Abstract:
:In an accompanying paper we reported the use of differential scanning calorimetry and optical densitometry to characterize the melting and aggregation of 160 bp fragments of calf thymus DNA during heating in the presence of divalent metal cations. Aggregation is observed as thermal denaturation begins and becomes more extensive with increasing temperature until the melting temperature Tm is reached, after which the aggregates dissolve extensively. The order of effectiveness of the metals in inducing aggregation is generally consistent with their ability to induce melting: Cd > Ni > Co > Mn approximately Ca > Mg. Under our experimental conditions (50 mg/ml DNA, 100 mM MCl2, [metal]/[DNA phosphate] approximately 0.6), no measurable aggregates were observed for BaDNA or SrDNA. In this paper we show that the Shibata-Schurr theory of aggregation in the thermal denaturation region provides a good model for our observations. Free energies of cross-linking, induced by the divalent cations, are estimated to be between 34% and 38% of the free energies of base stacking. The ability of a divalent metal cation to induce DNA aggregation can be attributed to its ability to disrupt DNA base pairing and simultaneously to link two different DNA sites.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Duguid JG,Bloomfield VAdoi
10.1016/S0006-3495(95)80134-7subject
Has Abstractpub_date
1995-12-01 00:00:00pages
2642-8issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(95)80134-7journal_volume
69pub_type
杂志文章abstract::Several suggestions have been made about the functional significance of dendritic spines in connection with synaptic plasticity. We investigated transient electrical behavior of spines with bulbous terminals in neurons with arbitrary dendritic geometries. It is shown that postsynaptic potential transform caused by a s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84008-4
更新日期:1984-08-01 00:00:00
abstract::In diseases of the brain, the distribution and properties of ion channels display deviations from healthy control subjects. We studied three cases of ion channel alteration related to epileptogenesis. The first case of ion channel alteration represents an enhanced sodium current, the second case addresses the downregu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.055
更新日期:2011-10-19 00:00:00
abstract::The wide use of lattice-sum strategies in biomolecular simulations has raised many questions on potential artifacts in these strategies. One interesting question is the artifacts in the counterion distributions of highly charged systems. As one would anticipate, Coulombic interactions under the periodic boundary condi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.05.012
更新日期:2009-07-22 00:00:00
abstract::Interactions between the graft copolymer poly(L-lysine)-g-poly(ethylene glycol), PLL-g-PEG, and two kinds of surface-supported lipidic systems (supported phospholipid bilayers and supported vesicular layers) were investigated by a combination of microscopic and spectroscopic techniques. It was found that the applicati...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.041780
更新日期:2004-09-01 00:00:00
abstract::The mechanism by which the cytoskeletal protein actin affects the conductance of amiloride-sensitive epithelial sodium channels (ENaC) was studied in planar lipid bilayers. In the presence of monomeric actin, we found a decrease in the single-channel conductance of alpha-ENaC that did not occur when the internal [Ca2+...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76190-5
更新日期:2001-05-01 00:00:00
abstract::A challenge in the understanding of creatine kinase (CK) fluxes reflected by NMR magnetization transfer in the perfused rat heart is the choice of a kinetic model of analysis. The complexity of the energetic pathways, due to the presence of adenosine triphosphate (ATP)-inorganic phosphate (Pi) exchange, of metabolite ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75940-1
更新日期:2001-12-01 00:00:00
abstract::The heterologous expression and purification of membrane proteins represent major limitations for their functional and structural analysis. Here we describe a new method of incorporation of transmembrane proteins in planar lipid bilayer starting from 1 pmol of solubilized proteins. The principle relies on the direct i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087791
更新日期:2006-11-01 00:00:00
abstract::The effect of peptides, corresponding to sequences in the skeletal muscle dihydropyridine receptor II-III loop, on Ca(2+) release from sarcoplasmic reticulum (SR) and on ryanodine receptor (RyR) calcium release channels have been compared in preparations from normal and malignant hyperthermia (MH)-susceptible pigs. Pe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76147-4
更新日期:2001-04-01 00:00:00
abstract::We demonstrate a novel method for stretching a long DNA molecule in agarose gel with alternating current (AC) electric fields. The molecular motion of a long DNA (T4 DNA; 165.6 kb) in agarose gel was studied using fluorescence microscopy. The effects of a wide range of field frequencies, field strengths, and gel conce...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75398-8
更新日期:2002-01-01 00:00:00
abstract::Synchrotron x-ray scattering measurements were performed on dilute solutions of the purified hemocyanin subunit (Bsin1) from scorpion (Buthus sindicus) and the N-terminal functional unit (Rta) from a marine snail (Rapana thomasiana). The model-independent approach based on spherical harmonics was applied to calculate ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(00)76655-0
更新日期:2000-02-01 00:00:00
abstract::Cell migration is based on an actin treadmill, which in turn depends on recycling of G-actin across the cell, from the rear where F-actin disassembles, to the front, where F-actin polymerizes. To analyze the rates of the actin transport, we used the Virtual Cell software to solve the diffusion-drift-reaction equations...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.130096
更新日期:2008-08-01 00:00:00
abstract::Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.10.016
更新日期:2018-12-04 00:00:00
abstract::We present here the parmbsc0 force field, a refinement of the AMBER parm99 force field, where emphasis has been made on the correct representation of the alpha/gamma concerted rotation in nucleic acids (NAs). The modified force field corrects overpopulations of the alpha/gamma = (g+,t) backbone that were seen in long ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.097782
更新日期:2007-06-01 00:00:00
abstract::We analyzed the microstructure in the first-order laser diffraction line from both resting and tetanically contracting single twitch fibers from frog anterior tibial muscle to see if the distribution of sarcomere lengths is continuous or discrete. Measuring the distance between adjacent microstructural elements lying ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84695-X
更新日期:1982-02-01 00:00:00
abstract::Microbes inhabiting Earth have adapted to diverse environments of water, air, soil, and often at the interfaces of multiple media. In this study, we focus on the behavior of Caulobacter crescentus, a singly flagellated bacterium, at the air/water interface. Forward swimming C. crescentus swarmer cells tend to get phys...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.05.026
更新日期:2013-07-02 00:00:00
abstract::We explore the means by which immobilization of a substrate on a surface can increase the rate of a diffusion-controlled enzymatic reaction. A quasichemical approach is developed and compared with Brownian dynamics simulations. We use these methods to show that restricting only the orientation of the enzyme by long-ra...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.072785
更新日期:2006-02-01 00:00:00
abstract::Intramolecular electron transfer between CuA and heme a in solubilized bacterial (Paracoccus denitrificans) cytochrome c oxidase was investigated by pulse radiolysis. CuA, the initial electron acceptor, was reduced by 1-methylnicotinamide radicals in a diffusion-controlled reaction, as monitored by absorption changes ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.075440
更新日期:2006-03-15 00:00:00
abstract::In this study stereochemically pure d-erythro-sphingomyelins (SMs) with either 16:0 or 18:1(cisDelta9) as the N-linked acyl-chain were synthesized. Our purpose was to examine the properties of these sphingomyelins and acyl-chain matched racemic (d-erythro/l-threo) sphingomyelins in model membranes. Liquid-expanded d-e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)76997-3
更新日期:1999-09-01 00:00:00
abstract::The kinetics of conformational changes of P-type ATPases necessary for the occlusion or deocclusion of transported ions are known to be sensitive to the composition of the surrounding membrane, e.g., phospholipid content, mole percentage of cholesterol, and the presence of lipid-bound anions. Research has shown that m...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2015.08.022
更新日期:2015-10-20 00:00:00
abstract::The cytoplasm of a living cell is a dynamic environment through which intracellular components must move and mix. In motile, rapidly deforming cells such as human neutrophils, bulk cytoplasmic flow couples cell deformation to the transport and dispersion of cytoplasmic particles. Using particle-tracking measurements i...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.09.009
更新日期:2017-11-07 00:00:00
abstract::We examined model mixed micelles consisting of the nonionic surfactant n-dodecyl-β-D-maltoside, 3-(3-cholamidopropyl)-dimethylammoniopropane sulfonate, and the cholesterol derivative cholesteryl hemisuccinate (CHS) to identify micellar properties that are correlated with the in vitro conformational stability and activ...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2010.12.3698
更新日期:2011-01-19 00:00:00
abstract::We present a detailed motion analysis of retrograde nerve growth factor (NGF) endosomes in axons to show that mechanical tugs-of-war and intracellular motor regulation are complimentary features of the near-unidirectional endosome directionality. We used quantum dots to fluorescently label NGF and acquired trajectorie...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.04.036
更新日期:2015-06-02 00:00:00
abstract::How calmodulin (CaM) acts in KRAS-driven cancers is a vastly important question. CaM binds to and stimulates PI3Kα/Akt signaling, promoting cell growth and proliferation. Phosphorylation of CaM at Tyr99 (pY99) enhances PI3Kα activation. PI3Kα is a lipid kinase. It phosphorylates PIP2 to produce PIP3, to which Akt bind...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.09.008
更新日期:2017-11-07 00:00:00
abstract::The extracellular matrix contains components with remarkable mechanical properties, including fibronectin (Fn) fibers with extensibilities of >700% strain. We utilized what we consider a novel technique to quantify the extent of molecular unfolding that contributes to Fn fiber extension, and we compared this behavior ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.029
更新日期:2011-10-05 00:00:00
abstract::Cartilage has a limited capacity for self-repair and focal damage can eventually lead to complete degradation of the tissue. Early diagnosis of degenerative changes in cartilage is therefore essential. Contrast agent-based computed tomography and magnetic resonance imaging provide promising tools for this purpose. How...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.04.041
更新日期:2014-07-15 00:00:00
abstract::Transient receptor potential (TRP) channels are members of a large family of ion channels located in membranes rich in cholesterol, some of whose functions are affected by the cholesterol content of the membrane. Here, cholesterol binding to TRPs is studied using a docking procedure that allows the transmembrane surfa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.011
更新日期:2019-11-19 00:00:00
abstract::Ion conduction across the cellular membrane requires the simultaneous opening of activation and inactivation gates of the K+ channel pore. The bacterial KcsA channel has served as a powerful system for dissecting the structural changes that are related to four major functional states associated with K+ gating. Yet, th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.12.001
更新日期:2017-01-10 00:00:00
abstract::We continue in this paper the presentation of theoretical and experimental methods for the joint refinement of neutron and x-ray lamellar diffraction data for the analysis of fluid (L alpha phase) bilayer structure (Wiener, M. C., and S. H. White. 1991 a, b, c. Biophys. J. 59:162-173 and 174-185; Biochemistry. 30:6997...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81848-9
更新日期:1992-02-01 00:00:00
abstract::Monolayers prepared from myelin conserve all the compositional complexity of the natural membrane when spread at the air-water interface. They show a complex pressure-dependent surface pattern that, on compression, changes from the coexistence of two liquid phases to a viscous fractal phase embedded in a liquid phase....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.112441
更新日期:2007-12-15 00:00:00
abstract::A structural model is suggested for axon membranes consisting of a double layer of lipid and phospholipid molecules in which the polar ends of certain phospholipids change their orientation and combining properties under the influence of an electric field. The phosphate groups act as ion exchange "gates" for the contr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(64)86776-x
更新日期:1964-05-01 00:00:00