Effect of oligonucleotide probes substituted by deoxyinosines on the specificity of SNP detection on the DNA microarray

One of the main factors that can affect the quality of microarray results is the microarray hybridization specificity. The key factor that affects hybridization specificity is the design of the probes. In this paper, we described a novel oligonucleotide probe containing deoxyinosines aimed at improving DNA hybridization specificity. We compared different probes to determine the distance between deoxyinosine base and SNPs site and the number of deoxyinosine bases. The new probe sequences contained two set of deoxyinosines (each set had two deoxyinosines), in which the interval between SNP site and each set of deoxyinosines was two bases. The new probes could obtain the highest hybridization specificity. The experimental results showed that probes containing deoxyinosines hybridized effectively to the perfectly matched target and improved the hybridization specificity of DNA microarray. By including a simple washing step after hybridization, these probes could distinguish matched targets from single‐base‐mismatched sequences perfectly. For the probes containing deoxyinosines, the fluorescence intensity of a match sequence was more than eight times stronger than that of a mismatch. However, the intensity ratio was only 1.3 times or less for the probes without deoxyinosines. Finally, using hybridization of the PCR product microarrays, we successfully genotyped SNP of 140 samples using these new labeled probes. Our results show that this is a useful new strategy for modifying oligonucleotide probes for use in DNA microarray analysis.     

金纳米粒子组装体的连续离散型纳米结构控制

采用柠檬酸钠还原氯金酸的方法,制备出粒径均一的金纳米粒子(AuNPs),通过加入二水合双(对-磺酰苯基)苯基膦化二钾盐(BSPP),增强了AuNPs体系的分散性与稳定性.选用直径为15和40nm的AuNPs,用不同序列巯基修饰的单链DNA连接到其表面,通过DNA链的杂交,形成不同结构的金纳米粒子组装体.通过改变加入DNA延长连接单元的比例,可以控制金纳米粒子组装体具有连续离散型的1∶1,2∶1和3∶1纳米结构.     

Hydrogels Triggered by Metal Ions as Precursors of Network CuS for DNA Detection

The gelation behavior of lithocholate (LC^?) with different metal ions in water was investigated. The microstructures of hydrogels were determined to be three‐dimensional (3D) networks of fibrous aggregates. The formation of fibrils was speculated to be mainly driven by the coordination between carboxylate of LC^? and metal ions, accompanied by the assistance of noncovalent interactions such as electrostatic and hydrophobic interactions. The hydrogels, which can maintain the mechanical strength at higher temperature, exhibit thermal stability. Their gelation capability was enhanced with the increase in acidity. The hydrogels of LC^? and Cu²⁺ mixtures served as the precursors for producing network nanostructures of CuS nanoparticles. These new CuS networks exhibit high fluorescence quenching ability and can act as an effective fluorescent sensing platform for ssDNA detection.     

Pyrrolo‐dC Metal‐Mediated Base Pairs in the Reverse Watson–Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6‐Pyridinyl Residues on Fluorescence and Silver‐Ion Binding

Reverse Watson–Crick DNA with parallel‐strand orientation (ps DNA) has been constructed. Pyrrolo‐dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3‐d]pyrimidine base have been incorporated in 12‐ and 25‐mer oligonucleotide duplexes and utilized as silver‐ion binding sites. Thermal‐stability studies on the parallel DNA strands demonstrated extremely strong silver‐ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single ^2pyPyrdC–^2pyPyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver‐ion base pair that aligns 7‐deazapurine bases head‐to‐tail instead of head‐to‐head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson–Crick base pairs stabilized by a dinuclear silver‐mediated PyrdC pair.     

Biofunctionalization of Polyoxometalates with DNA Primers,Their Use in the Polymerase Chain Reaction (PCR) and Electrochemical Detection of PCR Products

The bioconjugation of polyoxometalates (POMs), which are inorganic metal oxido clusters, to DNA strands to obtain functional labeled DNA primers and their potential use in electrochemical detection have been investigated. Activated monooxoacylated polyoxotungstates [SiW₁₁O₃₉{Sn(CH₂)₂CO}]^8? and [P₂W₁₇O₆₁{Sn(CH₂)₂CO}]^6? have been used to link to a 5′‐NH₂ terminated 21‐mer DNA forward primer through amide coupling. The functionalized primer was characterized by using a battery of techniques, including electrophoresis, mass spectrometry, as well as IR and Raman spectroscopy. The functionality of the POM‐labeled primers was demonstrated through hybridization with a surface‐immobilized probe. Finally, the labeled primers were successfully used in the polymerase chain reaction (PCR) and the PCR products were characterized by using electrophoresis.     

A Self‐Reporting Tetrazole‐Based Linker for the Biofunctionalization of Gold Nanorods

A photochemical approach based on nitrile imine‐mediated tetrazole‐ene cycloaddition is introduced to functionalize gold nanorods with biomolecules. For this purpose, a bifunctional, photoreactive linker containing thioctic acid as the Au anchoring group and a tetrazole moiety for the light‐induced reaction with maleimide‐capped DNA was prepared. The tetrazole‐based reaction on the nanoparticles’ surface results in a fluorescent pyrazoline product allowing for the spectroscopic monitoring of the reaction. This first example of nitrile imine‐mediated tetrazole‐ene cycloaddition (NITEC)‐mediated biofunctionalization of Au nanorods paves the way for the attachment of sensitive biomolecules, such as antibodies and other proteins, under mild conditions and expands the toolbox for the tailoring of nanomaterials.     

Photosensitized Thymine Dimerization via Delocalized Triplet Excited States

A new mechanism of photosensitized formation of thymine (Thy) dimers is proposed, which involves generation of a delocalized triplet excited state as the key step. This is supported by chemical evidence obtained by combining one benzophenone and two Thy units with different degrees of freedom, whereby the photoreactivity is switched from a clean Paternò–Büchi reaction to a fully chemo‐, regio‐, and stereoselective [2+2] cycloaddition.     

Fluorescence Polarization Based Nucleic Acid Testing for Rapid and Cost‐Effective Diagnosis of Infectious Disease

A new nucleic acid detection method was developed for a rapid and cost‐effective diagnosis of infectious disease. This approach relies on the three unique elements: 1) detection probes that regulate DNA polymerase activity in response to the complementary target DNA; 2) universal reporters conjugated with a single fluorophore; and 3) fluorescence polarization (FP) detection. As a proof‐of‐concept, the assay was used to detect and sub‐type Salmonella bacteria with sensitivities down to a single bacterium in less than three hours.     

Surviving Mass Extinctions through Biomineralized DNA

Even in the worst of conditions, such as those which occurred during mass extinction events, life on Earth never totally stopped. Aggressive chemical and physical attacks able to sterilize or poison living organisms occurred repeatedly. Surprisingly, DNA was not degraded, denatured or modified to the point of losing the capability of transferring the genetic information to the next generations. After the events of mass extinction life was able to survive and thrive. DNA was passed on despite being an extremely fragile biomolecule. The potential implications of hydroxyapatite protection of DNA are discussed in this Concept article including how DNA acts as a template for hydroxyapatite (HAp) formation, how cell death can trigger biomineralization, and how DNA can be successfully released from HAp when the conditions are favorable for life.     

Substituting CF2 for O4′ in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions

Intrinsic structural features and energetics of nucleotides containing variously fluorinated sugars as potential building blocks of DNA duplexes and quadruplexes are explored systematically using the modern methods of density functional theory (DFT) and quantum chemical topology (QCT). Our results suggest that fluorination at the 2′‐β or 2′‐α,β positions somewhat stabilizes in vacuo the AI relative to the BI conformations. In contrast, substitution of the CF₂ group for the O4′ atom (O4′‐CF₂ modification) leads to a preference of the BI relative to AI DNA‐like conformers. All the studied modifications result in a noticeable increase in the stability of the glycosidic bond [estimated by the relaxed force constants (RFC) approach], with particularly encouraging results for the O4′‐CF₂ derivative. Consequently, the O4′‐CF₂ modified systems are suggested and explored as promising scaffolds for the development of duplex and quadruplex structures with reduced propensity to form abasic lesions and to undergo DNA damage.