scholarly journals Three-dimensional graphene nanoribbons as a framework for molecular assembly and local probe chemistry

2020 ◽  
Vol 6 (9) ◽  
pp. eaay8913 ◽  
Author(s):  
Shigeki Kawai ◽  
Ondřej Krejčí ◽  
Tomohiko Nishiuchi ◽  
Keisuke Sahara ◽  
Takuya Kodama ◽  
...  
Keyword(s):  
Single Molecule ◽  
Graphene Nanoribbons ◽  
Theoretical Calculations ◽  
Bromine Atom ◽  
Three Dimensional ◽  
Fullerene Molecule ◽  
Molecular Assembly ◽  
Surface Chemical Reaction ◽  
Molecular Chemistry ◽  
Single Molecule Level

Recent advances in state-of-the-art probe microscopy allow us to conduct single molecular chemistry via tip-induced reactions and direct imaging of the inner structure of the products. Here, we synthesize three-dimensional graphene nanoribbons by on-surface chemical reaction and take advantage of tip-induced assembly to demonstrate their capability as a playground for local probe chemistry. We show that the radical caused by tip-induced debromination can be reversibly terminated by either a bromine atom or a fullerene molecule. The experimental results combined with theoretical calculations pave the way for sequential reactions, particularly addition reactions, by a local probe at the single-molecule level decoupled from the surface.

scholarly journals Nucleic acid-based nanoengineering: novel structures for biomedical applications

2011 ◽  
Vol 1 (5) ◽  
pp. 702-724 ◽  
Author(s):  
Hanying Li ◽  
Thomas H. LaBean ◽  
Kam W. Leong
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Single Molecule ◽  
Biomedical Applications ◽  
Three Dimensional ◽  
Base Pairs ◽  
Single Molecule Level ◽  
Stimulus Responsive ◽  
Bioactive Agents ◽  
Novel Structures

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

scholarly journals Nanopore microscope identifies RNA isoforms with structural colors

2021 ◽  
Author(s):  
Filip N Boskovic ◽  
Ulrich Felix Keyser
Keyword(s):  
Single Molecule ◽  
Three Dimensional ◽  
Rna Structures ◽  
Transcript Isoforms ◽  
Single Molecule Level ◽  
Structural Colors ◽  
Rna Targets ◽  
Dna Strands ◽  
One Step ◽  
Simultaneous Identification

Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colors. Structural colors consist of DNA structures, protein labels, native RNA structures, or a combination of all three. The sequence of structural colors of RNA IDs enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one step, enzyme-free reaction in a complex human transcriptome using single-molecule readout.

scholarly journals De Novo Design of a Nanopore for DNA Detection that Incorporates a β-Hairpin Peptide

2021 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Masataka Usami ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

Abstract The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length. Moreover, the larger sized nanopore can discriminate and human telomeric DNA (G-quadruplex, G4). The blocking current signals allowed us to investigate the translocation behavior of dsDNA or G4 structure at the single molecule level. Such de novo design of peptide sequences has the potential to create novel nanopores, which would be applicable in molecular transporter between across lipid membrane.

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

2020 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
Yoshio Hamada ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

scholarly journals De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

2020 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
Yoshio Hamada ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

scholarly journals Three-dimensional tracking of tethered particles for probing nanometer-scale single-molecule dynamics using plasmonic microscope

2021 ◽  
Author(s):  
Guangzhong Ma ◽  
Zijian Wan ◽  
Yunze Yang ◽  
Wenwen Jing ◽  
Shaopeng Wang
Keyword(s):  
Single Molecule ◽  
High Spatial Resolution ◽  
Imaging Technique ◽  
Three Dimensional ◽  
Axial Direction ◽  
Nanometer Scale ◽  
3D Tracking ◽  
Single Molecule Level ◽  
Plasmonic Imaging ◽  
Molecule Dynamics

Three-dimensional (3D) tracking of surface-tethered single-particle reveals the dynamics of the molecular tether. However, most 3D tracking techniques lack precision, especially in axial direction, for measuring the dynamics of biomolecules with spatial scale of several nanometers. Here we present a plasmonic imaging technique that can track the motion of ~100 tethered particles in 3D simultaneously with sub-nanometer axial precision at millisecond time resolution. By tracking the 3D coordinates of tethered particle with high spatial resolution, we are able to determine the dynamics of single short DNA and study its interaction with enzyme. We further show that the particle motion pattern can be used to identify specific and non-specific interactions in immunoassays. We anticipate that our 3D tracking technique can contribute to the understanding of molecular dynamics and interactions at the single-molecule level.

De Novo Design of a Nanopore for DNA Detection Incorporating a β-hairpin Peptide

2020 ◽  
Author(s):  
Keisuke Shimizu ◽  
Batsaikhan Mijiddorj ◽  
Shuhei Yoshida ◽  
Shiori Akayama ◽  
Yoshio Hamada ◽  
...  
Keyword(s):  
Single Molecule ◽  
Protein Design ◽  
Lipid Membrane ◽  
De Novo ◽  
Three Dimensional ◽  
Bilayer Lipid Membrane ◽  
De Novo Design ◽  
Dimensional Structure ◽  
Practical Applications ◽  
Single Molecule Level

The amino acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo protein design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device with practical applications. This peptide, named SV28, forms nanopore structures ranging from 1.6 to 6.2 nm in diameter assembled from 7 to 18 monomers. The nanopore formed with a diameter of 5 nm is able to detect long double-stranded DNA (dsDNA) with 1 kbp length, and measurement of current signals allowed us to investigate the translocation behavior of dsDNA at the single molecule level. Such de novo design of peptide sequences has the potential to create assembled structure in lipid membrane such as novel nanopores, which would also be applicable in molecular transporter between inside and outside of lipid membrane.

scholarly journals Tracking On-Surface Chemistry with Atomic Precision

Synlett ◽  
2017 ◽  
Vol 28 (19) ◽  
pp. 2509-2516 ◽  
Author(s):  
Peter Jacobse ◽  
Marc-Etienne Moret ◽  
Robertus Klein Gebbink ◽  
Ingmar Swart
Keyword(s):  
Atomic Force Microscopy ◽  
Single Molecule ◽  
Graphene Nanoribbons ◽  
Single Molecule Level ◽  
Force Microscopy ◽  
The Past ◽  
Atomic Force ◽  
Atomic Precision ◽  
Different Types ◽  
Insight Into

The field of on-surface synthesis has seen a tremendous development in the past decade as an exciting new methodology towards atomically well-defined nanostructures. A strong driving force in this respect is its inherent compatibility with scanning probe techniques, which allows one to ‘view’ the reactants and products at the single-molecule level. In this article, we review the ability of noncontact atomic force microscopy to study on-surface chemical reactions with atomic precision. We highlight recent advances in using noncontact atomic force microscopy to obtain mechanistic insight into reactions and focus on the recently elaborated mechanisms in the formation of different types of graphene nanoribbons.

scholarly journals Real-Time Video Imaging of Mechanical Motions of a Single Molecular Shuttle

2019 ◽  
Author(s):  
Toshiki Shimizu ◽  
Dominik Lungerich ◽  
Joshua Stuckner ◽  
Mitsuhiro Murayama ◽  
Koji Harano ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Quantum Control ◽  
Fullerene Molecule ◽  
Video Imaging ◽  
Strongly Coupled ◽  
Single Molecule Level ◽  
The Rich ◽  
Molecular Shuttle

Miniatured machines has open up a new dimension of chemistry, studied usually as an average over numerous molecules or for a single molecule bound on a robust substrate. Mechanical motions at a single molecule level, however, are under quantum control, strongly coupled with fluctuations of its environment -- a system rarely addressed because an efficient way of observing the nanomechanical motions in real time is lacking. Here, we report sub-ms sub-Å precision in situ video imaging of a single fullerene molecule shuttling, rotating, and interacting with a vibrating carbon nanotube, using an electron microscope, a fast camera, and a denoising algorithm. We have realized high spatial precision of distance measurement with the standard error of the mean as small as ± 0.01 nm, and revealed the rich molecular dynamics, where motions are non-linear, stochastic and often non-repeatable, and a work and energy relationship at a molecular level previously undetected by time-averaged measurements or microscopy.

scholarly journals Real-Time Video Imaging of Mechanical Motions of a Single Molecular Shuttle

2019 ◽  
Author(s):  
Toshiki Shimizu ◽  
Dominik Lungerich ◽  
Joshua Stuckner ◽  
Mitsuhiro Murayama ◽  
Koji Harano ◽  
...  
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Quantum Control ◽  
Fullerene Molecule ◽  
Video Imaging ◽  
Strongly Coupled ◽  
Single Molecule Level ◽  
The Rich ◽  
Molecular Shuttle

Miniatured machines has open up a new dimension of chemistry, studied usually as an average over numerous molecules or for a single molecule bound on a robust substrate. Mechanical motions at a single molecule level, however, are under quantum control, strongly coupled with fluctuations of its environment -- a system rarely addressed because an efficient way of observing the nanomechanical motions in real time is lacking. Here, we report sub-ms sub-Å precision in situ video imaging of a single fullerene molecule shuttling, rotating, and interacting with a vibrating carbon nanotube, using an electron microscope, a fast camera, and a denoising algorithm. We have realized high spatial precision of distance measurement with the standard error of the mean as small as ± 0.01 nm, and revealed the rich molecular dynamics, where motions are non-linear, stochastic and often non-repeatable, and a work and energy relationship at a molecular level previously undetected by time-averaged measurements or microscopy.

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