Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy

Next-Generation Sequencing and Emerging Technologies

Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.

Inkjet Printed Nanopatterned Aptamer-Based Sensors for Improved Optical Detection of Foodborne Pathogens

The increasing incidence of infectious outbreaks from contaminated food and water supply continues imposing a global burden for food safety, creating a market demand for on-site, disposable, easy-to-use, and cost-efficient devices. Despite of the rapid growth of biosensors field and the generation of breakthrough technologies, more than 80% of the platforms developed at lab-scale never will get to meet the market. This work aims to provide a cost-efficient, reliable, and repeatable approach for the detection of foodborne pathogens in real samples. For the first time an optimized inkjet printing platform is proposed taking advantage of a carefully controlled nanopatterning of novel carboxyl-functionalized aptameric ink on a nitrocellulose substrate for the highly efficient detection of E. coli O157:H7 (25 colony forming units (CFU) mL^-1 in pure culture and 233 CFU mL^-1 in ground beef) demonstrating the ability to control the variation within ±1 SD for at least 75% of the data collected even at very low concentrations. From the best of the knowledge this work reports the lowest limit of detection of the state of the art for paper-based optical detection of E. coli O157:H7, with enough evidence (p > 0.05) to prove its high specificity at genus, species, strain, and serotype level.

Quaternary Ammonium-Terminated Films Formed from Mixed Bidentate Adsorbates Provide a High-Capacity Platform for Oligonucleotide Delivery

The exposure of quaternary ammonium groups on surfaces allows self-assembled monolayers (SAMs) to serve as architectural platforms for immobilizing oligonucleotides. The current study describes the preparation of SAMs derived from four unique bidentate adsorbates containing two different ammonium termini (i.e., trimethyl- and triethyl-) and comparison to their monodentate analogs. Our studies found that SAMs derived from the bidentate adsorbates offered considerable enhancements in oligonucleotide binding when compared to SAMs derived from their monodentate analogs. The generated SAMs were analyzed using ellipsometry, X-ray photoelectron spectroscopy, contact angle goniometry, polarization modulation infrared reflection-absorption spectroscopy, and electrochemical quartz crystal microbalance. These analyses showed that the immobilization of oligonucleotides was affected by changes in the terminal functionalities and the relative packing densities of the monolayers. In efforts to enhance further the immobilization of oligonucleotides on these SAM surfaces, we explored the use of adsorbates having aliphatic linkers with systematically varying chain lengths to form binary SAMs on gold. Mixed monolayers with 50:50 ratios of adsorbates showed the greatest oligonucleotide binding. These studies lay the groundwork for oligonucleotide delivery using gold-based nanoparticles and nanoshells.

Electron Transfer in Spacer-Free DNA Duplexes Tethered to Gold via dA10 Tags

Electrical properties of DNA critically depend on the way DNA molecules are integrated within the electronics, particularly on DNA-electrode immobilization strategies. Here, we show that the rate of electron transport in DNA duplexes spacer-free tethered to gold via the adenosine terminal region (a dA₁₀ tag) is enhanced compared to the hitherto reported DNA-metal electrode tethering chemistries. The rate of DNA-mediated electron transfer (ET) between the electrode and methylene blue intercalated into the dA₁₀-tagged DNA duplex approached 361 s^-1 at a ca. half-monolayer DNA surface coverage Γ_DNA (with a linear regression limit of 670 s^-1 at Γ_DNA → 0), being 2.7-fold enhanced compared to phosphorothioated dA₅* tethering (6-fold for the C₆-alkanethiol linker representing an additional ET barrier). X-ray photoelectron spectroscopy evidenced dA₁₀ binding to the Au surface via the purine N, whereas dA₅* predominantly coordinated to the surface via sulfur atoms of phosphothioates. The latter apparently induces the DNA strand twist in the point of surface attachment affecting the local DNA conformation and, as a result, decreasing the ET rates through the duplex. Thus, a spacer-free DNA coupling to electrodes via dA₁₀ tags thus allows a perspective design of DNA electronic circuits and sensors with advanced electronic properties and no implication from more expensive, synthetic linkers.

Tautomerization of Thymine Using Ultraviolet Light

Ultraviolet-light-induced changes to the nucleobase thymine deposited onto a MoS₂ surface were studied using photoelectron spectroscopy and first-principles calculations. These measurements suggest changes in the molecular structure indicated by changes in core electron binding energies. The experimental work has been interpreted by means of ab initio calculations using coupled cluster singles and doubles (CCSD) linear response theory. Contrary to the expected behavior, i.e., the dimerization of two thymine molecules into a pyrimidine dimer, a shift between two tautomeric forms was observed upon UV-exposure. Exposure to ionizing radiation is known to induce damage in many biological molecules, and the present work gives additional insight into its effects on thymine, the interactions of the molecules, and finally how certain UV photoproducts may be avoided.