Exploring internal structures and properties of terpolymer fibers via real-space characterizations

• Michael R. Roenbeck and
• Kenneth E. Strawhecker

Beilstein J. Nanotechnol. 2023, 14, 1004–1017, doi:10.3762/bjnano.14.83

• chemistry of Kevlar® (Figure 1) leads to a well-ordered molecular structure (i.e., ‘ACACAC…’ in Figure 9), which should enhance load transfer at this scale compared to Technora®. Together, the more uniform molecular sequencing and the resulting microstructure in Kevlar® appear to explain why K29 has higher

• Technora® subdomains may be especially amenable to this characterization, which could shed more light on the sequencing of molecular subdomains (Figure 9) discussed here and in previous reports [2][3][4][5]. In addition, it would be interesting to apply the FIB notch technique to Kevlar® and Technora

• distributions. Solid vertical lines denote mean bulk values reported from published microscale experiments [8][19]. Schematic of possible molecular sequencing in Technora® fibers. (a) With random sequences of molecular subunits (e.g., ACBC, top left), adjacent extended chain molecules can form ordered or

DNA aptamer selection and construction of an aptasensor based on graphene FETs for Zika virus NS1 protein detection

• Nathalie B. F. Almeida,
• Thiago A. S. L. Sousa,
• Viviane C. F. Santos,
• Camila M. S. Lacerda,
• Thais G. Silva,
• Rafaella F. Q. Grenfell,
• Flavio Plentz and
• Antero S. R. Andrade

Beilstein J. Nanotechnol. 2022, 13, 873–881, doi:10.3762/bjnano.13.78

• repeated after each positive selection. DNA cloning and sequencing The ssDNA sequences obtained after the third cycle of the CE-SELEX procedure were cloned and sequenced [20]. PCR was performed, and the products were cloned into pGEM®-T easy vector systems (Promega). The plasmid was transformed into

• methodology using the M13 promoter primer. The sequencing was carried out at the René Rachou Institute (FIOCRUZ/Minas). Secondary structure prediction The secondary structure was predicted using Mfold analysis [21][22]. Determination of the dissociation constant Enzyme-linked oligonucleotide assay (ELONA) was

A review of defect engineering, ion implantation, and nanofabrication using the helium ion microscope

• Frances I. Allen

Beilstein J. Nanotechnol. 2021, 12, 633–664, doi:10.3762/bjnano.12.52

Bio-imaging with the helium-ion microscope: A review

• Matthias Schmidt,
• James M. Byrne and
• Ilari J. Maasilta

Beilstein J. Nanotechnol. 2021, 12, 1–23, doi:10.3762/bjnano.12.1

Using gold nanoparticles to detect single-nucleotide polymorphisms: toward liquid biopsy

• María Sanromán Iglesias and
• Marek Grzelczak

Beilstein J. Nanotechnol. 2020, 11, 263–284, doi:10.3762/bjnano.11.20

• -art of advanced techniques in the field of genomics such as digital PCR, next generation sequencing (NGS), fluorescence in situ hybridization (FISH) and BEAMing. These facilitate the fast design of mutational profiles of tumor DNA, helping the prioritization of anti-cancer therapy. Although these

• or the use of antifouling polymers such as polyethylene glycol. Finally, the availability of whole-genome sequencing as offered by recently established private companies (e.g., Veritas Genetics and Novogene) allows for the determination of hundreds of mutations from a single sample at relatively low

Serum type and concentration both affect the protein-corona composition of PLGA nanoparticles

• Katrin Partikel,
• Robin Korte,
• Dennis Mulac,
• Hans-Ulrich Humpf and
• Klaus Langer

Beilstein J. Nanotechnol. 2019, 10, 1002–1015, doi:10.3762/bjnano.10.101

• (Karlsruhe, Germany). The dye Coomassie Brilliant Blue G-250 was purchased from VWR Life science AMRESCO (Solon, Ohio). Bovine serum albumin (BSA), DL-dithiothreitol (DTT), and iodoacetamide (IAA) were obtained from Sigma-Aldrich (Steinheim, Germany). Trypsin (sequencing grade) for protein digestion was

Nanoporous silicon nitride-based membranes of controlled pore size, shape and areal density: Fabrication as well as electrophoretic and molecular filtering characterization

• Axel Seidenstücker,
• Stefan Beirle,
• Fabian Enderle,
• Paul Ziemann,
• Othmar Marti and
• Alfred Plettl

Beilstein J. Nanotechnol. 2018, 9, 1390–1398, doi:10.3762/bjnano.9.131

• mechanical stability together with chemical inertness. In general, thin single layers made from pure materials such as polymers, silicon, and silicon nitride are used. Recently, ultrathin graphene membranes became very promising for various applications including sequencing. However, the controlled

False positives and false negatives measure less than 0.001% in labeling ssDNA with osmium tetroxide 2,2’-bipyridine

• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 1434–1446, doi:10.3762/bjnano.7.135

• surrogate for nanopore-based DNA sequencing due to OsBp’s “perfect” label attributes. Osmylated deoxyoligos translocate unassisted and measurably slow via sub-2 nm SiN solid-state nanopores, as well as via the alpha-hemolysin (α-HL) pore. Both nanopores discriminate clearly between osmylated and intact

• properties of the degradation products via nanopore translocation can be evaluated to assure base calling quality in a DNA sequencing effort. Keywords: α-hemolysin; capillary electrophoresis; DNA sequencing; high-performance liquid chromatography; nanopores; osmium tetroxide bipyridine; osmylated oligos

• academia, government, and industry pushed DNA sequencing to next-generation technologies [3] that flourished exponentially due to technological advancements in parallelization, miniaturization, and bioinformatics. DNA sequencing was and still is an extension of the Sanger sequencing-by-synthesis (SBS

Reconstitution of the membrane protein OmpF into biomimetic block copolymer–phospholipid hybrid membranes

• Matthias Bieligmeyer,
• Franjo Artukovic,
• Stephan Nussberger,
• Thomas Hirth,
• Thomas Schiestel and
• Michaela Müller

Beilstein J. Nanotechnol. 2016, 7, 881–892, doi:10.3762/bjnano.7.80

• lipid membranes with high fidelity and selectivity. In the field of biotechnology, they are particularly attractive for single-molecule DNA sequencing [1][2][3][4][5] and stochastic sensing of ions and macromolecules [6][7][8][9][10]. The well-defined dimensions of the protein pores furthermore offer a

Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies

• Claudia Koch,
• Fabian J. Eber,
• Carlos Azucena,
• Alexander Förste,
• Stefan Walheim,
• Thomas Schimmel,
• Alexander M. Bittner,
• Holger Jeske,
• Hartmut Gliemann,
• Sabine Eiben,
• Fania C. Geiger and
• Christina Wege

Beilstein J. Nanotechnol. 2016, 7, 613–629, doi:10.3762/bjnano.7.54

• recent ICTV report from the end of 2011 [13] lists 87 families with 2,284 virus and viroid species and many yet unassigned viruses, which had increased to 3,186 species by end of 2015 [14]: The identification of further viruses is accelerating rapidly due to next generation sequencing techniques

Mismatch detection in DNA monolayers by atomic force microscopy and electrochemical impedance spectroscopy

• Maryse D. Nkoua Ngavouka,
• Pietro Capaldo,
• Elena Ambrosetti,
• Giacinto Scoles,
• Loredana Casalis and
• Pietro Parisse

Beilstein J. Nanotechnol. 2016, 7, 220–227, doi:10.3762/bjnano.7.20

• University of Trieste, Via Valerio 9, Trieste, Italy Department of Medical and Biological Sciences, University of Udine, Udine, Italy 10.3762/bjnano.7.20 Abstract Background: DNA hybridization is at the basis of most current technologies for genotyping and sequencing, due to the unique properties of DNA

• microRNAs or in genomic DNA. Keywords: atomic force microscopy; DNA monolayers; electrochemical impedance spectroscopy; hybridization; mismatches; Introduction Most current technologies for genotyping and sequencing are based on DNA hybridization, exploiting the high grade of selectivity due to the unique

Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore

• Yun Ding and
• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 91–101, doi:10.3762/bjnano.7.11

• the pore. With the assistance of a processing enzyme to slow down translocation, nanopore-based DNA sequencing is now a commercially available platform. However, accurate base calling is challenging because α-HL senses a sequence, and not a single nucleotide. Osmylated DNA was recently proposed as a

• surrogate for nanopore-based sequencing. Osmylation is the addition of osmium tetroxide 2,2’-bipyridine (OsBp) to the C5–C6 pyrimidine double bond. The process is simple, selective for deoxythymidine (dT) over deoxycytidine (dC), unreactive towards the purines, practically 100% effective, and strikingly

• above detection limits, may be further optimized, and clear the way for nanopore-based sequencing using osmylated DNA. Keywords: DNA sequencing; α-hemolysin; ion-channel measurements; nanopore; osmium tetroxide bipyridine; osmylated oligos; osmylation; single-stranded DNA (ssDNA); Introduction

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• need for standards and databases to house the extensive amount of data generated by gene expression and sequencing experiments, yielding such efforts as the development of the minimum information about a microarray experiment (MIAME) [16]. As a result, the MIAME guideline, and others, have been adopted

Functionalization of α-synuclein fibrils

• Simona Povilonienė,
• Vida Časaitė,
• Virginijus Bukauskas,
• Arūnas Šetkus,
• Juozas Staniulis and
• Rolandas Meškys

Beilstein J. Nanotechnol. 2015, 6, 124–133, doi:10.3762/bjnano.6.12

• screening and restriction analysis. The presence of the desired mutation was verified by DNA sequencing (Sequencing Center, Institute of Biotechnlogy, Vilnius University). Expression and purification of mutant α-SynC141 Wild-type α-Syn and α-SynC141 mutant were purified as described by Der-Sarkissian et al

Synthesis of hydrophobic photoluminescent carbon nanodots by using L-tyrosine and citric acid through a thermal oxidation route

• Venkatesh Gude

Beilstein J. Nanotechnol. 2014, 5, 1513–1522, doi:10.3762/bjnano.5.164

• : composite materials; fluorescence quenching; hydrophobic; luminescence; upconversion; Introduction The synthesis of fluorescent functional materials raised significant interest in order to understand biological processes such as DNA sequencing, detection of DNA-hybridization, protein sensing, single

Molecular biology approaches in bioadhesion research

• Marcelo Rodrigues,
• Birgit Lengerer,
• Thomas Ostermann and
• Peter Ladurner

Beilstein J. Nanotechnol. 2014, 5, 983–993, doi:10.3762/bjnano.5.112

• isolation of genes, and the study of their expression and function (Figure 1). Methods in the field have advanced tremendously in recent years, largely due to the recent advances in DNA and RNA sequencing, and protein analysis. These technologies allow research objectives to move from the analyses of single

• genes to the study of more complete sets of genes, or to examine all genes that are expressed at once. Now, functional genomics may reveal the transcriptional program of entire genomes by RNA sequencing. The recent advances in molecular biology have made available a wide range of research tools and

• temporary adhesives that contain a significant carbohydrate fraction usually also rely on proteins for adhesion. Review 1. Transcriptome sequencing and differential gene expression 1.1 What is a transcriptome? A transcriptome represents the entirety of RNA molecules expressed in an organism, a tissue or a

Controlled deposition and combing of DNA across lithographically defined patterns on silicon

• Zeinab Esmail Nazari and
• Leonid Gurevich

Beilstein J. Nanotechnol. 2013, 4, 72–76, doi:10.3762/bjnano.4.8

• nanoelectronics [7][8][15][16], many biomedical and genomic studies employ molecular combing as an effective tool for the generation of highly ordered alignments of DNA for various investigations, including gene mapping, DNA sequencing, and analysis [17][18]. Most combing methods reported so far involve

Nanolesions induced by heavy ions in human tissues: Experimental and theoretical studies

• Marcus Bleicher,
• Lucas Burigo,
• Marco Durante,
• Maren Herrlitz,
• Michael Krämer,
• Igor Mishustin,
• Iris Müller,
• Francesco Natale,
• Igor Pshenichnov,
• Stefan Schramm,
• Gisela Taucher-Scholz and
• Cathrin Wälzlein

Beilstein J. Nanotechnol. 2012, 3, 556–563, doi:10.3762/bjnano.3.64

• . We have also started a full-genome deep-sequencing approach to correlate the microscopy data with the cellular response. In principle, the nanolesion structure can be predicted by accurate Monte Carlo simulations of the energy deposition by the projectile and of the target structure. We used the

Distinction of nucleobases – a tip-enhanced Raman approach

• Regina Treffer,
• Xiumei Lin,
• Elena Bailo,
• Tanja Deckert-Gaudig and
• Volker Deckert

Beilstein J. Nanotechnol. 2011, 2, 628–637, doi:10.3762/bjnano.2.66

• , Jena University, Helmholtzweg 4, D-07743 Jena, Germany 10.3762/bjnano.2.66 Abstract The development of novel DNA sequencing methods is one of the ongoing challenges in various fields of research seeking to address the demand for sequence information. However, many of these techniques rely on some kind

• of labeling or amplification steps. Here we investigate the intrinsic properties of tip-enhanced Raman scattering (TERS) towards the development of a novel, label-free, direct sequencing method. It is known that TERS allows the acquisition of spectral information with high lateral resolution and

• of sensitivity and reproducibility shows that the crucial demands for a sequencing procedure are met. Keywords: DNA; nanoscale analysis; Raman; sequencing; TERS; Introduction The determination of the exact nucleobase sequence of DNA is of great importance for research in the life sciences. The