Nontarget DNA binding shapes the dynamic landscape for enzymatic recognition of DNA damage

The DNA repair enzyme human uracil DNA glycosylase (UNG) scans short stretches of genomic DNA and captures rare uracil bases as they transiently emerge from the DNA duplex via spontaneous base pair breathing motions. The process of DNA scanning requires that the enzyme transiently loosen its grip on DNA to allow stochastic movement along the DNA contour, while engaging extrahelical bases requires motions on a more rapid timescale. Here, we use NMR dynamic measurements to show that free UNG has no intrinsic dynamic properties in the millisecond to microsecond and subnanosecond time regimes, and that the act of binding to nontarget DNA reshapes the dynamic landscape to allow productive millisecond motions for scanning and damage recognition. These results suggest that DNA structure and the spontaneous dynamics of base pairs may drive the evolution of a protein sequence that is tuned to respond to this dynamic regime

Ameloblasts require active RhoA to generate normal dental enamel

RhoA plays a fundamental role in regulation of the actin cytoskeleton, intercellular attachment and cell proliferation. During amelogenesis, ameloblasts which produce the enamel proteins undergo dramatic cytoskeletal changes and RhoA protein level is upregulated. Transgenic mice were generated that express a dominant-negative RhoA transgene in ameloblasts using amelogenin gene regulatory sequences. Transgenic and WT molar tooth germs were incubated with NaF or NaCl in organ culture. F-actin stained with phalloidin was elevated significantly in WT ameloblasts treated with NaF compared to WT ameloblasts treated with NaCl or compared to transgenic ameloblasts treated with NaF, thereby confirming a block in the RhoA/ROCK pathway in the transgenic mice. Little difference in quantitative fluorescence (estimation of fluorosis) was observed between WT and transgenic incisors from mice provided NaF in their drinking water. We subsequently found reduced transgene expression in incisors compared to molars. Transgenic molar teeth had reduced amelogenin, E-cadherin and Ki67 compared to WT. Hypoplastic enamel in transgenic mice correlates with reduced expression of the enamel protein amelogenin, and E-cadherin and cell proliferation are regulated by RhoA in other tissues. Together these findings reveal deficits in molar ameloblast function when RhoA activity is inhibited

The Fpg/Nei Family of DNA Glycosylases

During the initial stages of the base excision DNA repair (BER) pathway, DNA glycosylases are responsible for locating and removing the majority of endogenous oxidative base lesions. The bifunctional formamidopyrimidine DNA glycosylase (Fpg) and endonuclease VIII (Nei) are members of the Fpg/Nei family, one of the two families of glycosylases that recognize oxidized DNA bases, the other being the HhH/GPD (or Nth) superfamily. Structural and biochemical developments over the past decades have led to novel insights into the mechanism of damage recognition by the Fpg/Nei family of enzymes. Despite the overall structural similarity among members of this family, these enzymes exhibit distinct features that make them unique. This review summarizes the current structural knowledge of the Fpg/Nei family members, emphasizes their substrate specificities, and describes how these enzymes search for lesions

Characterization of DNA with an 8-oxoguanine modification

The oxidation of DNA resulting from reactive oxygen species generated during aerobic respiration is a major cause of genetic damage that, if not repaired, can lead to mutations and potentially an increase in the incidence of cancer and aging. A major oxidation product generated in cells is 8-oxoguanine (oxoG), which is removed from the nucleotide pool by the enzymatic hydrolysis of 8-oxo-2′-deoxyguanosine triphosphate and from genomic DNA by 8-oxoguanine-DNA glycosylase. Finding and repairing oxoG in the midst of a large excess of unmodified DNA requires a combination of rapid scanning of the DNA for the lesion followed by specific excision of the damaged base. The repair of oxoG involves flipping the lesion out of the DNA stack and into the active site of the 8-oxoguanine-DNA glycosylase. This would suggest that thermodynamic stability, in terms of the rate for local denaturation, could play a role in lesion recognition. While prior X-ray crystal and NMR structures show that DNA with oxoG lesions appears virtually identical to the corresponding unmodified duplex, thermodynamic studies indicate that oxoG has a destabilizing influence. Our studies show that oxoG destabilizes DNA (ΔΔG of 2–8 kcal mol−1 over a 16–116 mM NaCl range) due to a significant reduction in the enthalpy term. The presence of oxoG has a profound effect on the level and nature of DNA hydration indicating that the environment around an oxoG•C is fundamentally different than that found at G•C. The temperature-dependent imino proton NMR spectrum of oxoG modified DNA confirms the destabilization of the oxoG•C pairing and those base pairs that are 5′ of the lesion. The instability of the oxoG modification is attributed to changes in the hydrophilicity of the base and its impact on major groove cation binding

Case Report-Mega-duodenum due to isolated segmental duodenal aganglionosis

Isolated segmental duodenal aganglionosis is an extremely rare condition. We report a case of mega-duodenum due to an isolated aganglionic segment in the second part of the duodenum. A 60-year-old female presented with a history of off-and-on non-bilious vomiting and upper abdominal fullness after each meal. Investigations suggested that the stomach and the first part of the duodenum were grossly dilated. On exploration, a narrowed segment in the second part of the duodenum with gross dilation of the proximal duodenum and the stomach was found. Retrocolic duodenojejunostomy was done and a biopsy was taken from the narrowed duodenal segment. Histopathology examination revealed near-complete absence of the ganglion cells in the narrowed segment