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Displaying 51 - 75 of 229

The Effects of Diffusion on an Exonuclease/Nanopore-Based DNA Sequencing Engine

December 7, 2012
Author(s)
Joseph E. Reiner, Joseph W. Robertson, Arvind Balijepalli, Daniel L. Burden, Bryon S. Drown, John J. Kasianowicz
The ability to electronically detect and characterize individual polynucleotides as they are driven through a single protein ion channel may eventually prove useful for rapidly sequencing DNA (base-by-base) in a ticker tape-like fashion. More recently, a

PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis

September 21, 2012
Author(s)
Shiv Kumar, Tao Chuanjuan, Chien Minchen, Hellner Brittney, Joseph W. Robertson, Arvind Balijepalli, Li Zengmin, James J. Russo, Joseph E. Reiner, John J. Kasianowicz, Jingyue Ju
There is a significant need to accurately sequence single DNA and RNA molecules for personalized medicine. We describe a novel nanopore-based sequencing by synthesis (SBS) strategy that will accurately differentiate at single molecule level four different

Structural and biochemical studies of a plant formamidopyrimidine-DNA glycosylase reveal why eukaryotic Fpg glycosylases do not excise 8-oxoguanine.

July 11, 2012
Author(s)
M Miral Dizdar, Pawel Jaruga, Susan Duclos, Pierre Aller, Susan Wallace, Susan Doublie
Formamidopyrimidine-DNA glycosylase (Fpg; MutM) is a DNA repair enzyme widely distributed in bacteria. Fpg recognizes and excises oxidatively modified purines, 4,6-diamino-5-formamidopyrimidine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 8-oxoguanine

Identification and quantification of DNA repair proteins by liquid chromatography/isotope-dilution tandem mass spectrometry using 15N-labeled whole proteins as internal standards

May 30, 2012
Author(s)
M Miral Dizdar, Prasad T. Reddy, Guldal Kirkali, Gamze Tuna, Bryant C. Nelson, Pawel Jaruga
Oxidatively induced DNA damage is implicated in disease, unless it is repaired by DNA repair. DNA repair proteins may be used as early detection and therapeutic biomarkers in cancer and other diseases. For this purpose, the measurement of the expression

Mechanisms of free radical-induced damage to DNA

April 1, 2012
Author(s)
M Miral Dizdar, Pawel Jaruga
Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates by

DNA Molecules Descending a Nanofluidic Staircase by Entropophoresis

January 26, 2012
Author(s)
Samuel M. Stavis, Jon C. Geist, Michael Gaitan, Laurie E. Locascio, Elizabeth A. Strychalski
A complex entropy gradient for confined DNA molecules was engineered for the first time. Following the second law of thermodynamics, this enabled the directed self-transport and self-concentration of DNA molecules. This new nanofluidic method is termed

Oxidatively Induced DNA Damage and Cancer

December 30, 2011
Author(s)
M Miral Dizdar, Pawel Jaruga
Oxidatively induced DNA damage is caused by endogenous and exogenous sources in living organisms. Many resulting DNA lesions are mutagenic and lead to mutations commonly found in cancer. Repairs mechanisms exist to repair this type of DNA damage

Evidence for upregulated repair of oxidatively induced DNA damage in human colorectal cancer

September 15, 2011
Author(s)
M Miral Dizdar, Pawel Jaruga, Prasad T. Reddy, Guldal Kirkali, Didem Keles, Gulgun Oktay, Aras E. Canda
Molecular pathways that play a role in the development of colorectal cancer involve multiple genetic changes in cancer-related genes that may be caused by overproduction of oxygen-derived species including free radicals, which are capable of damaging DNA

Stable isotope-labeling of DNA repair proteins, and their purification and characterization

July 1, 2011
Author(s)
M Miral Dizdar, Pawel Jaruga, Prasad T. Reddy, Bryant C. Nelson, Mark S. Lowenthal
Reduced DNA repair capacity is associated with increased risk for a variety of disease processes including carcinogenesis. Thus, DNA repair proteins have the potential to be used as important predictive, prognostic and therapeutic biomarkers in cancer and

PDH-locked, frequency-stabilized cavity ring-down spectrometer

June 16, 2011
Author(s)
Joseph T. Hodges, A. Cygan, Piotr Maslowski, Katarzyna E. Bielska, S. Wojtewicz, J. Domyslawska, Hisashi Abe, R.S. Trawinski, R. Ciurylo
We describe a high sensitivity and high spectral resolution laser absorption spectrometer based upon the frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) technique. We used the Pound-Drever-Hall (PDH) method to lock the probe laser to the high

Metrology Needs and NIST Resources for the Forensic DNA Community

June 1, 2011
Author(s)
Michael D. Coble, Margaret C. Kline, John M. Butler
With the advent of Forensic DNA profiling in the mid-1980s, this technology has had a positive impact on the criminal justice system, helping to convict the guilty and exonerate the innocent. The field has evolved from focusing on multi-locus markers

A Major Role for Non-Enzymatic Antioxidant Processes in the Radioresistance of Halobacterium salinarum

April 1, 2011
Author(s)
M Miral Dizdar, Pawel Jaruga, Courtney K. Robinson, Kim Webb, Amardeep Kaur, Nitin S. Baliga, Allen Place, Jocelyne DiRuggiero
Oxidative stress occurs when the generation of reactive oxygen species (ROS) exceeds the capacity of the cell’s endogenous systems to neutralize them. We analyzed the oxidative stress responses and cellular damage of the archaeon Halobacterium salinarum

Mechanisms and Measurement of Nanomaterial-Induced Oxidative Damage to DNA

June 22, 2010
Author(s)
Bryant C. Nelson, Elijah J. Petersen
Many of the current investigations on the environmental health and human safety risks of engineered nanomaterials focus on their short-term acute effects. However, the long-term chronic effects of nanomaterials on living systems, and in particular, on the

Development and Demonstration of a Method to Evaluate Bio-Sampling Strategies Using Building Simulation and Sample Planning Software

June 10, 2010
Author(s)
William S. Dols, Jayne B. Morrow, Andrew K. Persily, Brett Matzke, Landon Sego, Lisa Nuffer, Brent Pulsipher
response and recovery sampling approaches and technologies, the U.S. Department of Homeland Security (DHS), along with several other agencies, have simulated a biothreat agent release within a facility at Idaho National Laboratory (INL) on two separate

The mouse ortholog of NEIL3 is a functional DNA glycosylase in vitro and in vivo

March 16, 2010
Author(s)
Minin Liu, Viswanath Bandaru, Jeffrey Bond, Pawel Jaruga, Xiaobei Zhao, Plamen P. Christov, Cynthia Burrows, Carmelo J. Rizzo, Miral M. Dizdar, Susan Wallace
To protect cells from oxidative DNA damage and mutagenesis, organisms possess multiple glycosylases to recognize the damaged bases and to initiate the Base Excision Repair (BER) pathway. Recently, three DNA glycosylases were identified in mammals that are
Displaying 51 - 75 of 229