Abstract:
:Competitive hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place when the targets can hybridize with free complementary chains in the solution. The effects of competitive hybridization on the thermodynamically attainable performance of DNA chips are quantified in terms of the hybridization isotherms of the spots. These relate the equilibrium degree of the hybridization to the bulk composition. The hybridization isotherm emerges as a Langmuir isotherm modified for electrostatic interactions within the probe layer. The sensitivity of the assay in equilibrium is directly related to the slope of the isotherm. A simpler description is possible, in terms of c(50) values specifying the bulk composition corresponding to 50% hybridization at the surface. The effects of competitive hybridization are important for the quantitative analysis of DNA chip results, especially when used to study point mutations.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Halperin A,Buhot A,Zhulina EBdoi
10.1016/S0006-3495(04)74150-8subject
Has Abstractpub_date
2004-02-01 00:00:00pages
718-30issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(04)74150-8journal_volume
86pub_type
杂志文章abstract::We showed recently that the high-salt transition of poly[d(G-C)]. poly[d(G-C)] between B-DNA and Z-DNA (at [NaCl] = 2.25 M or [MgCl(2)] = 0.7 M) can be ascribed to the lesser electrostatic free energy of the B form, due to better immersion of the phosphates in the solution. This property was incorporated in cylindrica...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(00)76665-3
更新日期:2000-02-01 00:00:00
abstract::The molecular motor protein myosin VI moves toward the minus-end of actin filaments with a step size of 30-36 nm. Such large step size either drastically limits the degree of complex formation between dimer subunits to leave enough length for the lever arms, or requires an extension of the lever arms' crystallographic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.010
更新日期:2011-06-22 00:00:00
abstract::The absolute direction of the retinal chromophore of bacterio-rhodopsin relative to the membrane plane is investigated by using an optical second-harmonic interference technique. Compared with the known adsorbed geometry of free retinylidene Schiff base on a glass substrate, our data indicate the beta-ionone ring of t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82883-8
更新日期:1989-05-01 00:00:00
abstract::This article shows that colchicine and taxol strongly influence the kinetics of L-type Ca channels in intact cardiac cells, and it suggests a mechanism for this action. It is known that colchicine disassociates microtubules into tubulin, and that taxol stabilizes microtubules. We have found that colchicine increases t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80715-5
更新日期:1994-12-01 00:00:00
abstract::In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem pro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.01.065
更新日期:2011-03-16 00:00:00
abstract::The crowded environment of cells poses a challenge for rapid protein-protein association. Yet, it has been established that the rates of association are similar in crowded and in dilute solutions. Here we probe the pathway leading to fast association between TEM1 β-lactamase and its inhibitor protein BLIP in crowded s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.009
更新日期:2012-09-05 00:00:00
abstract::Time-resolved photovoltage measurements were performed with the acid-blue (bR605A) and acid-purple (bR565A) forms of bacteriorhodopsin (bR) in the time range from 25 ns to 100 s. The bR605A and bR565A pigments were formed by titration with H2SO4 in the absence and presence of 150 mM KCI, respectively. Qualitatively th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80077-9
更新日期:1995-11-01 00:00:00
abstract::It is shown that alpha-helical content of eleven proteins is well correlated with alanine plus leucine content. These residues, taken singly or together, are to a first approximation randomly distributed in the four proteins whose tertiary structures have been determined (i.e., myoglobin, lysozyme, ribonuclease, alpha...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(68)86553-1
更新日期:1968-11-01 00:00:00
abstract::We present a new approach to probing single-particle dynamics that uses dynamic light scattering from a localized region. By scattering a focused laser beam from a micron-size particle, we measure its spatial fluctuations via the temporal autocorrelation of the scattered intensity. We demonstrate the applicability of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77866-X
更新日期:1998-03-01 00:00:00
abstract::The mating pathway in Saccharomyces cerevisiae is one of the best understood signal transduction pathways in eukaryotes. It transmits the mating signal from plasma membrane into the nucleus through the G-protein coupled receptor and the mitogen-activated protein kinase (MAPK) cascade. According to current understandin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.081661
更新日期:2006-12-01 00:00:00
abstract::The cytoplasmic surface of the BR (initial) state of bacteriorhodopsin is characterized by a cluster of three carboxylates that function as a proton-collecting antenna. Systematic replacement of most of the surface carboxylates indicated that the cluster is made of D104, E161, and E234 (Checover, S., Y. Marantz, E. Na...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75179-5
更新日期:2002-07-01 00:00:00
abstract::Gigaohm recordings have been made from glutamate receptor channels in excised, outside-out patches of collagenase-treated locust muscle membrane. The channels in the excised patches exhibit the kinetic state switching first seen in megaohm recordings from intact muscle fibers. Analysis of channel dwell time distributi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82367-5
更新日期:1990-07-01 00:00:00
abstract::Here we extend the ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, to models with lower, residue-level resolution. Whereas in the former case there is one bead per nonhydrogen atom,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.06.046
更新日期:2011-08-17 00:00:00
abstract::Cytotoxic lymphocytes are key elements of the immune system that are primarily responsible for targeting cells infected with intracellular pathogens, or cells that have become malignantly transformed. Target cells are killed mainly via lymphocyte exocytosis of specialized lysosomes containing perforin, a pore-forming ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.06.045
更新日期:2015-08-04 00:00:00
abstract::This paper describes a new technique that can be used to study chloroplast volume regulation in vivo. Nuclear magnetic resonance spectroscopy was used to measure relative amounts of chloroplast water in Acer platanoides leaves as they dried in air, and also in leaf disks exposed to aqueous polyethylene glycol, sucrose...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81930-6
更新日期:1992-05-01 00:00:00
abstract::The products of MgATP hydrolysis bind to the nucleotide site of myosin and thus may be expected to inhibit the contraction of muscle fibers. We measured the effects of phosphate and MgADP on the isometric tensions and isotonic contraction velocities of glycerinated rabbit psoas muscle at 10 degrees C. Addition of phos...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83837-6
更新日期:1985-11-01 00:00:00
abstract::Fatty acid binding proteins play an important role in the transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the gap is lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.005
更新日期:2020-01-21 00:00:00
abstract::Many biological processes exhibit complex kinetic behavior that involves a nontrivial distribution of rate constants. Characterization of the rate constant distribution is often critical for mechanistic understandings of these processes. However, it is difficult to extract a rate constant distribution from data measur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.090688
更新日期:2006-12-01 00:00:00
abstract::Molecular dynamics simulations supplement single-molecule pulling experiments by providing the possibility of examining the full free energy landscape using many coordinates. Here, we use an all-atom structure-based model to study the force and temperature dependence of the unfolding of the protein filamin by applying...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.10.021
更新日期:2014-12-16 00:00:00
abstract::In this new method for studying the shape recovery of deformed red blood cells, three optical traps ("optical tweezers") induce a parachute-shaped red cell deformation, which is comparable to the deformation in small capillaries. The shape recovery is recorded, and a relaxation time is obtained for each individual red...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80084-6
更新日期:1995-11-01 00:00:00
abstract::One theory of freezing damage suggests that slowly cooled cells are killed by being exposed to increasing concentrations of electrolytes as the suspending medium freezes. A corollary to this view is that protective additives such as glycerol protect cells by acting colligatively to reduce the electrolyte concentration...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85436-8
更新日期:1978-07-01 00:00:00
abstract::The conformational flexibility of the DNA double helix is of great interest because of its potential role in protein recognition, packaging into chromosomes, formation of photodefects, and interaction with drugs. Theory finds that DNA is very flexible; however, there is a scarcity of experimental results that examine ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79755-2
更新日期:1996-04-01 00:00:00
abstract::Theoretical studies of the electronic structure and spectra of models for the ferric resting state and Compound I intermediates of horseradish peroxidase (HRP-I) and catalase (CAT-I) have been performed using the INDO-RHF/CI method. The goals of these studies were twofold: i) to determine whether the axial ligand of H...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80160-8
更新日期:1995-01-01 00:00:00
abstract::Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically enc...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2012.09.031
更新日期:2012-11-07 00:00:00
abstract::A two-dimensional (2D) model of lipid bilayers was developed and used to investigate a possible role of membrane lateral tension in membrane fusion. We found that an increase of lateral tension in contacting monolayers of 2D analogs of liposomes and planar membranes could cause not only hemifusion, but also complete f...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75648-8
更新日期:2002-06-01 00:00:00
abstract::Cubic insulin crystals contain a binding site for monovalent cations in a cavity of the crystal dyad in which the bound cation is ligated by protein atomic dipoles and water molecules. These types of interaction are analogous to interactions that occur in small cation-selective carrier and channel molecules. X-ray dif...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(94)80795-7
更新日期:1994-02-01 00:00:00
abstract::Investigations into the spatiotemporal dynamics of DNA repair using live-cell imaging are aided by the ability to generate well defined regions of ultravioletlike photolesions in an optical microscope. We demonstrate that multiphoton excitation of DNA in live cells with visible femtosecond pulses produces thymine cycl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.09.031
更新日期:2011-11-02 00:00:00
abstract::Tropomyosin (Tm) paracrystal formation induced by Mg2+ was studied by monitoring increases in light scattering. Paracrystals formed above a critical Tm concentration with lag phases in the time courses at pH 7.5 and 6.0, indicating that condensation polymerization processes are involved. The kinetic data at pH 7.5 rea...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82655-4
更新日期:1989-07-01 00:00:00
abstract::Sedimentation velocity analytical ultracentrifugation is an important tool in the characterization of macromolecules and nanoparticles in solution. The sedimentation coefficient distribution c(s) of Lamm equation solutions is based on the approximation of a single, weight-average frictional coefficient of all particle...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.081372
更新日期:2006-06-15 00:00:00
abstract::Eukaryotic DNA is packaged into the cell nucleus as a nucleoprotein complex, chromatin. Despite this condensed state, access to the DNA sequence must occur during gene expression and other essential genetic events. Here we employ optical tweezers stretching of reconstituted chromatin fibers to investigate the release ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.053074
更新日期:2005-05-01 00:00:00