Oxidative DNA glycosylases: recipes from cloning to characterization.

abstract：:Since its major launch into academia in the mid-1990s, spotted DNA microarray technology has expanded and matured into an important mainstream tool for genomic-scale gene expression studies across many species with many applications. Based on the principles of enzymatic nucleic acid labeling and DNA hybridization, the...

journal_title：Methods in enzymology

authors： Hager J

更新日期：2006-01-01 00:00:00

abstract：:Anomalous small angle X-ray scattering (ASAXS) exploits contrast variation methods to highlight the scattering from one elemental component in a multielement sample, such as one ion species in an ion-DNA system. The ASAXS method has been applied to measure ions condensed around short nucleic acid duplexes. This chapte...

journal_title：Methods in enzymology

authors： Pabit SA,Finkelstein KD,Pollack L

更新日期：2009-01-01 00:00:00

abstract：:A genetic interaction occurs when the combination of two mutations leads to an unexpected phenotype. Screens for synthetic genetic interactions have been used extensively to identify genes whose products are functionally related. In particular, synthetic lethal genetic interactions often identify genes that buffer one...

journal_title：Methods in enzymology

authors： Baryshnikova A,Costanzo M,Dixon S,Vizeacoumar FJ,Myers CL,Andrews B,Boone C

更新日期：2010-01-01 00:00:00

abstract：:Circadian clocks are present in most cells and are essential for maintenance of daily rhythms in physiology, mood, and cognition. Thus, not only neurons of the central circadian pacemaker but also many other peripheral tissues possess the same functional and self-sustained circadian clocks. Surprisingly, however, thei...

journal_title：Methods in enzymology

authors： Gaspar L,Brown SA

更新日期：2015-01-01 00:00:00

abstract：:In the presence of specialized proteins or peptides, a biological membrane can spontaneously restructure itself to allow communication between the intracellular and the extracellular sides. Examples of these proteins include cell-penetrating peptides and antimicrobial peptides (AMPs), which interact with cell membrane...

journal_title：Methods in enzymology

authors： Mishra A,Tai KP,Schmidt NW,Ouellette AJ,Wong GC

更新日期：2011-01-01 00:00:00

abstract：:Critical to the advancement of tumor immunotherapy is the reliable identification of responders and the quantification of the tumor-specific immune response elicited by treatments. In this regard, Enzyme-Linked Immunospot assay (ELISpot) is an ideal monitoring technique due to its high sensitivity, ease of execution a...

journal_title：Methods in enzymology

authors： Negri D,Sestili P,Borghi M,Ciccolella M,Bracci L

更新日期：2020-01-01 00:00:00

abstract：:Polyacrylamide gel electrophoresis under native conditions (native PAGE) is a well-established and versatile method for probing nucleic acid conformation and nucleic acid-protein interactions. Native PAGE has been used to measure RNA folding equilibria and kinetics under a wide variety of conditions. Advantages of thi...

journal_title：Methods in enzymology

authors： Woodson SA,Koculi E

更新日期：2009-01-01 00:00:00

abstract：:Antibodies are excellent binding proteins that have found numerous applications in biological research, biotechnology, and medicine. Characterization of their ligand binding properties has long been, and continues to be, the focus of many researchers. Antibodies are also perfect test systems which can be used for the ...

journal_title：Methods in enzymology

authors： Tetin SY,Ruan Q,Skinner JP

更新日期：2013-01-01 00:00:00

abstract：:Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, an...

journal_title：Methods in enzymology

authors： Revsbech NP

更新日期：2005-01-01 00:00:00

abstract：:Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides ...

journal_title：Methods in enzymology

authors： Lima LM,Iranzo O

更新日期：2016-01-01 00:00:00

abstract：:Recent work demonstrates that RNA interference (RNAi) can coordinate protein expression. Inhibitory RNAs are expressed naturally in cells as microRNAs (miRNAs) or introduced into cells as small interfering RNAs (siRNAs). Both types of small RNAs can be used at the bench to silence mRNA expression. For many researchers...

journal_title：Methods in enzymology

authors： Davidson BL,Harper SQ

更新日期：2005-01-01 00:00:00

abstract：:Vertebrate odorant-binding proteins (OBPs) are small soluble proteins abundantly secreted in the olfactory mucus of many animal species, including humans. Vertebrate OBPs reversibly bind odorant molecules with micromolar range affinities. Although their physiological role is not clearly understood, OBPs are proposed t...

journal_title：Methods in enzymology

authors： Brulé M,Glaz M,Belloir C,Poirier N,Moitrier L,Neiers F,Briand L

更新日期：2020-01-01 00:00:00

abstract：:Rarely is any solution simply solute and water. In vivo, solutes, such as proteins and nucleic acids, swim in a sea of water, salts, ions, small molecules, and lipids, not to mention other macromolecules. In vitro, virtually all solutions contain a mixture of aqueous solvents, or "cosolvents" [i.e., solvent(s) in addi...

journal_title：Methods in enzymology

authors： Beck DA,Bennion BJ,Alonso DO,Daggett V

更新日期：2007-01-01 00:00:00

abstract：:Isothermal Titration Calorimetry (ITC) provides a sensitive and accurate means by which to study the thermodynamics of RNA folding, RNA binding to small molecules, and RNA-protein interactions. The advent of extremely sensitive instrumentation and the increasing availability of ITC in shared facilities have made it in...

journal_title：Methods in enzymology

authors： Feig AL

更新日期：2009-01-01 00:00:00

abstract：:Embryonic stem (ES) cells are cells derived from the inner cell mass of a blastocyst stage embryo. These self-renewing multipotent cells are able to differentiate to the three embryonic germ layers, the endoderm, ectoderm, and mesoderm, and are thus able to produce virtually all cell types. The ES cell capacity to gen...

journal_title：Methods in enzymology

authors： Goldberg-Cohen I,Beck G,Ziskind A,Itskovitz-Eldor J

更新日期：2006-01-01 00:00:00

abstract：:Current methodologies available to quantify changes in mitochondrial turnover are limited to pulse-chase assays or specific assays that quantify mitophagy. Accordingly, new tools that can assess mitochondrial turnover are needed for the study of cellular, subcellular, and spatial parameters of mitochondrial turnover a...

journal_title：Methods in enzymology

authors： Trudeau KM,Gottlieb RA,Shirihai OS

更新日期：2014-01-01 00:00:00

abstract：:A- and B-type lamins support the nuclear envelope, contribute to heterochromatin organization, and regulate a myriad of nuclear processes. The mechanisms by which lamins function in different cell types and the mechanisms by which lamin mutations cause over a dozen human diseases (laminopathies) remain unclear. The id...

journal_title：Methods in enzymology

authors： Mehus AA,Anderson RH,Roux KJ

更新日期：2016-01-01 00:00:00

abstract：:Precisely imaging and tracking dynamic biological processes in live cells are crucial for both fundamental research in life sciences and biomedical applications. Nonfluorescent nanoparticles are emerging as important optical probes in live-cell imaging because of their excellent photostability, large optical cross sec...

journal_title：Methods in enzymology

authors： Wang G,Fang N

更新日期：2012-01-01 00:00:00

abstract：:Embryonic stem cells (ESCs) have the ability to expand indefinitely in vitro and give rise to cells of all three germ layers as well as germ cells. For these reasons, ESCs hold great promise for biomedicine. In order to harness the potential of pluripotent cells, it is necessary to first understand the molecular mecha...

journal_title：Methods in enzymology

authors： Schaniel C,Lee DF,Lemischka IR

更新日期：2010-01-01 00:00:00

abstract：:Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus...

journal_title：Methods in enzymology

authors： Yang F,Ouma WZ,Li W,Doseff AI,Grotewold E

更新日期：2016-01-01 00:00:00

abstract：:Cells belonging to the monocyte/macrophage lineage are in general highly resistant to peroxynitrite. Resistance is not dependent on the scavenging of peroxynitrite itself, or of other secondary reactive species, but is rather associated with the prompt activation of a survival signaling leading to the prevention of to...

journal_title：Methods in enzymology

authors： Cantoni O,Tommasini I,Cerioni L

更新日期：2008-01-01 00:00:00

abstract：:When isolating ribonucleoprotein (RNP) complexes by an affinity selection approach, tagging the RNA component can prove to be strategically important. This is especially true for purifying single types of snoRNPs, because in most cases the snoRNA is thought to be the only unique component. Here, we present a general s...

journal_title：Methods in enzymology

authors： Piekna-Przybylska D,Liu B,Fournier MJ

更新日期：2007-01-01 00:00:00

abstract：:The programmed death 1 (PD-1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) are negative regulators of T-cell immune function. Removal of these "brakes" in T cells results in increased activation of the immune system and controlling and eradicating tumor. The development of immune checkpoint inhibitors (ICI...

journal_title：Methods in enzymology

authors： Nomura N,Nomura Y,Sato Y,Iwata S

更新日期：2019-01-01 00:00:00

abstract：:Extracellular thiol/disulfide redox environments are highly regulated in healthy individuals and become oxidized in disease. This oxidation affects the function of cell surface receptors, ion channels, and structural proteins. Downstream signaling due to changes in extracellular redox potential can be studied using a ...

journal_title：Methods in enzymology

authors： Go YM,Jones DP

更新日期：2010-01-01 00:00:00

abstract：:The breaking of RNA strands by 2'-O-transphosphorylation is a ubiquitous reaction in biology, and enzymes that catalyze this reaction play key roles in RNA metabolism. The mechanisms of 2'-O-transphosphorylation in solution are relatively well studied, but complex and can involve different transition states depending ...

journal_title：Methods in enzymology

authors： Harris ME,York DM,Piccirilli JA,Anderson VE

更新日期：2017-01-01 00:00:00

abstract：:The elucidation of structure-affinity relationships in EF-hand proteins requires a reliable assay of divalent ion affinity. In principle, isothermal titration calorimetry (ITC) should be capable of furnishing estimates for Ca2+- and Mg2+-binding constants in these systems. And because the method yields the binding ent...

journal_title：Methods in enzymology

authors： Henzl MT

更新日期：2009-01-01 00:00:00

abstract：:Assessment of protein nitration is commonly used as a footprint for the formation of reactive nitrogen species in vivo. However, one of the major disadvantages of measuring nitrotyrosine in proteins is that nitrated proteins are broken down at variable rates, and the resulting free nitrotyrosine is taken up by cells, ...

journal_title：Methods in enzymology

authors： Mani AR,Moore KP

更新日期：2005-01-01 00:00:00

abstract：:Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttrans...

journal_title：Methods in enzymology

authors： Egli M

更新日期：2015-01-01 00:00:00

abstract：:Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, flu...

journal_title：Methods in enzymology

authors： Sanford L,Palmer A

更新日期：2017-01-01 00:00:00

abstract：:Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly ...

journal_title：Methods in enzymology

authors： Freibert SA,Weiler BD,Bill E,Pierik AJ,Mühlenhoff U,Lill R

更新日期：2018-01-01 00:00:00