Highly selective and sensitive DNA assay based on electrocatalytic oxidation of ferrocene bearing zinc(II)-cyclen complexes with diethylamine

A highly selective and sensitive electrochemical biosensor has been developed that detects DNA hybridization by employing the electrocatalytic activity of ferrocene (Fc) bearing cyclen complexes (cyclen = 1,4,7,10-tetraazacyclododecane, Fc[Zn(cyclen)H2O]2(ClO4)4 (R1), Fc(cyclen)2 (R2), Fc[Zn(cyclen)H2O](ClO4)2 (R3), and Fc(cyclen) (R4)). A sandwich-type approach, which involves hybridization of a target probe hybridized with the preimmobilized thiolated capture probe attached to a gold electrode, is employed to fabricate a DNA duplex layer. Electrochemical signals are generated by voltammetric interrogation of a Fc bearing Zn−cyclen complexes that selectively and quantitatively binds to the duplex layers through strong chelation between the cyclen complexes and particular nucleobases within the DNA sequence. Chelate formation between R1 or R3 and thymine bases leads to the perturbation of base-pair (A−T) stacking in the duplex structure, which greatly diminishes the yield of DNA-mediated charge transport and displays a marked selectivity to the presence of the target DNA sequence. Coupling the redox chemistry of the surface-bound Fc bearing Zn−cyclen complex and dimethylamine provides an electrocatalytic pathway that increases sensitivity of the assay and allows the 100 fM target DNA sequence to be detected. Excellent selectivity against even single-base sequence mismatches is achieved, and the DNA sensor is stable and reusable.

Simulation and analysis of a sub-wavelength grating based multilayer surface plasmon resonance biosensor

This paper presents a subwavelength grating based multilayer surface plasmon resonance biosensor (SPRB) which includes a periodic array of subwavelength grating on top of a layer of graphene sheet in the biosensor. The proposed biosensor is named grating-graphene SPRB (GG-SPRB). The aim of the proposed multilayer structure is to improve the sensitivity of the SPRB through monitoring of the biomolecular interactions of DNA hybridization. Significant sensitivity improvement is obtained for the GG-SPRB compared with the conventional SPRB. The result of the numerical investigation of the GG-SPRB is presented and compared with a theoretically developed multilayer matrix formalism, and a good agreement has been observed. In addition, an optimization of the grating dimensions including volume factor, grating depth, grating angle, grating period, and grating geometry (e.g., rectangular, sinusoidal and triangular) is presented. The outcome of the investigation presented in this paper identifies desired functioning conditions corresponding to the best design parameters for the GG-SPRB.

Numerical investigation of a grating and graphene-based multilayer surface plasmon resonance biosensor

A multilayer surface plasmon resonance biosensor (SPRB) incorporating a grating-graphene configuration is investigated for enhanced sensitivity. The numerical analysis of the impact of integrating a periodic array of subwavelength grating on top of a layer of graphene sheet for improving sensitivity is presented. The result of monitoring the biomolecular interactions of DNA hybridization is compared against the outcome of the conventional SPRB, a graphene-based multilayer SPRB, and a multilayer layer grating SPRB, and is mathematically validated. It is demonstrated that the inclusion of a grating and graphene layer on top of the gold thin film is an excellent candidate for a highly sensitive SPRB. To achieve further enhancement of sensitivity, the subwavelength grating is numerically optimized against its geometry including grating configurations (rectangular, sinusoidal, and triangular), grating depth, volume factor, and grating period. © 2014 Taylor & Francis.

Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo

The taxonomic status of a bacterium, strain NCCP-246(T), isolated from rhizosphere of Vigna mungo, was determined using a polyphasic taxonomic approach. The strain NCCP-246(T) can grow at 16-37 °C (optimum 32 °C), at pH ranges of 6-8 (optimum growth occurs at pH 7) and in 0-4 % (w/v) NaCl. Phylogenetic analysis based upon on 16S rRNA gene sequence comparison revealed that strain NCCP-246(T) belonged to genus Sphingobacterium. Strain NCCP-246(T) showed highest similarity to the type strain of Sphingobacterium canadense CR11(T) (97.67 %) and less than 97 % with other species of the genus. The DNA-DNA relatedness value of strain NCCP-246(T) with S. canadense CR11(T) and Sphingobacterium thalpophilum JCM 21153(T) was 55 and 44.4 %, respectively. The chemotaxonomic data revealed the major menaquinone as MK-7 and dominant cellular fatty acids were summed feature 3 [C16:1 ω7c/C16:1 ω6c] (37.07 %), iso-C15:0 (28.03 %), C16:0 (11.85 %), C17:0 cyclo (8.84 %) and C14:0 (2.42 %). The G+C content of the strain was 39.2 mol%. On the basis of DNA-DNA hybridization, phylogenetic analyses, physiological and, biochemical data, strain NCCP-246(T) can be differentiated from the validly named members of genus Sphingobacterium and thus represents as a new species, for which the name, Sphingobacterium pakistanensis sp. nov. is proposed with the type strain NCCP-246(T) (= JCM18974 (T) = KCTC 23914(T)).