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Imaging inside nanowires DNA amplification without thermocycling In the popular PCR method of DNA amplification, a DNA sample is cycled through three different temperatures. Although a few isothermal amplification methods exist, they have complicated reaction schemes and are only able to copy short templates. Huimin Kong and colleagues at New England Biolabs have developed an isothermal amplification method, however, that is simple and can copy long templates. The approach is ideal for point-of-care diagnostic tests, they say. In conventional PCR, the reaction mixture is heated to ~95 ºC for a while to denature the double-stranded template DNA (dsDNA). This step requires special thermostable DNA polymerases. Primer hybridization to the template and extension of
Anders Mikkelsen and colleagues at Lund University (Sweden) have used scanning tunneling microscopy (STM), combined with an embedding technique, to visualize the interior of semiconductor nanowires with atomic resolution. Semiconductor nanowires are predicted to have a major impact in the future of nanoelectronics and photonics. They have already been used successfully to create biological and chemical sensors and singlenanowire lasers. Because the properties of nanowires are largely dependent on their structure, it is important to study the interior architecture of nanowire atoms. Using high-magnification STM imaging, Mikkelsen and his colleagues showed that the interior of GaAs nanowires wrapped in AlGaAs could be directly examined at the atomic level. The wires they examined were mostly defect-free, but the areas with defects had atomic vacancies and protrusions. The researchers say that their technique can also be used to study different types of semiconductor nanowires, dopants, and heterostructures inside nanowires. (Nat. Mater. 2004, 3, 519–523)
the primer to produce a copy occur at lower temperatures. In the helicase-dependent amplification (HDA) method developed by Kong and colleagues, extremely high temperatures are not necessary, so less expensive and more commonly available DNA polymerases can be used. And because the entire reaction is performed at 37 ºC, costly and bulky thermocycler machines are also not needed. When DNA is replicated in a cell, a helicase unwinds the two strands, allowing replication proteins to bind the strands and begin copying. The researchers take advantage of this process by using a bacterial helicase to unwind dsDNA templates in the HDA reaction. Proteins that bind to single-stranded DNA are included in the reaction, which may help prevent rehybridization of the template. The rest of the process is similar to PCR—primers bind to the template, and the polymerase copies the DNA. In the next cycle, the products of the HDA reaction are unwound by the helicase, and the process starts again. The researchers typically ran the reaction for 1–2 h. Kong and colleagues successfully tested the method using plasmid, genomic DNA, or whole bacterial cells as starting material. At present, the method can amplify samples >10 million-fold, but the researchers predict that with optimization even greater amplification can be achieved. (EMBO Rep. 2004, 5, doi 10.1038/sj.embor.7400200)
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