Ion beam processing of DNA origami nanostructures

• Leo Sala,
• Agnes Zerolová,
• Violaine Vizcaino,
• Alain Mery,
• Alicja Domaracka,
• Hermann Rothard,
• Philippe Boduch,
• Dominik Pinkas and
• Jaroslav Kocišek

Beilstein J. Nanotechnol. 2024, 15, 207–214, doi:10.3762/bjnano.15.20

• modifications, which can be further exploited in novel material processing at the nanoscale. Experimental DNA origami synthesis Rothemund 2D triangles were synthesized by mixing 6 nM M13mp18 scaffold ssDNA with 144 nM staple strands in 1× TAE buffer supplemented with 12.5 mM MgCl2 (folding buffer, FOB) and

Rapid and sensitive detection of box turtles using an electrochemical DNA biosensor based on a gold/graphene nanocomposite

• Abu Hashem,
• M. A. Motalib Hossain,
• Ab Rahman Marlinda,
• Mohammad Al Mamun,
• Khanom Simarani and
• Mohd Rafie Johan

Beilstein J. Nanotechnol. 2022, 13, 1458–1472, doi:10.3762/bjnano.13.120

• ssDNA recognition elements [31]. As per our observation, this is the first application of an electrochemical DNA biosensor for BT detection. Kusnin et al. [57] employed silicon nanowires/platinum nanoparticles (SiNWs/PtNPs) on a SPCE for the detection of porcine DNA. The few studies conducted earlier

• GENEWIZ (China) with the following sequence (the underlined bases indicate the number of mismatches with the probe sequence). Thiolated ssDNA probe (ssBT): HS-S-(CH2)6-5′-GATCATTACTAGGCACCTGCCTAATCCTTCA-3′ Reverse complementary (RC) ssDNA: 5′-TGAAGGATTAGGCAGGTGCCTAGTAATGATC-3′ RC one base mismatch ssDNA

• (1MN): 5′-TGAAGGATTAGGCAAGTGCCTAGTAATGATC-3′ RC three base mismatch ssDNA (3MN): 5′-TGAAGGATTAGGTGAGTGCCTAGTAATGATC-3′ Cow RC ssDNA (CW): 5′-TGTAGGATTAGGCAGATTCCCAGGAGGGAAC-3′ Buffalo RC ssDNA (BF): 5′-TGCAGGATTAGGCAGATGCCTAGGAGAGAGC-3′ Horse RC ssDNA (GT): 5′-TGGAGGATTAGGCAGATTCCTAGGAGGGAGC-3′ Duck RC

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

• , and specific virus identification. However, these techniques require professional expertise and expensive laboratory equipment and reagents. These conditions are frequently unavailable in endemic regions [8][9][10]. Nucleic acid aptamers are single-strand oligonucleotides (ssDNA or ssRNA) that can

• , and T at each position and was purchased from IDT DNA Technologies [18]. CE-SELEX Three CE-SELEX selection cycles were performed. To initiate in vitro selection, 800 μM ssDNA was heated at 95 °C for 5 min, snap-cooled on ice for 15 min and left at room temperature for 10 min. After that, it was

• MaxiSorp plates (Thermo Fisher) was used [19]. The sequences unbound to these proteins were collected, amplified by conventional PCR, further amplified by asymmetric PCR, and the obtained ssDNA product was used for the next positive selection cycle with the ZIKV NS1 protein. The counterselections were

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

• -stabilized gold nanoparticles of 13 nm in diameter (Figure 3a). A target oligonucleotide (24–30 bases) that was complementary to the single-stranded DNA (ssDNA) of both types of nanoparticles induced an aggregation through hybridization. The main advantage of this method is the low risk of false positives

• principle of this system rests on the fact that ssDNA exhibits a higher affinity to the surface of metallic gold as dsDNA. This is because ssDNA molecules contain a large number of functional groups facilitating electrostatic interactions with the gold surface (Figure 3c). Therefore, at a high salt

• concentration, adsorbed ssDNA stabilizes the nanoparticles against aggregation. In contrast, the preferential hybridization of target DNA with complementary strands left the nanoparticles uncovered, facilitating aggregation. The authors were able to detect single-base mismatches at the level of 43 nM using gold

Molecular architectonics of DNA for functional nanoarchitectures

• Debasis Ghosh,
• Lakshmi P. Datta and
• Thimmaiah Govindaraju

Beilstein J. Nanotechnol. 2020, 11, 124–140, doi:10.3762/bjnano.11.11

• sequence specificity, molecular recognition properties, and the formation of regular and defined structures of DNA made it possible to custom the design and to engineer a range of molecular architectures [5][6][7][8][9]. In DNA, two polydeoxyoligonucleotides (single-stranded DNA, ssDNA) are held together

• . 40–50 nm. Moreover, ssDNA sequences can be used as molecular glue to construct diverse and well-defined nanoarchitectures. In this context, Seeman and co-workers introduced the disruptive idea of using DNA as a molecular building block to design and construct nanosystems and materials, which paved

• functional properties and practical applications [12][13][18][19][20][21]. In functional DNA nanoarchitectonics, short oligonucleotides (ssDNA) with sequences of less than persistence length (ca. 40–50 nucleotides) are co-organized with SFMs or their assemblies to generate hybrid DNA ensembles [18][20]. The

Streptavidin-coated gold nanoparticles: critical role of oligonucleotides on stability and fractal aggregation

• Roberta D'Agata,
• Pasquale Palladino and
• Giuseppe Spoto

Beilstein J. Nanotechnol. 2017, 8, 1–11, doi:10.3762/bjnano.8.1

• further investigate the behaviour of ssDNA, which is adsorbed on AuNP surface more easily than dsDNA. Both citrate-stabilized AuNPs and oligonucleotides are negatively charged, therefore ssDNA adsorption is linked to the long-range electrostatic repulsion, which is related to the Debye length and is

• much research into the contribution of the hydrophobic effect which has been claimed to play a dominant role in ssDNA adsorption [51]. The incubation of BiotinDNA with bare AuNPs at pH 6 produced a plasmon band at 524 nm (Figure 7) thus testifying the adsorption of the oligonucleotide sequence onto the

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

• Anastassia Kanavarioti Yenos Analytical LLC, El Dorado Hills, CA, USA 10.3762/bjnano.7.135 Abstract Osmium tetroxide 2,2’-bipyridine (OsBp) is known to react with pyrimidines in ssDNA and preferentially label deoxythymine (T) over deoxycytosine (C). The product, osmylated DNA, was proposed as a

• nucleobase; α-HL was also shown to discriminate between osmylated T and osmylated C. Experiments presented here confirm that the kinetics of osmylation are comparable for short oligos and long ssDNA and show that pyrimidine osmylation is practically complete in two hours at room temperature with less than 15

• ; osmylation; ssDNA; Introduction At the time the human genome was completed in 2001 [1][2], it was becoming clear that the relationships between genes, noncoding regions, epigenetic modifications, and the transcriptome were intertwined and led to health vs disease in complex patterns. A large effort in

Hierarchical coassembly of DNA–triptycene hybrid molecular building blocks and zinc protoporphyrin IX

• Rina Kumari,
• Sumit Singh,
• Mohan Monisha,
• Sourav Bhowmick,
• Anindya Roy,
• Neeladri Das and
• Prolay Das

Beilstein J. Nanotechnol. 2016, 7, 697–707, doi:10.3762/bjnano.7.62

• ′-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser

• polymeric networks [46][47]. In this study, we report the synthesis of the DNA–TPA scaffolds by covalent conjugation of 2,6,14-triptycenetripropiolic acid (TPA) with amine-modified 12-mer ssDNA and coassembly with zinc protoporphyrin IX(Zn PpIX) to form composite DNA nanostructures (Scheme 1). Porphyrins

• in the present study is two-fold. Firstly, in the interaction of Zn PpIX with DNA, the former is hypothesized to provide template for assembly formation [45]. Secondly, the generation of ROS through excitation of porphyrins is an established fact [48]. The covalent conjugation of TPA with ssDNA was

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

• ssDNA anchors after partial TMV disassembly, exposing a 5'-terminal stretch of their RNA, e.g., under mild alkaline conditions, as it has been demonstrated for TMV labeled with distinct dyes [135][136]. This allows for the installation of blends of distinct TMV-exposed effector molecules (as exemplified

• reaction. The resulting nanowell template was incubated with OAs-containing RNA, to allow its hybridization to ssDNA exposed on the bottom of the holes. After assembly-competent CP was applied, TMV-like rods were detected protruding in almost upright orientations (Figure 8B). Further improvements of the

• cascade of [SA]-GOx and [SA]-HRP can be established in a PDMS flow cell. B: TMV-like particles mounted in an upright position in a nanowell template fabricated as follows: A flat substrate was equipped with ssDNA and covered with a 60 nm thin, perforated metal-organic film produced by metal polymer blend

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

• differentiate devices read-out of fully and partially matching sequences. Results: We present here two platforms based on different sensing strategies, to detect mismatched and/or perfectly matched complementary DNA strands hybridization into ssDNA oligonucleotide monolayers. The first platform exploits atomic

• force microscopy-based nanolithography to create ssDNA nano-arrays on gold surfaces. AFM topography measurements then monitor the variation of height of the nanostructures upon biorecognition and then follow annealing at different temperatures. This strategy allowed us to clearly detect the presence of

• mismatches. The second strategy exploits the change in capacitance at the interface between an ssDNA-functionalized gold electrode and the solution due to the hybridization process in a miniaturized electrochemical cell. Through electrochemical impedance spectroscopy measurements on extended ssDNA self

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

• produces a constant ion flux through the pore. Nucleic acids added to one compartment traverse the pore, and modulate the current in a sequence-dependent manner. While translocation is faster than detection, the α-hemolysin nanopore (α-HL) successfully senses base modifications in ssDNA immobilized within

• 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

• such as the α-HL, a modified version of the Mycobacterium smegmatis porin A (MspA), and the Ph29 connector channel have been investigated as single molecule sensing devices for ssDNA, RNA, dsDNA, and proteins [12][13][14]. The advantage of the natural pores is that they are well defined and highly

DNA–melamine hybrid molecules: from self-assembly to nanostructures

• Rina Kumari,
• Shib Shankar Banerjee,
• Anil K. Bhowmick and
• Prolay Das

Beilstein J. Nanotechnol. 2015, 6, 1432–1438, doi:10.3762/bjnano.6.148

• ]. However, the directionality of the single-stranded DNA (ssDNA) sequences obtained through a DNA synthesizer is limited only to the terminal positions. This could limit further DNA extension in both directions. As a recent trend, DNA–organic molecule hybrid structures are being produced post-synthesis to

• , planar, heterocyclic, aromatic compound, having multiple pendant amine functionality. Although, melamine has been previously used to generate nanostructures, it has not been explored to create self-assembled nanostructures exclusively with DNA [25][26]. The covalent conjugation of ssDNA with aromatic

• reaction between aliphatic primary amine moieties and a terminal phosphate group of DNA was previously reported [27][28]. We optimized the reaction for the coupling of the aromatic amines of melamine with the 5’-terminal phosphate groups of two self-complementary ssDNA molecules (24 bases long, Supporting

Sequence-dependent electrical response of ssDNA-decorated carbon nanotube, field-effect transistors to dopamine

• Hari Krishna Salila Vijayalal Mohan,
• Jianing An and
• Lianxi Zheng

Beilstein J. Nanotechnol. 2014, 5, 2113–2121, doi:10.3762/bjnano.5.220

• FETs lack responsivity and selectivity for its detection due to the presence of interfering compounds such as uric acid (UA). Surface modification of CNTs using single-stranded deoxyribonucleic acid (ssDNA) renders the surface responsive to DA and screens the interferent. Due to the presence of

• different bases in ssDNA, it is necessary to investigate the effect of sequence on the FET-based molecular recognition of DA. SWCNT FETs were decorated with homo- and repeated-base ssDNA sequences, and the electrical response induced by DA in the presence and absence of UA was gauged in terms of the

• variation in transistor electrical parameters including conductance, transconductance, threshold voltage and hysteresis gap. Our results showed that the response of ssDNA-decorated devices to DA, irrespective of the presence or absence of UA, was DNA sequence dependent and exhibited the trend: G > A > C and

Non-covalent and reversible functionalization of carbon nanotubes

• Antonello Di Crescenzo,
• Valeria Ettorre and
• Antonella Fontana

Beilstein J. Nanotechnol. 2014, 5, 1675–1690, doi:10.3762/bjnano.5.178

• , the most representative one is DNA and different examples of non-covalently functionalized SWCNTs with DNA have been published. While double-stranded DNA (dsDNA), being more rigid, displayed a less efficient wrapping, single-stranded DNA (ssDNA) has been used to disperse CNTs or to separate and purify

• them. Indeed, by sonicating ssDNA with HiPco SWCNTs for ca. 1 h a solution as concentrated as 25 mg/L has been obtained [75]. These functionalized SWCNTs have proved to be able to internalize oligonucleotide chains into living cells whereas ssDNAs have been translocated into cell nucleus upon endosomal

DNA origami deposition on native and passivated molybdenum disulfide substrates

• Xiaoning Zhang,
• Masudur Rahman,
• David Neff and
• Michael L. Norton

Beilstein J. Nanotechnol. 2014, 5, 501–506, doi:10.3762/bjnano.5.58

• extra staples present in the synthesis solution were removed via dialysis, debris is observed in the background of these images and is attributed to small quantities of additional staple DNA released from the DNA origami structures. It may be observed that these ssDNA staples adsorbed to the pristine

• hydrochloride were obtained from Sigma-Aldrich. We used M13mp18 ssDNA plasmid (7249 bp) and short complementary DNA staple strands to program the cross-shaped DNA origami (the details are provided in Supporting Information File 1). To remove the excess staple strands, the DNA origami solutions were dialyzed