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Special Issue "Single Biomolecule Detection"

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A special issue of Sensors (ISSN 1424-8220). This special issue belongs to the section "Biosensors".

Deadline for manuscript submissions: closed (15 August 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Masateru Taniguchi (Website)

The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
Phone: +81-6-6879-8445
Fax: +81-6-6875-2440
Interests: single molecular science; single molecular devices; nanofabrications

Special Issue Information

Dear Colleagues,

Single-biomolecule detection technologies with high throughput and high accuracy can provide new information in the fields of medical science and biology, and they are expected to be utilized as innovative technologies in the future development of medical treatments and drugs. An ideal single-biomolecule detection technology can identify targeted biomolecules and analyze blood and spittle containing specific biomolecules using an integrated chip, where pretreatment devices exclude all molecules except targeted molecules and after-treatment devices identify and treat targeted molecules. For example, using an integrated chip composed of MEMS/NEMS and nanopores, DNA molecules are separated/extracted from blood and sequenced by MEMS/NEMS and nanopore devices, respectively. However, pretreatment and after-treatment devices are developed individually in different fields, and there are few integrated devices that facilitate both pretreatment and after-treatment processes. Integration is a big barrier for practical single-biomolecule detection technologies.

The aim of this special issue is to furnish an opportunity to break through the barrier and discover innovative single-biomolecule detection technologies. Therefore, the papers include a wide range of studies regarding pretreatment, after-treatment, and integration devices, including MEMS, NEMS, fluid devices, nanopore devices, and single-molecule optical and electrical detection technologies.

Both review articles and original research papers relating to pretreatment and after-treatment devices are solicited. There is particular interest in papers concerning technologies where optical, electrical, and magnetic detections are performed using pretreatment and after-treatment devices fabricated by microfabrication technologies in order to focus on practical applications of single-biomolecule detection technologies using integrated devices.

Prof. Dr. Masateru Taniguchi
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Sensors is an international peer-reviewed Open Access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs).

Keywords

  • Single biomolecules
  • MEMS/NEMS
  • Nanopore
  • Pretreatment devices
  • After-treatment devices

Related Special Issue

Published Papers (5 papers)

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Research

Jump to: Review

Open AccessArticle Nanomechanical DNA Origami pH Sensors
Sensors 2014, 14(10), 19329-19335; doi:10.3390/s141019329
Received: 25 August 2014 / Revised: 30 September 2014 / Accepted: 8 October 2014 / Published: 16 October 2014
Cited by 5 | PDF Full-text (1756 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA [...] Read more.
Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5'-AACCCCAACCCC-3'), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors. Full article
(This article belongs to the Special Issue Single Biomolecule Detection)
Figures

Open AccessArticle Electroless Deposition and Nanolithography Can Control the Formation of Materials at the Nano-Scale for Plasmonic Applications
Sensors 2014, 14(4), 6056-6083; doi:10.3390/s140406056
Received: 20 December 2013 / Revised: 10 March 2014 / Accepted: 21 March 2014 / Published: 27 March 2014
Cited by 10 | PDF Full-text (1056 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The new revolution in materials science is being driven by our ability to manipulate matter at the molecular level to create structures with novel functions and properties. The aim of this paper is to explore new strategies to obtain plasmonic metal nanostructures [...] Read more.
The new revolution in materials science is being driven by our ability to manipulate matter at the molecular level to create structures with novel functions and properties. The aim of this paper is to explore new strategies to obtain plasmonic metal nanostructures through the combination of a top down method, that is electron beam lithography, and a bottom up technique, that is the chemical electroless deposition. This technique allows a tight control over the shape and size of bi- and three-dimensional metal patterns at the nano scale. The resulting nanostructures can be used as constituents of Surface Enhanced Raman Spectroscopy (SERS) substrates, where the electromagnetic field is strongly amplified. Our results indicate that, in electroless growth, high quality metal nanostructures with sizes below 50 nm may be easily obtained. These findings were explained within the framework of a diffusion limited aggregation (DLA) model, that is a simulation model that makes it possible to decipher, at an atomic level, the rules governing the evolution of the growth front; moreover, we give a description of the physical mechanisms of growth at a basic level. In the discussion, we show how these findings can be utilized to fabricate dimers of silver nanospheres where the size and shape of those spheres is controlled with extreme precision and can be used for very large area SERS substrates and nano-optics, for single molecule detection. Full article
(This article belongs to the Special Issue Single Biomolecule Detection)
Figures

Open AccessArticle A New Direct Single-Molecule Observation Method for DNA Synthesis Reaction Using Fluorescent Replication Protein A
Sensors 2014, 14(3), 5174-5182; doi:10.3390/s140305174
Received: 9 December 2013 / Revised: 25 February 2014 / Accepted: 7 March 2014 / Published: 12 March 2014
Cited by 1 | PDF Full-text (383 KB) | HTML Full-text | XML Full-text
Abstract
Using a single-stranded region tracing system, single-molecule DNA synthesis reactions were directly observed in microflow channels. The direct single-molecule observations of DNA synthesis were labeled with a fusion protein consisting of the ssDNA-binding domain of a 70-kDa subunit of replication protein A [...] Read more.
Using a single-stranded region tracing system, single-molecule DNA synthesis reactions were directly observed in microflow channels. The direct single-molecule observations of DNA synthesis were labeled with a fusion protein consisting of the ssDNA-binding domain of a 70-kDa subunit of replication protein A and enhanced yellow fluorescent protein (RPA-YFP). Our method was suitable for measurement of DNA synthesis reaction rates with control of the ssλDNA form as stretched ssλDNA (+flow) and random coiled ssλDNA (−flow) via buffer flow. Sequentially captured photographs demonstrated that the synthesized region of an ssλDNA molecule monotonously increased with the reaction time. The DNA synthesis reaction rate of random coiled ssλDNA (−flow) was nearly the same as that measured in a previous ensemble molecule experiment (52 vs. 50 bases/s). This suggested that the random coiled form of DNA (−flow) reflected the DNA form in the bulk experiment in the case of DNA synthesis reactions. In addition, the DNA synthesis reaction rate of stretched ssλDNA (+flow) was approximately 75% higher than that of random coiled ssλDNA (−flow) (91 vs. 52 bases/s). The DNA synthesis reaction rate of the Klenow fragment (3’-5’exo–) was promoted by DNA stretching with buffer flow. Full article
(This article belongs to the Special Issue Single Biomolecule Detection)
Open AccessArticle Topoisomerase I as a Biomarker: Detection of Activity at the Single Molecule Level
Sensors 2014, 14(1), 1195-1207; doi:10.3390/s140101195
Received: 18 December 2013 / Revised: 3 January 2014 / Accepted: 7 January 2014 / Published: 10 January 2014
Cited by 5 | PDF Full-text (370 KB) | HTML Full-text | XML Full-text
Abstract
Human topoisomerase I (hTopI) is an essential cellular enzyme. The enzyme is often upregulated in cancer cells, and it is a target for chemotherapeutic drugs of the camptothecin (CPT) family. Response to CPT-based treatment is dependent on hTopI activity, and reduction in [...] Read more.
Human topoisomerase I (hTopI) is an essential cellular enzyme. The enzyme is often upregulated in cancer cells, and it is a target for chemotherapeutic drugs of the camptothecin (CPT) family. Response to CPT-based treatment is dependent on hTopI activity, and reduction in activity, and mutations in hTopI have been reported to result in CPT resistance. Therefore, hTOPI gene copy number, mRNA level, protein amount, and enzyme activity have been studied to explain differences in cellular response to CPT. We show that Rolling Circle Enhanced Enzyme Activity Detection (REEAD), allowing measurement of hTopI cleavage-religation activity at the single molecule level, may be used to detect posttranslational enzymatic differences influencing CPT response. These differences cannot be detected by analysis of hTopI gene copy number, mRNA amount, or protein amount, and only become apparent upon measuring the activity of hTopI in the presence of CPT. Furthermore, we detected differences in the activity of the repair enzyme tyrosyl-DNA phosphodiesterase 1, which is involved in repair of hTopI-induced DNA damage. Since increased TDP1 activity can reduce cellular CPT sensitivity we suggest that a combined measurement of TDP1 activity and hTopI activity in presence of CPT will be the best determinant for CPT response. Full article
(This article belongs to the Special Issue Single Biomolecule Detection)

Review

Jump to: Research

Open AccessReview Electron Transfer-Based Single Molecule Fluorescence as a Probe for Nano-Environment Dynamics
Sensors 2014, 14(2), 2449-2467; doi:10.3390/s140202449
Received: 14 December 2013 / Revised: 22 January 2014 / Accepted: 27 January 2014 / Published: 3 February 2014
Cited by 3 | PDF Full-text (2667 KB) | HTML Full-text | XML Full-text
Abstract
Electron transfer (ET) is one of the most important elementary processes that takes place in fundamental aspects of biology, chemistry, and physics. In this review, we discuss recent research on single molecule probes based on ET. We review some applications, including the [...] Read more.
Electron transfer (ET) is one of the most important elementary processes that takes place in fundamental aspects of biology, chemistry, and physics. In this review, we discuss recent research on single molecule probes based on ET. We review some applications, including the dynamics of glass-forming systems, surface binding events, interfacial ET on semiconductors, and the external field-induced dynamics of polymers. All these examples show that the ET-induced changes of fluorescence trajectory and lifetime of single molecules can be used to sensitively probe the surrounding nano-environments. Full article
(This article belongs to the Special Issue Single Biomolecule Detection)

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Site-Directed Synthesis of Freestanding Graphene Nano-Membrane Arrays
Authors:
Pradeep Waduge, Joseph Larkin, Moneesh Upmanyu, Swastik Kar, and Meni Wanunu
Affiliation:
Department of Physics, Northeastern University, 110 Forsyth St, Dana 111, Boston MA 02115, USA; E-Mail: wanunu@neu.edu
Abstract:
Freestanding graphene membranes are unique materials: the combination of atomically thin dimensions, remarkable mechanical robustness, and chemical stability, make porous graphene membrane devices attractive for various purification and detection applications. Nanopores in graphene and other 2D materials have been identified as promising devices for next-generation DNA sequencing, based on readout of either transverse DNA base-gated current or through-pore ion current. While several ground breaking studies of graphene-based nanopores for DNA analysis have been reported, all methods reported to date require a physical transfer of the graphene from its source of production onto an aperture support. The transfer process suffers from several drawbacks that include contamination, mechanical strain, and a low device throughput that arises from mechanical damage. In this work, we report a novel scalable approach for site-directed fabrication of pinhole-free graphene nano-membranes. Our approach yields high quality few-layer graphene membranes produced in less than a day on sub-micron apertures using a few steps. We highlight the functionality of these graphene devices by measuring DNA translocation through electron-beam fabricated nanopores in such membranes.

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