandeep Verma
- Department of Chemistry
- Indian Institute of Technology Kanpur
- Kanpur, 208016
- India
- Centre for Nanoscience
| |
Collapse
|
12
|
Vinje J, Falck M, Mazzola F, Cooil SP, Koch H, Høyvik IM, Wells J. Tautomerization of Thymine Using Ultraviolet Light. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:9666-9672. [PMID: 28835097 DOI: 10.1021/acs.langmuir.7b02473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultraviolet-light-induced changes to the nucleobase thymine deposited onto a MoS2 surface were studied using photoelectron spectroscopy and first-principles calculations. These measurements suggest changes in the molecular structure indicated by changes in core electron binding energies. The experimental work has been interpreted by means of ab initio calculations using coupled cluster singles and doubles (CCSD) linear response theory. Contrary to the expected behavior, i.e., the dimerization of two thymine molecules into a pyrimidine dimer, a shift between two tautomeric forms was observed upon UV-exposure. Exposure to ionizing radiation is known to induce damage in many biological molecules, and the present work gives additional insight into its effects on thymine, the interactions of the molecules, and finally how certain UV photoproducts may be avoided.
Collapse
Affiliation(s)
- Jakob Vinje
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Merete Falck
- NTNU Nanomechanical Lab, Department of Structural Engineering, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Federico Mazzola
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Simon Phillip Cooil
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| | - Justin Wells
- Department of Physics, Norwegian University of Science and Technology (NTNU) , N-7491 Trondheim, Norway
| |
Collapse
|
13
|
Ding Y, Xie L, Zhang C, Xu W. Real-space evidence of the formation of the GCGC tetrad and its competition with the G-quartet on the Au(111) surface. Chem Commun (Camb) 2017; 53:9846-9849. [PMID: 28825090 DOI: 10.1039/c7cc05548j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we show the first real-space evidence of the formation of GCGC tetrad on an Au(111) surface, and further investigate its competition with the well-known G-quartet with the aid of NaCl under ultrahigh vacuum (UHV) conditions.
Collapse
Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
| | | | | | | |
Collapse
|
14
|
Zhao H, Li Y, Chen D, Liu B. Investigating the Co-Adsorption Behavior of Nucleic-Acid Base (Thymine and Cytosine) and Melamine at Liquid/Solid Interface. NANOSCALE RESEARCH LETTERS 2016; 11:552. [PMID: 28000170 PMCID: PMC5174008 DOI: 10.1186/s11671-016-1767-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
The co-adsorption behavior of nucleic-acid base (thymine; cytosine) and melamine was investigated by scanning tunneling microscopy (STM) technique at liquid/solid (1-octanol/graphite) interface. STM characterization results indicate that phase separation happened after dropping the mixed solution of thymine-melamine onto highly oriented pyrolytic graphite (HOPG) surface, while the hetero-component cluster-like structure was observed when cytosine-melamine binary assembly system is used. From the viewpoints of non-covalent interactions calculated by using density functional theory (DFT) method, the formation mechanisms of these assembled structures were explored in detail. This work will supply a methodology to design the supramolecular assembled structures and the hetero-component materials composed by biological and chemical compound.
Collapse
Affiliation(s)
- Huiling Zhao
- Institute of Photo-biophysics, School of Physics and Electronics, Henan University, Kaifeng, 475004 People’s Republic of China
| | - Yinli Li
- Institute of Photo-biophysics, School of Physics and Electronics, Henan University, Kaifeng, 475004 People’s Republic of China
| | - Dong Chen
- Institute of Photo-biophysics, School of Physics and Electronics, Henan University, Kaifeng, 475004 People’s Republic of China
| | - Bo Liu
- Institute of Photo-biophysics, School of Physics and Electronics, Henan University, Kaifeng, 475004 People’s Republic of China
| |
Collapse
|
15
|
Ciesielski A, El Garah M, Masiero S, Samorì P. Self-assembly of Natural and Unnatural Nucleobases at Surfaces and Interfaces. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:83-95. [PMID: 26488679 DOI: 10.1002/smll.201501017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/19/2015] [Indexed: 06/05/2023]
Abstract
The self-assembly of small organic molecules interacting via non-covalent forces is a viable approach towards the construction of highly ordered nanostructured materials. Among various molecular components, natural and unnatural nucleobases can undergo non-covalent self-association to form supramolecular architectures with ad hoc structural motifs. Such structures, when decorated with appropriate electrically/optically active units, can be used as scaffolds to locate such units in pre-determined positions in 2D on a surface, thereby paving the way towards a wide range of applications, e.g., in optoelectronics. This review discusses some of the basic concepts of the supramolecular engineering of natural and unnatural nucleobases and derivatives thereof as well as self-assembly processes on conductive solid substrates, as investigated by scanning tunnelling microscopy in ultra-high vacuum and at the solid/liquid interface. By unravelling the structure and dynamics of these self-assembled architectures with a sub-nanometer resolution, a greater control over the formation of increasingly sophisticated functional systems is achieved. The ability to understand and predict how nucleobases interact, both among themselves as well as with other molecules, is extremely important, since it provides access to ever more complex DNA- and RNA-based nanostructures and nanomaterials as key components in nanomechanical devices.
Collapse
Affiliation(s)
- Artur Ciesielski
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Mohamed El Garah
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Stefano Masiero
- Dipartimento di Chimica "G. Caimician", Alma Mater Studiorum - Università di Bologna, v. San Giacomo, 11 - 40126, Bologna, Italy
| | - Paolo Samorì
- ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| |
Collapse
|
16
|
Zhao H, Song X, Aslan H, Liu B, Wang J, Wang L, Besenbacher F, Dong M. Self-assembly of hydrogen-bonded supramolecular complexes of nucleic-acid-base and fatty-acid at the liquid–solid interface. Phys Chem Chem Phys 2016; 18:14168-71. [DOI: 10.1039/c6cp00112b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interesting sandwich-like architectures were formed at the liquid–solid interface by using a binary system consisting of guanine and stearic acid.
Collapse
Affiliation(s)
- Huiling Zhao
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Xin Song
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Hüsnü Aslan
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Bo Liu
- Institute of Photo-biophysics
- School of Physics and Electronics
- Henan University
- Kaifeng 475004
- China
| | - Jianguo Wang
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Li Wang
- Department of Physics
- Nanchang University
- Nanchang 330031
- China
| | - Flemming Besenbacher
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO)
- Center for DNA Nanotechnology (CDNA)
- Aarhus University
- DK-8000 Aarhus C
- Denmark
| |
Collapse
|
17
|
Liu L, Xia D, Klausen LH, Dong M. The self-assembled behavior of DNA bases on the interface. Int J Mol Sci 2014; 15:1901-14. [PMID: 24473140 PMCID: PMC3958828 DOI: 10.3390/ijms15021901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 12/31/2013] [Accepted: 01/07/2014] [Indexed: 11/16/2022] Open
Abstract
A successful example of self-assembly in a biological system is that DNA can be an excellent agent to self-assemble into desirable two and three-dimensional nanostructures in a well-ordered manner by specific hydrogen bonding interactions between the DNA bases. The self-assembly of DNA bases have played a significant role in constructing the hierarchical nanostructures. In this review article we will introduce the study of nucleic acid base self-assembly by scanning tunneling microscopy (STM) at vacuum and ambient condition (the liquid/solid interface), respectively. From the ideal condition to a more realistic environment, the self-assembled behaviors of DNA bases are introduced. In a vacuum system, the energetic advantages will dominate the assembly formation of DNA bases, while at ambient condition, more factors such as conformational freedom and the biochemical environment will be considered. Therefore, the assemblies of DNA bases at ambient condition are different from the ones obtained under vacuum. We present the ordered nanostructures formed by DNA bases at both vacuum and ambient condition. To construct and tailor the nanostructure through the interaction between DNA bases, it is important to understand the assembly behavior and features of DNA bases and their derivatives at ambient condition. The utilization of STM offers the advantage of investigating DNA base self-assembly with sub-molecular level resolution at the surface.
Collapse
Affiliation(s)
- Lei Liu
- Institute for Advanced Materials, Jiangsu University, 301 Xuefu Road, Jiangsu 212013, China.
| | - Dan Xia
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
| | - Lasse H Klausen
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
| | - Mingdong Dong
- Interdisciplinary nanoscience Center (iNANO), Gustav Wieds vej 14, DK-8000 Aarhus C, Denmark.
| |
Collapse
|
18
|
Liu L, Besenbacher F, Dong M. Self-Assembly of DNA Bases via Hydrogen Bonding Studied by Scanning Tunneling Microscopy. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2014. [DOI: 10.1007/978-3-642-38815-6_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Linkov P, Artemyev M, Efimov AE, Nabiev I. Comparative advantages and limitations of the basic metrology methods applied to the characterization of nanomaterials. NANOSCALE 2013; 5:8781-8798. [PMID: 23934544 DOI: 10.1039/c3nr02372a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Fabrication of modern nanomaterials and nanostructures with specific functional properties is both scientifically promising and commercially profitable. The preparation and use of nanomaterials require adequate methods for the control and characterization of their size, shape, chemical composition, crystalline structure, energy levels, pathways and dynamics of physical and chemical processes during their fabrication and further use. In this review, we discuss different instrumental methods for the analysis and metrology of materials and evaluate their advantages and limitations at the nanolevel.
Collapse
Affiliation(s)
- Pavel Linkov
- Laboratory of Nano-Bioengineering, National Research Nuclear University, Moscow Engineering Physics Institute, 31 Kashirskoe sh., 115409 Moscow, Russian Federation.
| | | | | | | |
Collapse
|
20
|
Mu Z, Rubner O, Bamler M, Blömker T, Kehr G, Erker G, Heuer A, Fuchs H, Chi L. Temperature-dependent self-assembly of adenine derivative on HOPG. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10737-10743. [PMID: 23902468 DOI: 10.1021/la401974t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Temperature-dependent self-assembly formed by the adsorption of the nucleobase adenine derivative on a graphite surface were investigated by in situ scanning tunneling microscopy (STM). The high-resolution STM images reveal two types of structures, α phase and β phase, which are mainly driven by either hydrogen bonding or aromatic π-π interactions between adenine bases, respectively, as well as the interactions of alkyl chains. α-Phase structures can be transformed into β-phase structures by increasing temperature. The reverse is true for decreasing temperature. This reflects structural stabilities resulting from the different interactions. Density functional theory (DFT) calculations were performed to characterize possible arrangements of adjacent adenine moieties systematically in terms of binding energies and structural properties. Via a systematic search algorithm, all possible network structures were determined on a microscopic level. In this way, it is possible to rationalize the structural parameters as found in the STM images.
Collapse
Affiliation(s)
- Zhongcheng Mu
- Faculty of Chemistry, Northeast Normal University, 130024 Changchun, Jilin, PR China
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Roxbury D, Jagota A, Mittal J. Structural Characteristics of Oligomeric DNA Strands Adsorbed onto Single-Walled Carbon Nanotubes. J Phys Chem B 2012. [DOI: 10.1021/jp309523a] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Roxbury
- Department
of Chemical Engineering, and ‡Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United
States
| | - Anand Jagota
- Department
of Chemical Engineering, and ‡Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United
States
| | - Jeetain Mittal
- Department
of Chemical Engineering, and ‡Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United
States
| |
Collapse
|
22
|
Lipton-Duffin J, Miwa JA, Urquhart SG, Contini G, Cossaro A, Casalis L, Barth JV, Floreano L, Morgante A, Rosei F. Binding geometry of hydrogen-bonded chain motif in self-assembled gratings and layers on Ag(111). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:14291-14300. [PMID: 22970746 DOI: 10.1021/la303010p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Upon adsorption on the (111) facet of Ag, 4-[trans-2-(pyrid-4-yl-vinyl)] benzoic acid (PVBA) self-assembles into a highly ordered, chiral twin chain structure at submonolayer coverages with domains that can extend for micrometers in one dimension. Using polarization-dependent measurements of C and N K-shell excitations in near-edge X-ray absorption fine structure (NEXAFS) spectra, we determine the binding geometry of single PVBA molecules within this unique ensemble for both low and high coverage regimes. At submonolayer coverage, the molecule is twisted to facilitate the formation of hydrogen bonds. The gas-phase planarity is gradually recovered as the coverage is increased, with complete planarity coinciding with loss of order in the overlayer. Thermal treatment of the PVBA film results in deprotonation of the carboxyl tail of the molecule, but despite the suppression of the stabilizing hydrogen-bonds, the overlayer remains ordered.
Collapse
Affiliation(s)
- J Lipton-Duffin
- Centre Énergie, Matériaux et Télécommunications, Institut National de la Recherche Scientifique, Université du Québec, 1650 Boulevard Lionel-Boulet, Varennes, QC, J3X 1S2, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Langner A, Tait SL, Lin N, Chandrasekar R, Meded V, Fink K, Ruben M, Kern K. Selective Coordination Bonding in Metallo-Supramolecular Systems on Surfaces. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
24
|
Langner A, Tait SL, Lin N, Chandrasekar R, Meded V, Fink K, Ruben M, Kern K. Selective coordination bonding in metallo-supramolecular systems on surfaces. Angew Chem Int Ed Engl 2012; 51:4327-31. [PMID: 22441822 DOI: 10.1002/anie.201108530] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/17/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander Langner
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Guo Z, De Cat I, Van Averbeke B, Lin J, Wang G, Xu H, Lazzaroni R, Beljonne D, Meijer EW, Schenning APHJ, De Feyter S. Nucleoside-Assisted Self-Assembly of Oligo(p-phenylenevinylene)s at Liquid/Solid Interface: Chirality and Nanostructures. J Am Chem Soc 2011; 133:17764-71. [DOI: 10.1021/ja206437c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zongxia Guo
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Inge De Cat
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Bernard Van Averbeke
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Jianbin Lin
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Guojie Wang
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Hong Xu
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| | - Roberto Lazzaroni
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - David Beljonne
- Service de Chimie des Matériaux Nouveaux, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - E. W. Meijer
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Albertus P. H. J. Schenning
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Steven De Feyter
- Division of Molecular Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven (K.U. Leuven), Celestijnenlaan 200 F, B-3001 Leuven, Belgium
| |
Collapse
|
26
|
Wazir M, Arora V, Bakhshi A. Electronic Structures and Conduction Properties of Biopolymers. Biopolymers 2011. [DOI: 10.1002/9781118164792.ch15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
27
|
Roxbury D, Tu X, Zheng M, Jagota A. Recognition ability of DNA for carbon nanotubes correlates with their binding affinity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:8282-8293. [PMID: 21650196 DOI: 10.1021/la2007793] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ability to sort mixtures of carbon nanotubes (CNTs) based on chirality has recently been demonstrated using special short DNA sequences that recognize certain matching CNTs of specific chirality. In this work, we report on a study of the relationship between recognition sequences and the strength of their binding to the recognized CNT. We have chosen the (6,5) CNT and its corresponding DNA recognition sequences for investigation in this study. Binding strength is quantified by studying the kinetics of DNA replacement by a surfactant, which is monitored by following shifts in the absorption spectrum. We find that recognition ability correlates strongly with binding strength thus measured; addition or subtraction of just one base from the recognition sequence can enhance the kinetics of DNA displacement some 20-fold. The surfactant displaces DNA in two steps: a rapid first stage lasting less than a few seconds, followed by progressive removal lasting tens of minutes. The kinetics of the second stage is analyzed to extract activation energies. Fluorescence studies support the finding that the DNA sequence that recognizes the (6,5)-CNT forms a more stable hybrid than its close relatives.
Collapse
Affiliation(s)
- Daniel Roxbury
- Department of Chemical Engineering and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | | | | | | |
Collapse
|
28
|
Singh P, Toma FM, Kumar J, Venkatesh V, Raya J, Prato M, Verma S, Bianco A. Carbon Nanotube-Nucleobase Hybrids: Nanorings from Uracil-Modified Single-Walled Carbon Nanotubes. Chemistry 2011; 17:6772-80. [DOI: 10.1002/chem.201100312] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Indexed: 11/11/2022]
|
29
|
Bald I, Wang YG, Dong M, Rosen CB, Ravnsbaek JB, Zhuang GL, Gothelf KV, Wang JG, Besenbacher F. Control of self-assembled 2D nanostructures by methylation of guanine. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:939-949. [PMID: 21394906 DOI: 10.1002/smll.201002033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/01/2011] [Indexed: 05/30/2023]
Abstract
Methylation of DNA nucleobases is an important control mechanism in biology applied, for example, in the regulation of gene expression. The effect of methylation on the intermolecular interactions between guanine molecules is studied through an interplay between scanning tunneling microscopy (STM) and density functional theory with empirical dispersion correction (DFT-D). The present STM and DFT-D results show that methylation of guanine can have subtle effects on the hydrogen-bond strength with a strong dependence on the position of methylation. It is demonstrated that the methylation of DNA nucleobases is a precise means to tune intermolecular interactions and consequently enables very specific recognition of DNA methylation by enzymes. This scheme is used to generate four different types of artificial 2D nanostructures from methylated guanine. For instance, a 2D guanine windmill motif that is stabilized by cooperative hydrogen bonding is revealed. It forms by self-assembly on a graphite surface under ambient conditions at the liquid-solid interface when the hydrogen-bonding donor at the N1 site of guanine is blocked by a methyl group.
Collapse
Affiliation(s)
- Ilko Bald
- Interdisciplinary Nanoscience Center (iNANO), Centre for DNA Nanotechnology (CDNA), Aarhus University, Denmark.
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Gutzler R, Cardenas L, Rosei F. Kinetics and thermodynamics in surface-confined molecular self-assembly. Chem Sci 2011. [DOI: 10.1039/c1sc00531f] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
31
|
Li Y, Liu L, Subramani R, Pan Y, Liu B, Yang Y, Wang C, Mamdouh W, Besenbacher F, Dong M. Building layer-by-layer 3D supramolecular nanostructures at the terephthalic acid/stearic acid interface. Chem Commun (Camb) 2011; 47:9155-7. [PMID: 21755081 DOI: 10.1039/c1cc11443c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Yinli Li
- Institute of photo-biophysics, School of Physics and Electronics, Henan University, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Xu W, Wang JG, Jacobsen MF, Mura M, Yu M, Kelly REA, Meng QQ, Laegsgaard E, Stensgaard I, Linderoth TR, Kjems J, Kantorovich LN, Gothelf KV, Besenbacher F. Supramolecular Porous Network Formed by Molecular Recognition between Chemically Modified Nucleobases Guanine and Cytosine. Angew Chem Int Ed Engl 2010; 49:9373-7. [DOI: 10.1002/anie.201003390] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
33
|
Xu W, Wang JG, Jacobsen MF, Mura M, Yu M, Kelly REA, Meng QQ, Laegsgaard E, Stensgaard I, Linderoth TR, Kjems J, Kantorovich LN, Gothelf KV, Besenbacher F. Supramolecular Porous Network Formed by Molecular Recognition between Chemically Modified Nucleobases Guanine and Cytosine. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201003390] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
34
|
Andrews KM, Pearl TP. Modification of Ag(111) surface electronic structure via weak molecular adsorption of adenine measured with low temperature scanning tunneling microscopy and spectroscopy. J Chem Phys 2010; 132:214701. [PMID: 20528035 DOI: 10.1063/1.3427248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Low temperature scanning tunneling microscopy and spectroscopy have been used to resolve modifications to the Ag(111) surface electronic structure due to the weak adsorption of the nucleobase adenine. Differential conductance spectroscopy recorded at 15 K reveals an upward energetic shift of the surface state native to Ag(111) from a band edge of -67 meV on the clean surface to +82.5 meV recorded over adenine islands. Differential conductance images show the impact of adenine domains on the density of available states as a function of energy relative to the uncovered Ag terraces as well as free-electron-like scattering in the adenine domains. Dispersion of the parallel wave vector of scattered electrons in the adenine domains is compared with the dispersion for electron scattering in bare silver and the ratio of effective masses for electrons in those bands is 1.1+/-0.2. It is hypothesized that this shift occurs due to a combination of effects brought on by the adsorption of adenine including dielectric screening of the first image potential.
Collapse
Affiliation(s)
- Katie M Andrews
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-7518, USA
| | | |
Collapse
|
35
|
Mansley CP, Smith CI, Bowfield A, Fernig DG, Edwards C, Weightman P. Prevention of surface reconstruction at the Au(110)/electrolyte interface by the adsorption of cytosine. J Chem Phys 2010; 132:214708. [DOI: 10.1063/1.3436715] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
36
|
Gonzalez-Lakunza N, Cañas-Ventura ME, Ruffieux P, Rieger R, Müllen K, Fasel R, Arnau A. Hydrogen-Bonding Fingerprints in Electronic States of Two-Dimensional Supramolecular Assemblies. Chemphyschem 2009; 10:2943-6. [DOI: 10.1002/cphc.200900722] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
37
|
Singh P, Kumar J, Toma FM, Raya J, Prato M, Fabre B, Verma S, Bianco A. Synthesis and Characterization of Nucleobase−Carbon Nanotube Hybrids. J Am Chem Soc 2009; 131:13555-62. [DOI: 10.1021/ja905041b] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prabhpreet Singh
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Jitendra Kumar
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Francesca Maria Toma
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Jesus Raya
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Maurizio Prato
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Bruno Fabre
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Sandeep Verma
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| | - Alberto Bianco
- CNRS, Institut de Biologie Moléculaire et Cellulaire, Laboratoire d’Immunologie et Chimie Thérapeutiques, 67000 Strasbourg, France, Department of Chemistry, Indian Institute of Technology, Kanpur-208016 UP, India, Dipartimento di Scienze Farmaceutiche, Università di Trieste, 34127 Trieste, Italy, SISSA, Via Beirut 2−4, 34151 Trieste, Italy, Laboratoire de RMN et de biophysique des membranes, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, 67000 Strasbourg, France, Matière Condensée et
| |
Collapse
|
38
|
Mamdouh W, Kelly REA, Dong M, Jacobsen MF, Ferapontova EE, Kantorovich LN, Gothelf KV, Besenbacher F. Self-Assembly of Artificial Nucleobase 1H-Benzimidazole-4,7-dione at the Liquid/Solid Interface. J Phys Chem B 2009; 113:8675-81. [DOI: 10.1021/jp9029419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wael Mamdouh
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Ross E. A. Kelly
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Mingdong Dong
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Mikkel F. Jacobsen
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Elena E. Ferapontova
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Lev N. Kantorovich
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Kurt V. Gothelf
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| | - Flemming Besenbacher
- Centre for DNA Nanotechnology (CDNA), The Interdisciplinary Nanoscience Center (iNANO), and Departments of Physics and Astronomy and of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark, Department of Physics and Astronomy, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom, and Department of Physics, School of Physical Sciences and Engineering, King’s College London, Strand, London WC2R 2LS, United Kingdom
| |
Collapse
|
39
|
Viladoms J, Escaja N, Frieden M, Gómez-Pinto I, Pedroso E, González C. Self-association of short DNA loops through minor groove C:G:G:C tetrads. Nucleic Acids Res 2009; 37:3264-75. [PMID: 19321501 PMCID: PMC2691830 DOI: 10.1093/nar/gkp191] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d<pCGCTCCGT>, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes.
Collapse
Affiliation(s)
- Júlia Viladoms
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, C/. Martí i Franquès 1-11, 08028 Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
40
|
Kim S, Pike R, D'Acchioli J, Walder B, Carpenter G, Sweigart D. Patterned Monolayers of Neutral and Charged Functionalized Manganese Arene Complexes on a Highly Ordered Pyrolytic Graphite Surface. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
41
|
Kim S, Pike R, D'Acchioli J, Walder B, Carpenter G, Sweigart D. Patterned Monolayers of Neutral and Charged Functionalized Manganese Arene Complexes on a Highly Ordered Pyrolytic Graphite Surface. Angew Chem Int Ed Engl 2009; 48:1762-5. [DOI: 10.1002/anie.200805760] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
42
|
Kumar AMS, Fox JD, Buerkle LE, Marchant RE, Rowan SJ. Effect of monomer structure and solvent on the growth of supramolecular nanoassemblies on a graphite surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:653-6. [PMID: 19086887 PMCID: PMC2635022 DOI: 10.1021/la803369j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The self-assembly of high aspect ratio hierarchical surface assemblies, as observed by fluid tapping mode AFM, can be achieved through careful design of the supramolecular interactions between low-molecular-weight adsorbates. Needlelike assemblies of monotopic guanine end-capped alkanes grow on a graphite surface when deposited from a water/DMSO solution. The growth of these assemblies can be monitored by AFM in real time, and the growth rate along the two different axes can be understood (through molecular modeling) in terms of the specific adsorbate-adsorbate interactions along those axes. Additionally, through judicious solvent selection (e.g., use of non-H-bonding solvents such as o-dichlorobenzene), which allows the formation of hydrogen-bonding aggregates in solution and influences the surface-adsorbate interactions, dramatically different surface assemblies of these guanine derivatives are obtained.
Collapse
Affiliation(s)
- Aryavarta M. S. Kumar
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106
| | - Justin D. Fox
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106
| | - Lauren E. Buerkle
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106
| | - Roger E. Marchant
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106
| | - Stuart J. Rowan
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, OH 44106
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106
| |
Collapse
|
43
|
Lukas M, Kelly REA, Kantorovich LN, Otero R, Xu W, Laegsgaard E, Stensgaard I, Besenbacher F. Adenine monolayers on the Au(111) surface: Structure identification by scanning tunneling microscopy experiment and ab initio calculations. J Chem Phys 2009; 130:024705. [DOI: 10.1063/1.3046690] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
44
|
Otero R, Xu W, Lukas M, Kelly REA, Laegsgaard E, Stensgaard I, Kjems J, Kantorovich LN, Besenbacher F. Specificity of watson-crick base pairing on a solid surface studied at the atomic scale. Angew Chem Int Ed Engl 2008; 47:9673-6. [PMID: 19003837 DOI: 10.1002/anie.200803333] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Roberto Otero
- Interdisciplinary Nanoscience Center (iNANO), Center for DNA Nanotechnology (CDNA), and Department of Physics and Astronomy, University of Aarhus, Ny Munkegade, 8000 Aarhus, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Höök F, Kasemo B, Grunze M, Zauscher S. Quantitative biological surface science: challenges and recent advances. ACS NANO 2008; 2:2428-2436. [PMID: 19206275 DOI: 10.1021/nn800800v] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological surface science is a broad, interdisciplinary subfield of surface science, where properties and processes at biological and synthetic surfaces and interfaces are investigated, and where biofunctional surfaces are fabricated. The need to study and to understand biological surfaces and interfaces in liquid environments provides sizable challenges as well as fascinating opportunities. Here, we report on recent progress in biological surface science that was described within the program assembled by the Biomaterial Interface Division of the Science and Technology of Materials, Interfaces and Processes (www.avs.org) during their 55th International Symposium and Exhibition held in Boston, October 19-24, 2008. The selected examples show that the rapid progress in nanoscience and nanotechnology, hand-in-hand with theory and simulation, provides increasingly sophisticated methods and tools to unravel the mechanisms and details of complex processes at biological surfaces and in-depth understanding of biomolecular surface interactions.
Collapse
Affiliation(s)
- Fredrik Höök
- Department of Applied Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | | | | | |
Collapse
|
46
|
Otero R, Xu W, Lukas M, Kelly R, Laegsgaard E, Stensgaard I, Kjems J, Kantorovich L, Besenbacher F. Specificity of Watson-Crick Base Pairing on a Solid Surface Studied at the Atomic Scale. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200803333] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
47
|
Klappenberger F, Cañas-Ventura ME, Clair S, Pons S, Schlickum U, Qu ZR, Strunskus T, Comisso A, Wöll C, Brune H, Kern K, De Vita A, Ruben M, Barth JV. Does the Surface Matter? Hydrogen-Bonded Chain Formation of an Oxalic Amide Derivative in a Two- and Three-Dimensional Environment. Chemphyschem 2008; 9:2522-30. [DOI: 10.1002/cphc.200800590] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
48
|
Lee WJ, Weng MH, Ju SP, Chen HC. Lock and key behaviours of an aromatic carboxylic acid molecule with differing conformations on an Au (111) surface. Mol Phys 2008. [DOI: 10.1080/00268970802473976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Wen-Jay Lee
- a Department of Mechanical and Electro-Mechanical Engineering , Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University Kaohsiung , Taiwan 804
| | - Meng-Hsiung Weng
- a Department of Mechanical and Electro-Mechanical Engineering , Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University Kaohsiung , Taiwan 804
| | - Shin-Pon Ju
- a Department of Mechanical and Electro-Mechanical Engineering , Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University Kaohsiung , Taiwan 804
| | - Hui-Chuan Chen
- a Department of Mechanical and Electro-Mechanical Engineering , Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University Kaohsiung , Taiwan 804
| |
Collapse
|
49
|
Kelly REA, Lukas M, Kantorovich LN, Otero R, Xu W, Mura M, Lægsgaard E, Stensgaard I, Besenbacher F. Understanding the disorder of the DNA base cytosine on the Au(111) surface. J Chem Phys 2008; 129:184707. [DOI: 10.1063/1.3001585] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
50
|
Popoff A, Fichou D. Immobilization of paracetamol and benzocaine pro-drug derivatives as long-range self-organized monolayers on graphite. Colloids Surf B Biointerfaces 2008; 63:153-8. [DOI: 10.1016/j.colsurfb.2007.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/01/2007] [Accepted: 11/06/2007] [Indexed: 11/16/2022]
|