In this chapter, we describe a gene-specific quantitative PCR (QPCR)-based assay for the measurement of DNA damage, using amplification of long DNA targets. This assay has been used extensively to measure the integrity of both nuclear and mitochondrial genomes exposed to different genotoxins and has proven to be particularly valuable in identifying reactive oxygen species-mediated mitochondrial DNA damage. QPCR can be used to quantify both the formation of DNA damage as well as the kinetics of damage removal. One of the main strengths of the assay is that it permits monitoring the integrity of mtDNA directly from total cellular DNA without the need for isolating mitochondria or a separate step of mitochondrial DNA purification. Here we discuss advantages and limitations of using QPCR to assay DNA damage in mammalian cells. In addition, we give a detailed protocol of the QPCR assay that helps facilitate its successful deployment in any molecular biology laboratory.

Recent data in invertebrates demonstrated that huntingtin (htt) is essential for fast axonal trafficking. Here, we provide direct and functional evidence that htt is involved in fast axonal trafficking in mammals. Moreover, expression of full-length mutant htt (mhtt) impairs vesicular and mitochondrial trafficking in mammalian neurons in vitro and in whole animals in vivo. Particularly, mitochondria become progressively immobilized and stop more frequently in neurons from transgenic animals. These defects occurred early in development prior to the onset of measurable neurological or mitochondrial abnormalities. Consistent with a progressive loss of function, wild-type htt, trafficking motors, and mitochondrial components were selectively sequestered by mhtt in human Huntington's disease-affected brain. Data provide a model for how loss of htt function causes toxicity; mhtt-mediated aggregation sequesters htt and components of trafficking machinery leading to loss of mitochondrial motility and eventual mitochondrial dysfunction.Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion mutation in the coding region of a novel gene. The mechanism of HD is unknown. However, most data suggest that polyglutamine-mediated aggregation contributes to the pathology (32). Studies of human brain (14), mouse models (48), and cells (8, 28) demonstrate that mutant huntingtin (mhtt) binds and sequesters its normal counterpart as well as many cellular proteins (41). But whether pathophysiology results from a loss of normal function or a gain of a new function in adult neurons is not well understood.A major gap in our understanding of the disease mechanism is the absence of a known function for normal huntingtin (htt). Emerging evidence suggests that htt is likely to be a multifunctional protein that can mediate transactions in both the nucleus and the cytoplasm. Transcriptional dysfunction caused by mhtt has been proposed to lead to toxicity. The mutation in full-length htt prevents its normal ability to bind and sequester a repressor of brain-derived neurotrophic factor expression, reducing the availability of brain-derived neurotrophic factor to striatal neurons (54). The N-terminal, truncated form of mhtt can bind to and interfere with nuclear factors such as CREB (51), CREB binding protein (30, 39), corepressor (22), and transcriptional activator Sp1 (12,23).Cytoplasmic dysfunction has also been implicated as a toxic mechanism. Recently, novel data obtained with Drosophila (17) and isolated squid axoplasm (42) have provided direct evidence that htt is an essential protein involved in fast axonal trafficking. Additionally, these data demonstrate that the mutation in htt causes trafficking abnormalities. Reduction of htt expression in Drosophila caused axonal transport defects in larval nerves and the same neurodegenerative phenotype in adult eyes as expression of mutant dynein or p150 Glued (17). In invertebrate models for HD, expression of truncated proteins with an expanded gluta...

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