Predicting G-quadruplex Formation

Guanine-rich regions of genomic DNA can spontaneously fold into secondary structures called G-quadruplexes (GQs). Akin to tiny switches, GQs regulate genetic processes through their folding and unfolding. Their interest to basic science, as well as their potential as therapeutic targets for human diseases, has motivated the creation of computational tools for their prediction. Currently, GQ folding predictors are based on results from studies of GQs formed in single-stranded DNA. As a result, existing tools perform poorly when applied to the prediction of GQ formation in double-stranded (ds) DNA, the native context within which genomic GQs are found. Here, we present a probabilistic model of GQ formation, which is learned from large-scale human genomic pull-down experiments and applied to the analysis of gene ontological data. Advances in the characterization of GQs in dsDNA have enabled us to integrate results from small-molecule binding assays and singlemolecule FRET microscopy into our model. In order to obtain training sets of sequences, we identified nearly 700,000 unique, potential GQs and categorized them according to pulldown experiment outcomes. Model parameters learned from these training sets agree with experimental evidence and, when asked to predict the folding of dsDNA GQ sequences, outperformed existing models of GQ folding. This tool can be applied to genomic sequences to locate the most strongly forming GQs, revealing valuable information for the design of GQ-targeting therapies, and represents the next step toward the practical, widespread use of GQs in medicine and technology.Ope

G-quadruplex DNA and the Regulation of Human Telomere Accessibility

Human telomeres are nucleoprotein structures that cap the ends of chromosomes, preventing them from degradation. In normal cells, they are shortened due to the end replication problem. However, most cancer cells overcome this inherent growth limitation by upregulating telomerase, an enzyme that elongates telomeres to yield an immortal phenotype. The remaining cancerous cells immortalize by activating the alternative telomerelengthening pathway (ALT). Thus, treatments that directly target the telomere could disrupt both mechanisms the cancer cell employs for unlimited proliferation. The telomere overhang is G-rich DNA that spontaneously folds into a G-quadruplex. In vitro, the G-quadruplex structure has been shown to inhibit telomere extension by telomerase, making it an attractive potential therapeutic target. However, G-quadruplex capping properties and regulatory roles are still poorly understood. In this study, we used a FRET-based assay to probe the stability and accessibility of the G-quadruplex. We examined the folding behavior of variable telomeric repeat lengths (4- 8). Accessibility of the G-quadruplex was measured by the rate of quadruplex unfolding after the addition of complementary DNA, ALT pathway proteins, and telomerase. These measurements revealed a distinct periodic pattern of overhang accessibility where DNA and protein binding is limited for multiples of four TTAGGG repeats, whereas five to seven repeats are more accessible (7>6>5). Contrastingly, POT1, a telomere-specific binding protein, showed accessibility independent of the number of repeats. These results demonstrate the role of G-quadruplexes as physical impedances to the binding of telomere associated proteins and as critical regulatory structures for theOpe

Telomeric Overhang Length Determines Structural Dynamics and Accessibility to Telomerase and ALT-Associated Proteins

SummaryThe G-rich single-stranded DNA at the 3′ end of human telomeres can self-fold into G-quaduplex (GQ). However, telomere lengthening by telomerase or the recombination-based alternative lengthening of telomere (ALT) mechanism requires protein loading on the overhang. Using single-molecule fluorescence spectroscopy, we discovered that lengthening the telomeric overhang also increased the rate of dynamic exchanges between structural conformations. Overhangs with five to seven TTAGGG repeats, compared with four repeats, showed much greater dynamics and accessibility to telomerase binding and activity and loading of the ALT-associated proteins RAD51, WRN, and BLM. Although the eight repeats are highly dynamic, they can fold into two GQs, which limited protein accessibility. In contrast, the telomere-specific protein POT1 is unique in that it binds independently of repeat number. Our results suggest that the telomeric overhang length and dynamics may contribute to the regulation of telomere extension via telomerase action and the ALT mechanism

Self-Powered Neutron Detector Calibration Using a Large Vertical Irradiation Hole of HANARO

A calibration technology of the self-powered neutron detectors (SPNDs) using a large vertical irradiation hole of HANARO is developed. The 40 Rh-SPNDs are installed on the polycarbonate plastic support, and the gold wires with the same length as the effective length of the rhodium emitter of the SPND are also installed to measure the neutron flux on the SPND. They are irradiated at a low reactor power, and the SPND current is measured using the pico-ammeter. The external gamma-rays which affect the SPND current response are analyzed using the Monte Carlo simulation for various irradiation conditions in HANARO. It is confirmed that the effect of the external gamma-rays to the SPND current is dependent on the reactor characteristics, and that it is affected by materials around the detector. The current signals due to the external gamma-rays can be either positive or negative, in that the net flow of the current may be either in the same or the opposite direction as the neutron-induced current by the rhodium emitter. From the above procedure, the effective calibration methodology of multiple SPNDs using the large hole of HANARO is developed. It could be useful for the calibration experiment of the neutron detectors in the research reactors

Using Online Planning and Acting to Recover from Cyberattacks on Software-defined Networks

We describe ACR-SDN, a system to monitor, diagnose, and quickly respond to attacks or failures that may occur in software-defined networks (SDNs). An integral part of ACR-SDN is its use of RAE+UPOM, an automated acting and planning engine that uses hierarchical refinement. To advise ACR-SDN on how to recover a target system from faults and attacks, RAE+UPOM uses attack recovery procedures written as hierarchical operational models. Our experimental results show that the use of refinement planning in ACR-SDN is successful in recovering SDNs from attacks with respect to five performance metrics: estimated time for recovery, efficiency, retry ratio, success ratio, and costEffectiveness

University of Michigan Undergraduate Research Journal presents: The Zine, Winter 2010

Articlehttp://deepblue.lib.umich.edu/bitstream/2027.42/97011/1/UMURJ-Zine_2010.pd