New application of bimetallic Ag/Pt nanoplates in a colorimetric biosensor for specific detection of E. coli in water

• Azam Bagheri Pebdeni,
• Mohammad N. AL-Baiati and
• Morteza Hosseini

Beilstein J. Nanotechnol. 2024, 15, 95–103, doi:10.3762/bjnano.15.9

• ], photocatalytic degradation and bactericidal action [21], sensors and biosensors [22][23][24][25], and as electrocatalysts [26]. Aptamers are single-stranded DNA or RNA oligonucleotides that attach to their targets with great affinity and specificity. Aptamers have high stability in a variety of environments and

• structure of the oligonucleotides the UNAfold program was employed, as illustrated in Supporting Information File 1, Figure S1. Peroxidase-like activity of Ag/Pt NPLs Supporting Information File 1, Figure S2a illustrated a comparison of the inherent peroxidase activity of Ag/Pt NPLs. The intrinsic

Antibody-conjugated nanoparticles for target-specific drug delivery of chemotherapeutics

• Mamta Kumari,
• Amitabha Acharya and
• Praveen Thaggikuppe Krishnamurthy

Beilstein J. Nanotechnol. 2023, 14, 912–926, doi:10.3762/bjnano.14.75

• of nanoscale chemotherapeutics is accomplished by two different approaches, namely the exploitation of leaky tumor vasculature (EPR effect) and the surface modification of nanoparticles (NPs) with various tumor-homing peptides, aptamers, oligonucleotides, and monoclonal antibodies (mAbs). Because of

Polymer nanoparticles from low-energy nanoemulsions for biomedical applications

• Santiago Grijalvo and
• Carlos Rodriguez-Abreu

Beilstein J. Nanotechnol. 2023, 14, 339–350, doi:10.3762/bjnano.14.29

• by TEM) were surface-decorated with carbosilane cationic dendrons via carbodiimide chemistry [54] for conjugation with antisense oligonucleotides (ASO). The conjugated nanoparticles with a hydrodynamic diameter between 80 and 160 nm (depending on dendron generation) showed high colloidal stability

• composed of carbosilane dendron functionalized nanoparticles prepared from nanoemulsions as non-viral carriers for antisense oligonucleotides”, pages 113-123, Copyright (2014), with permission from Elsevier. This content is not subject to CC BY 4.0. (a) Partial phase diagram of the system PBS/Polysorbate

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

• peptide nucleic acid (PNA) probes [64]. Methylene blue is a very prominent intercalator for DNA-based sensors and biosensors [31][65][66][67][68][69]. For example, Plaxco's group reported the preparation of electrode-immobilised methylene-blue-modified oligonucleotides for electrochemical DNA and aptamer

• hydrochloride (EDC) were used to covalently link DNA and oligonucleotides to a carboxylate-terminated alkanethiol self-assembled monolayer (SAM) performed on a gold electrode (AuE) [70]. The Lisdat group described a label-free impedimetric sensor for the detection of hybridisation events which is based on short

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

• mandatory. Acid nucleic aptamers are oligonucleotides that bind to a specific target molecule with high affinity and specificity. Because of their unique characteristics, aptamers are promising tools for biosensor development. Aptamers are usually obtained through a procedure called “systematic evolution of

• , 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

• “systematic evolution of ligands by exponential enrichment” (SELEX), first introduced in 1990 [13]. This methodology includes the exposure of the target molecule to a chemically synthesized random-sequence library (1014–1015 sequences) to allow for the interaction of all binding oligonucleotides to the target

Recent advances in nanoarchitectures of monocrystalline coordination polymers through confined assembly

• Lingling Xia,
• Qinyue Wang and
• Ming Hu

Beilstein J. Nanotechnol. 2022, 13, 763–777, doi:10.3762/bjnano.13.67

• strategies. With surface modifications, the interparticle interactions can be stronger and well defined. With the assistance of interactions among the oligonucleotides, the packing of coordination polymers could be programmed (Figure 6) [134]. 2D and 3D structures, that is, face-centered cubic, body-centered

Theranostic potential of self-luminescent branched polyethyleneimine-coated superparamagnetic iron oxide nanoparticles

• Rouhollah Khodadust,
• Ozlem Unal and
• Havva Yagci Acar

Beilstein J. Nanotechnol. 2022, 13, 82–95, doi:10.3762/bjnano.13.6

• signal was demonstrated. Then, a pro-apoptotic oligonucleotide (polyinosinic–polycytidylic acid sodium salt) (PIC) was transfected into HeLa cells to demonstrate that luminescent bPEI coating is still an effective component for the delivery of an anionic cargo and it may deliver oligonucleotides in a

• capable of delivering oligonucleotides as proven here by two different cargoes. Poly I:C, a pro-apoptotic agent, was loaded on these nanoparticles (N/P = 30), and was effectively delivered to HeLa cells, reducing the viability by 40% in 48 h at a nontoxic dose of the nanoparticle. Besides, PIC loading did

Modification of a SERS-active Ag surface to promote adsorption of charged analytes: effect of Cu²⁺ ions

• Bahdan V. Ranishenka,
• Andrei Yu. Panarin,
• Irina A. Chelnokova,
• Sergei N. Terekhov,
• Peter Mojzes and
• Vadim V. Shmanai

Beilstein J. Nanotechnol. 2021, 12, 902–912, doi:10.3762/bjnano.12.67

• ; oligonucleotides; porphyrin; silver nanoparticles; substrate modification; surface-enhanced Raman spectroscopy (SERS); Introduction Surface-enhanced Raman scattering (SERS) with its advantages of extreme sensitivity, high selectivity, and non-destructive nature has demonstrated great potential for the quick

• oligonucleotides [19]. Finally, recent work [20] demonstrates the detection of anionic analytes by addition of multicharged metal cations. The abovementioned papers devoted to the chemical SERS activation of silver-based substrates, with the exception of [23][24], described colloidal NPs. The work [20] reports the

• remaining polymer molecules are not able to generate a strong positive charge at the surface but they improve the adsorption of the analyte molecules due to hydrogen bonding and donor–acceptor and lipophilic interactions. SERS analysis of dye-labeled oligonucleotides Biomolecules such as nucleotides and

The impact of molecular tumor profiling on the design strategies for targeting myeloid leukemia and EGFR/CD44-positive solid tumors

• Nikola Geskovski,
• Nadica Matevska-Geshkovska,
• Simona Dimchevska Sazdovska,
• Marija Glavas Dodov,
• Kristina Mladenovska and
• Katerina Goracinova

Beilstein J. Nanotechnol. 2021, 12, 375–401, doi:10.3762/bjnano.12.31

Poly(1-vinylimidazole) polyplexes as novel therapeutic gene carriers for lung cancer therapy

• Gayathri Kandasamy,
• Elena N. Danilovtseva,
• Vadim V. Annenkov and
• Uma Maheswari Krishnan

Beilstein J. Nanotechnol. 2020, 11, 354–369, doi:10.3762/bjnano.11.26

• the endosomes and the red fluorescence of the fluorophore-tagged siRNA are perfectly merged indicating that the free siRNA is unable to escape from the endosome. This is expected as it has been established earlier that double-stranded oligonucleotides tend to accumulate in the endosomal compartment

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

• oligonucleotides upon hybridization on a DNA template), and (4) invasive cleavage (nuclease-based cleavage of the 3D structure formed when two overlapping oligonucleotides hybridize perfectly to a target DNA). The genotyping method should meet several requirements, namely, facile development from sequence

• cyclically amplify the process of DNA self-assembly. The strategies based on enzymatic tools, on the other hand, are characterized by an extraordinary potential for signal amplification. The main advantages of using enzymes involve: a) the capability of modifying oligonucleotides (e.g., polymerases

• magnetic beads coated with a sequence of oligonucleotides and Au@DNA modified with two types of oligonucleotides (1:100 ratio), one that was complementary to the target sequence and the other complementary to a bar-code sequence. The magnetic beads and the Au@DNA formed a sandwich structure linked by the

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

• researchers to design new DNA-based functional materials with chemical and biological properties distinct from their parent components. The modulation of structural and functional properties of hybrid DNA ensembles of small functional molecules (SFMs) and short oligonucleotides by adapting the principles of

• 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

• short oligonucleotides are inexpensive to synthesize in-house or commercially available, and their coassembly with SFMs assures to generate novel nanoarchitectures with functional properties and applications. Although the field of classical DNA nanotechnology exploited the supramolecular bottom-up self

Internalization mechanisms of cell-penetrating peptides

• Ivana Ruseska and
• Andreas Zimmer

Beilstein J. Nanotechnol. 2020, 11, 101–123, doi:10.3762/bjnano.11.10

• cargo by chemical cross-linking or by cloning, followed by the expression of a CPP fusion protein. Such interactions have been seen in several CPPs such as TAT derivatives, penetratin or polyarginines [10]. It seems that covalent modification is most suitable for charge-neutral oligonucleotides such as

• peptide nucleic acids (PNAs) and phosphorodiamidate morpholino oligonucleotides (PMOs) [3][12]. Concerning charged molecules such as siRNA or miRNA, the covalent conjugation leads to restricted biological activity, most likely due to the steric hindrance caused by the covalently-linked CPP, which is an

• process [30]. Membrane perturbation as an internalization mechanism has also been proposed for the MPG-family of amphipathic peptides (Figure 2) [3][17][31]. MPG carriers are amphipathic peptides able to form stable complexes with antisense oligonucleotides, plasmid DNA, siRNA and peptides, which improve

Long-term stability and scale-up of noncovalently bound gold nanoparticle-siRNA suspensions

• Anna V. Epanchintseva,
• Julia E. Poletaeva,
• Dmitrii V. Pyshnyi,
• Elena I. Ryabchikova and
• Inna A. Pyshnaya

Beilstein J. Nanotechnol. 2019, 10, 2568–2578, doi:10.3762/bjnano.10.248

• solid-phase phosphoramidite synthesis [32]. The following oligonucleotides were synthesized: sense-GFP (5'-CAAGCUGACCCUGAAGUUCTT'), antisense-GFP (5'-GAACUUCAGGGUCAGCUUGTT), and 5’-fluorescently labeled sense-GFP-Cy5.5 (5'-Cy5.5-CAAGCUGACCCUGAAGUUCTT), which was synthesized with the use of Cy-5.5

• phosphoramidite at the final stage of the synthesis. The oligonucleotides were isolated by electrophoresis in 15% polyacrylamide gel (acrylamide/N,N’-bisacrylamide (29:1) and 8 M urea) in TBE buffer (89 mM Tris, 89 mM H3BO3, and 2 mM EDTA, рН 8.3) for 1.5 h at 20 V/cm and 40 °С. The oligonucleotides were eluted

Experimental study of an evanescent-field biosensor based on 1D photonic bandgap structures

• Jad Sabek,
• Francisco Javier Díaz-Fernández,
• Luis Torrijos-Morán,
• Zeneida Díaz-Betancor,
• Ángel Maquieira,
• María-José Bañuls,
• Elena Pinilla-Cienfuegos and
• Jaime García-Rupérez

Beilstein J. Nanotechnol. 2019, 10, 967–974, doi:10.3762/bjnano.10.97

• femtomolar range for oligonucleotides detection [6]. A particular type of photonic sensing devices are photonic bandgap (PBG) biosensors based on evanescent-wave detection [7]. PBG structures consist of a periodic dielectric configuration for which the propagation of a certain wavelength range is forbidden

Non-agglomerated silicon–organic nanoparticles and their nanocomplexes with oligonucleotides: synthesis and properties

• Asya S. Levina,
• Marina N. Repkova,
• Nadezhda V. Shikina,
• Zinfer R. Ismagilov,
• Svetlana A. Yashnik,
• Dmitrii V. Semenov,
• Yulia I. Savinovskaya,
• Natalia A. Mazurkova,
• Inna A. Pyshnaya and
• Valentina F. Zarytova

Beilstein J. Nanotechnol. 2018, 9, 2516–2525, doi:10.3762/bjnano.9.234

• of low molecular weight polymer chains with [─Si(OH)(C3H6NH2)O─] monomer units. Oligonucleotides (ODN) were conjugated to the prepared Si–NH2 nanoparticles using the electrostatic interaction between positively charged amino groups of nanoparticles and negatively charged internucleotide phosphate

• groups in oligonucleotides. The Si–NH2 nanoparticles and Si–NH2·ODN nanocomplexes were characterized by transmission electron microscopy, atomic force microscopy and IR and electron spectroscopy. The size and zeta potential values of the prepared nanoparticles and nanocomplexes were evaluated

• . Oligonucleotides in Si–NH2·ODN complexes retain their ability to form complementary duplexes. The Si–NH2Flu nanoparticles and Si–NH2·ODNFlu nanocomplexes were shown by fluorescence microscopy to penetrate into human cells. The Si–NH2Flu nanoparticles predominantly accumulated in the cytoplasm whereas ODNFlu

Mechanistic insights into plasmonic photocatalysts in utilizing visible light

• Kah Hon Leong,
• Azrina Abd Aziz,
• Lan Ching Sim,
• Pichiah Saravanan,
• Min Jang and
• Detlef Bahnemann

Beilstein J. Nanotechnol. 2018, 9, 628–648, doi:10.3762/bjnano.9.59

• achieve tunable light absorption and emission. Prior works reported the use of DNA oligonucleotides [152][153] and virus capsids [154] as tunable spacers to control the distance between Au NPs and fluorophores. The assembly hierarchy of the plasmonic photocatalysts were carried out using both MS2 virus

Wafer-scale bioactive substrate patterning by chemical lift-off lithography

• Chong-You Chen,
• Chang-Ming Wang,
• Hsiang-Hua Li,
• Hong-Hseng Chan and
• Wei-Ssu Liao

Beilstein J. Nanotechnol. 2018, 9, 311–320, doi:10.3762/bjnano.9.31

• ). Deionized water (>18 MΩ·cm) was obtained from the ELGA PURELAB classic system (Taipei, Taiwan). Oligonucleotide sequences. Oligonucleotides purified by HPLC were purchased from PURIGO Biotechnology Co., Ltd. (Taipei, Taiwan). The oligonucleotide sequences are listed in the following: Hg2+-specific probe (30

Selective detection of Mg²⁺ ions via enhanced fluorescence emission using Au–DNA nanocomposites

• Tanushree Basu,
• Khyati Rana,
• Niranjan Das and
• Bonamali Pal

Beilstein J. Nanotechnol. 2017, 8, 762–771, doi:10.3762/bjnano.8.79

• [37]. Preparation and characterization of Au–DNA nanocomposites Herring sperm DNA (20 μL, 3.5 mg mL−1) was diluted with 2 mL sterile, deionized water [38] and 5 μL MPA was added to it, which was then incubated in a laminar hood at 21 °C for 24 h to ensure the binding of alkanethiol to oligonucleotides

• phosphate buffer) was added to the above solution and again incubated at room temperature for 1 h to cleave the disulfide bonds formed by the oligonucleotides upon addition of MPA. DNA functionalized gold nanoparticles were then washed twice by centrifugation (13,000 rpm, 15 min) to remove all unbound

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

• compared to citrate-stabilized AuNPs ζ-potential (Table 1) contributes to improving the stability of functionalized nanoparticles dispersions. Nanoparticles modified with biotinylated oligonucleotides are spontaneously redispersed because of steric and electrostatic repulsion provided by the introduction

• oligonucleotides) no similar changes were observed in the absorbance spectrum (Figure 4B) where one single absorption peak at 524 nm is displayed, thus demonstrating that AuNP-SA are stable in the presence of a large amount of free biotin (Figure 4D). These results suggest that the aggregation of AuNP-SA-BiotinDNA

• interaction of single-stranded DNA with citrate-stabilized AuNPs has been widely investigated and controversial mechanisms have been proposed for this process [51][56]. The discovery of a different propensity of single- or double-stranded oligonucleotides to adsorb onto citrate-stabilized AuNPs [57] led to

A novel electrochemical nanobiosensor for the ultrasensitive and specific detection of femtomolar-level gastric cancer biomarker miRNA-106a

• Maryam Daneshpour,
• Kobra Omidfar and
• Hossein Ghanbarian

Beilstein J. Nanotechnol. 2016, 7, 2023–2036, doi:10.3762/bjnano.7.193

• with TMC polymer and gold NPs. However, the zero remanence and coercivity values indicated the superparamagnetic nature of gold–magnetic NPs with an acceptable VSM value (59.05 emu/g) [20]. Preparation of gold–magnetic nanoprobes The oligonucleotides can be immobilized on the gold NPs through various

Controlled supramolecular structure of guanosine monophosphate in the interlayer space of layered double hydroxide

• Gyeong-Hyeon Gwak,
• Istvan Kocsis,
• Yves-Marie Legrand,
• Mihail Barboiu and
• Jae-Min Oh

Beilstein J. Nanotechnol. 2016, 7, 1928–1935, doi:10.3762/bjnano.7.184

• condensation of amino acids was determined to favor heteropeptide rather than homopeptide. Besides polymerization of amino acids, it was reported that abiotic oligomerization of RNA nucleotides was catalyzed by montmorillonite clay [7]. In the presence of clay, the length of polymerized RNA oligonucleotides

High antiviral effect of TiO₂·PL–DNA nanocomposites targeted to conservative regions of (−)RNA and (+)RNA of influenza A virus in cell culture

• Asya S. Levina,
• Marina N. Repkova,
• Elena V. Bessudnova,
• Ekaterina I. Filippova,
• Natalia A. Mazurkova and
• Valentina F. Zarytova

Beilstein J. Nanotechnol. 2016, 7, 1166–1173, doi:10.3762/bjnano.7.108

• TiO2·PL–DNA nanocomposite consisting of titanium dioxide nanoparticles and polylysine (PL)-containing oligonucleotides. Results: The TiO2·PL–DNA nanocomposites bearing the DNA fragments targeted to different conservative regions of (−)RNA and (+)RNA of segment 5 of influenza A virus (IAV) were studied

• (oligonucleotides and their derivatives and analogs) can be used for this purpose because they are known to site specifically interact with certain regions of nucleic acid (NA) targets. The development of antisense technology for the creation of drugs that can gene specifically affect the genes responsible for

• NA-based drugs of various nature [8][9][10][11][12][13][14][15][16]. However, there is still no unified concept for the most vulnerable regions of this segment. In this work, we attempt to find some relationships in this aspect for IAV segment 5. To deliver antisense oligonucleotides into cells, we

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

• Anja Henning-Knechtel,
• Matthew Wiens,
• Mathias Lakatos,
• Andreas Heerwig,
• Frieder Ostermaier,
• Nora Haufe and
• Michael Mertig

Beilstein J. Nanotechnol. 2016, 7, 948–956, doi:10.3762/bjnano.7.87

• electrodes confirming that the trapping only occurs in the presence of an electrical field. We then conjugated 15 nm gold nanoparticles to oligonucleotides with a poly(T) sequence, and further attached them to the ten double-sticky-end locations along the DNA nanostructure through hybridization. Figure 4b

• 30 min and the supernatant carefully removed. The remaining pellet was resuspended in a mixture of 100 µL of 2.5 mM BSPP and 100 µL of methanol. The solution was once more spun down to dissolve the pellet in 2.5 mM BSPP. The gold nanoparticles were further modified with oligonucleotides that included

• a thiol functionality at the 3′ end (sequence: 5′TTTTT TTTTT TTTTT TTT–C3H5SH3′, HPLC purified, Biomers.net). For this, 3.2 pmol phosphinated gold nanoparticles were mixed in equivalent ratio with the oligonucleotides in Na+-TBE buffer solution (50 mM NaCl, 89 mM Tris, 89 mM boric acid, 1 mM EDTA pH

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

• , the AFM tip is scanned at high load (approx. 100 nN) over the TOEG6 SAM, operating in a buffer solution (10 mM Tris-HCl, 1 mM EDTA, (hereafter TE), 1 M NaCl, pH 7.1) containing 5 μM thiolated ssDNA oligonucleotides. The applied load is sufficient to displace the TOEG6 molecules from the gold surface

• strategies based on the use of ssDNA monolayers tethered to gold substrates, for the detection of mismatches in DNA oligonucleotides. Both the strategies are label-free and are sensitive enough to detect point mutations. In Table 2 we report a comparison between the performance of our two approaches (nano