Nanostructured DNA Microarrays for Dual SERS and Electrochemical Read‐out

We present a strategy to fabricate nanostructured microarrays ready to perform a dual read‐out, namely electrochemical (EC) as well as surface‐enhanced Raman spectroscopy (SERS) based detection of DNA hydridization. A polystyrene nanobeads monolayer assembly, obtained by means of a Langmuir Blodgett type technique, followed by electrochemical Au deposition, was employed to construct homogeneous nanostructures in the form of inverse‐opal nanovoids on a 32‐electrode Au microarray chip. Characterization of the obtained nanostructured electrodes of the array by means of cyclic voltammetry demonstrated high reproducibility of the surface modification process. The performance of the obtained array platform was investigated by modifying the microarray electrodes with three different oligonucleotide capture probes using a previously developed potential‐assisted surface modification protocol. Two ferrocene‐labeled target DNA sequences and one target RNA sequence with a Texas red label were detected electrochemically and via SERS, respectively.     

Bioelectrochemistry for miRNA detection

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The prize-collecting generalized minimum spanning tree problem

We introduce the prize-collecting generalized minimum spanning tree problem. In this problem a network of node clusters needs to be connected via a tree architecture using exactly one node per cluster. Nodes in each cluster compete by offering a payment for selection. This problem is NP-hard, and we describe several heuristic strategies, including local search and a genetic algorithm. Further, we present a simple and computationally efficient branch-and-cut algorithm. Our computational study indicates that our branch-and-cut algorithm finds optimal solutions for networks with up to 200 nodes within two hours of CPU time, while the heuristic search procedures rapidly find near-optimal solutions for all of the test instances.     

Potential‐Assisted DNA Immobilization as a Prerequisite for Fast and Controlled Formation of DNA Monolayers

Highly reproducible and fast potential‐assisted immobilization of single‐stranded (ss)DNA on gold surfaces is achieved by applying a pulse‐type potential modulation. The desired DNA coverage can be obtained in a highly reproducible way within minutes. Understanding the underlying processes occurring during potential‐assisted ssDNA immobilization is crucial. We propose a model that considers the role of ions surrounding the DNA strands, the distance dependence of the applied potentials within the electrolyte solution, and most importantly the shift of the potential of zero charge during the immobilization due to the surface modification with DNA. The control of the surface coverage of ssDNA as well as the achieved speed and high reproducibility are seen as prerequisites for improved DNA‐based bioassays.     

Designing WDM Optical Networks Using Branch-and-Price

In this paper, we present an exact solution procedure for the design of two-layer wavelength division multiplexing (WDM) optical networks with wavelength changers and bifurcated flows. This design problem closely resembles the traditional multicommodity flow problem, except that in the case of WDM optical networks, we are concerned with the routing of multiple commodities in two network layers. Consequently, the corresponding optimization models have to deal with two types of multicommodity variables defined for each of the network layers. The proposed procedure represents one of the first branch-and-price algorithms for a general WDM optical network setting with no assumptions on the number of logical links that can be established between nodes in the network. We apply our procedure in a computational study with four different network configurations. Our results show that for the three tested network configurations our branch-and-price algorithm provides solutions that are on average less than 5 % from optimality. We also provide a comparison of our branch-and-price algorithm with two simple variants of the upper bounding heuristic procedure HLDA that is commonly used for WDM optical network design.     

Controlling DNA/Surface Interactions for Potential Pulse‐Assisted Preparation of Multi‐Probe DNA Microarrays

The possibility of selectively modifying microarray electrodes with different DNA sequences in a controlled way without the need for local positioning of solutions or local modification of array surfaces is demonstrated. Potential pulse sequences are employed to perform sequential surface modification of a 32‐gold‐electrode array with two different thiolated DNA capture sequences, surface passivation and regeneration of selected microarray electrodes, all by adjusting the potential intensities of the same potential pulse‐assisted method. We achieve reproducible and controlled DNA immobilization together with minimization of false signals originating from unspecific adsorption or undesired co‐immobilization. This methodology is not limited to DNA chips and it is potentially suitable for a wide range of applications employing Au?S chemistry. It can be employed in laboratory conditions for localizing different reactive chemistries onto predefined electrodes of an array without the need for complex and expensive apparatus and special conditions.