BioTechniques' Advance Online Publication is a monthly e-mail alert featuring select abstracts with links to their full-text articles of papers posted online prior to publication. Each month you'll receive selected hot papers before they are published.

Scanning conductance microscopy investigations on fixed human
Casper Hyttel Clausen, Jacob Moresco Lange, Linda Boye Jensen, Pranjul Jaykumar Shah, Maria Ioannou Dimaki, and Winnie Edith Svendsen
Scanning conductance microscopy investigations were carried out in air on human chromosomes fixed on pre-fabricated SiO surfaces with a backgate. The point of the investigation was to estimate the dielectric constant of fixed human chromosomes in order to use it for microfluidic device optimization. The phase shift caused by the electrostatic forces, together with geometrical measurements of the atomic force microscopy (AFM) cantilever and the chromosomes were used to estimate a value for the dielectric constant of different human chromosomes.

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Rapid capture of DNA targets
Judy St. John and Thomas W. Quinn
A rapid capture technique was developed to efficiently isolate specific DNA targets from a variety of genomes. The specificity can be easily adapted to any target for which partial sequence is known, allowing for the isolation of a wide set of target molecules from either characterized or uncharacterized genomes. These targets include but are not limited to transposable elements, microsatellites, repetitive sequences, and possibly unique sequences. Additionally, because the thermodynamics of nucleic acid hybridizations differ from processes such as PCR, a wider variety of targets with a range of mismatches to any customized probe can be isolated. Further, this method allows sequences flanking known internal regions to be co-isolated, facilitating the development of flanking primers for downstream applications. Considerable reduction in the frequency of nonspecific binding between key components (background) obviates the need for subsequent screening steps. Rapid capture of DNA targets quickly provides information about target and flanking sequences.

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An oligonucleotide microarray for multiplex real-time PCR identification of HIV-1, HBV, and HCV
Dmitry A. Khodakov, Natalia V. Zakharova, Dmitry A. Gryadunov, Felix P. Filatov, Alexander S. Zasedatelev, and Vladimir M. Mikhailovich
We describe a novel microarray-based approach for simultaneous identification and quantification of human immunodeficiency virus type 1 (HIV-1) and hepatitis B and C viruses (HBV and HCV) in donor plasma specimens. The method is based on multiplex real-time RT-PCR performed within the microarray hydrogel pads. Double-stranded amplification products are simultaneously detected using nonspecific SYBR Green I dye due to the reaction run in separate pads bearing 5′-immobilized specific primers. Both the sensitivity and specificity of the assay, based on 132 blood specimens analyzed, were 100% (56, 26, and 8 specimens were seropositive to HBV, HCV, and HIV-1, respectively; 22 were positive to both HIV-1 and HCV, and 2 positive to all three viruses; 18 samples were pathogen-negative). The dynamic range of the quantitative analysis covered a six-order interval ranging from 10⁰ to 10⁶ genome equivalents per assay. The 95% detection limits were 14 gEq for HIV-1, 10 gEq (1.7 IU) for HBV, and 15 gEq (7.5 IU) for HCV per assay. The proposed approach is considered to be versatile and could be adapted for simultaneous identification and quantification of numerous genetic targets.

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