Abstract:
:Using CD spectroscopy, guanine tetraplex formation was studied with short DNA fragments in which cytosine residues were systematically added to runs of guanine either at the 5' or 3' ends. Potassium cations induced the G-tetraplex more easily with fragments having the guanine run at the 5' end, which is just an opposite tendency to what was reported for (G+T) oligonucleotides. However, the present (G+C) fragments simultaneously adopted other conformers that complicated the analysis. We demonstrate that repeated freezing/thawing, performed at low ionic strength, is a suitable method to exclusively stabilize the tetraplex in the (G+C) DNA fragments. In contrast to KCl, the repeated freeze/thaw cycles better stabilized the tetraplex with fragments having the guanine run on the 3' end. The tendency of guanine blocks to generate the tetraplex destabilized the d(G5).d(C5) duplex whose strands dissociated, giving rise to a stable tetraplex of (dG5) and single-stranded (dC5). In contrast to d(G3C3) and d(G5C5), repeated freezing/thawing induced the tetraplex even with the self-complementary d(C3G3) or d(C5G5); hence the latter oligonucleotides preferred the tetraplex to the apparently very stable duplex. The tetraplexes only included guanine blocks while the 5' end cytosines interfered neither with the tetraplex formation nor the tetraplex structure.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Penázová H,Vorlicková Mdoi
10.1016/S0006-3495(97)78235-3subject
Has Abstractpub_date
1997-10-01 00:00:00pages
2054-63issue
4eissn
0006-3495issn
1542-0086pii
S0006-3495(97)78235-3journal_volume
73pub_type
杂志文章abstract::2H-nuclear magnetic resonance (NMR) has been used to study the dynamics of amino acid residues in bacteriorhodopsin with results that depend on the method of sample preparation. We show here that in [2H]-leucine-labeled samples the intensity of the isotropic signal varies according to the degree of residual contaminat...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83278-2
更新日期:1987-11-01 00:00:00
abstract::Solid phase amplification (SPA), a new method to amplify DNA, is characterized by the use of surface-bound primers. This limits the amplification to two-dimensional surfaces and therefore allows the easy parallelization of DNA amplification in a single system. SPA leads to the formation of small but dense DNA brushes,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.051904
更新日期:2005-07-01 00:00:00
abstract::We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformatio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.009
更新日期:2009-02-01 00:00:00
abstract::The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76092-4
更新日期:2001-03-01 00:00:00
abstract::Three-dimensional structures were determined for three crystal forms of the antigen binding fragment (Fab) of anti-fluorescein antibody 4-4-20 in complex with fluorescein. These included 1) a triclinic (P1) form crystallized in 47% (v/v) 2-methyl-2,4-pentanediol (MPD); 2) a triclinic (P1) form crystallized in 16% (w/v...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80738-6
更新日期:1994-12-01 00:00:00
abstract::The time correlation function of the shape fluctuations of large (greater than 10 micron), cylindrical, hydrated, phospholipid-membrane vesicles consisting of one bimolecular layer was measured. The restoring force of the membrane was due to the excess curvature of a membrane element. A value for the curvature elastic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84235-6
更新日期:1984-05-01 00:00:00
abstract::Calcium ions act presynaptically to modulate synaptic strength and to trigger neurotransmitter release. Here we detect stimulus-evoked changes in residual free calcium ([Ca2+]i) in rat cerebellar granule cell presynaptic terminals. Granule cell axons, known as parallel fibers, and their associated boutons, were labele...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80398-X
更新日期:1995-05-01 00:00:00
abstract::Embryonic and adult fibroblasts can be returned to pluripotency by the expression of reprogramming genes. Multiple lines of evidence suggest that these human induced pluripotent stem (hiPS) cells and human embryonic stem (hES) cells are behaviorally, karyotypically, and morphologically similar. Here we sought to deter...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.10.007
更新日期:2010-12-01 00:00:00
abstract::The thermal stability of a Schizolobium parahyba chymotrypsin inhibitor (SPCI) as a function of pH has been investigated using fluorescence, circular dichroism, and differential scanning calorimetry (DSC). The thermodynamic parameters derived from all methods are remarkably similar and strongly suggest the high stabil...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.045682
更新日期:2005-05-01 00:00:00
abstract::Association of transmembrane (TM) helices is facilitated by the close packing of small residues present along the amino-acid sequence. Extensive studies have established the role of such small residue motifs (GxxxG) in the dimerization of Glycophorin A (GpA) and helped to elucidate the association of TM domains in the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.10.023
更新日期:2010-12-01 00:00:00
abstract::Global analysis techniques are described for frequency domain fluorescence lifetime imaging microscopy (FLIM) data. These algorithms exploit the prior knowledge that only a limited number of fluorescent molecule species whose lifetimes do not vary spatially are present in the sample. Two approaches to implementing the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76759-2
更新日期:2000-04-01 00:00:00
abstract::In an open circuit there can be no net cation flux through membranes containing only cation-selective channels, because electroneutrality must be maintained. If the channels are so narrow that water and cations cannot pass by each other, then the net water flux through those "single-file" channels that contain a catio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84804-7
更新日期:1981-08-01 00:00:00
abstract::In the first issue, on the first page of the Biophysical Journal in 1960, Cole and Moore provided the first confirmation of the Hodgkin and Huxley formulation of the sodium and potassium conductances that underlie the action potential. In addition, working with the squid giant axon, Cole and Moore noted that strong hy...
journal_title:Biophysical journal
pub_type: 历史文章,杂志文章
doi:10.1016/j.bpj.2015.07.052
更新日期:2015-10-06 00:00:00
abstract::Myosin II is a central mechanoenzyme in a wide range of cellular morphogenic processes. Its cellular localization is dependent not only on signal transduction pathways, but also on mechanical stress. We suggest that this stress-dependent distribution is the result of both the force-dependent binding to actin filaments...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.12.020
更新日期:2012-01-18 00:00:00
abstract::Atherosclerosis is a disease initiated by lipoprotein aggregation and deposition in artery walls. In this study, the de novo low-density lipoprotein aggregation process was examined. Nine major intermediates were identified in two stages of the aggregation process. In the aggregation stage, low-density lipoprotein mol...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75887-0
更新日期:2001-10-01 00:00:00
abstract::Two-dimensional solid-state 31P NMR has been used to investigate the orientational exchange of phospholipids in gel and liquid-crystalline aqueous multilamellar dispersions and oriented multibilayers, and in biological membranes. In liquid-crystalline L alpha multilamellar dispersions, orientational exchange originate...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82198-1
更新日期:1991-01-01 00:00:00
abstract::All-atom molecular dynamics simulations of the ion current through OmpF, the major porin in the outer membrane of Escherichia coli, were performed. Starting from the crystal structure, the all-atom modeling allows us to calculate a parameter-free ion conductance in semiquantitative agreement with experiment. Discrepan...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.07.018
更新日期:2009-10-07 00:00:00
abstract::This article describes the application of a change-point algorithm to the analysis of stochastic signals in biological systems whose underlying state dynamics consist of transitions between discrete states. Applications of this analysis include molecular-motor stepping, fluorophore bleaching, electrophysiology, partic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.05.038
更新日期:2015-07-21 00:00:00
abstract::Transmembrane osmotic gradients applied on large unilamellar 1-palmitoyl-2-oleoyl-phosphatidylcholine vesicles were used to modulate the potency of melittin to induce leakage. Melittin, an amphipathic peptide, changes the permeability of vesicles, as studied using the release of entrapped calcein, a fluorescent marker...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79622-4
更新日期:1996-02-01 00:00:00
abstract::We have measured light-induced voltage changes (electrogenic events) in photosystem II (PSII) core complexes oriented in phospholipid monolayers. These events are compared to those measured in the functionally and structurally closely related reaction centers from the photosynthetic bacterium Rhodobacter sphaeroides. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)81001-X
更新日期:1994-06-01 00:00:00
abstract::Under the assumption that vesicles are the anatomic correlate of quantal release, the forces governing the movement of synaptic vesicles inside neurons are analyzed. Semiquantitative calculations are presented to show that a diffuse layer field penetrates a few Debye lengths into the axoplasm. This field binds tightly...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(73)85973-9
更新日期:1973-02-01 00:00:00
abstract::We have used electron paramagnetic resonance (EPR) to probe the homo- and heterooligomeric interactions of reconstituted sarcoplasmic reticulum Ca-ATPase (SERCA) and its regulator phospholamban (PLB). SERCA is responsible for restoring calcium to the sarcoplasmic reticulum to allow muscle relaxation, whereas PLB inhib...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.032
更新日期:2012-09-19 00:00:00
abstract::By combining the osmotic stress technique with small-angle x-ray scattering measurements, we followed the structural response of the casein micelle to an overall increase in concentration. When the aqueous phase that separates the micelles is extracted, they behave as polydisperse repelling spheres and their internal ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.10.019
更新日期:2010-12-01 00:00:00
abstract::Normal coordinate analyses and vibrational assignments are presented for the dimethyl phosphate anion [(CH3O)2PO2-] and its deuteriomethyl [(CD3O)2PO2-] and carbon-13 [(13CH3O)2PO2-] derivatives in the gauche-gauche conformation. The dimethyl phosphate anion, which is the simplest model for the nucleic acid phosphodie...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80767-2
更新日期:1994-01-01 00:00:00
abstract::Multiple nanosecond duration molecular dynamics simulations were performed on the transmembrane region of the Torpedo nicotinic acetylcholine receptor embedded within a bilayer mimetic octane slab. The M2 helices and M2-M3 loop regions were free to move, whereas the outer (M1, M3, M4) helix bundle was backbone restrai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.052878
更新日期:2005-05-01 00:00:00
abstract::Critical to biological processes such as secretion and transport, protein-lipid interactions within the membrane and at the membrane-water interface still raise many questions. Here we examine the role of lipid headgroups in these interactions by using gramicidin A (gA) channels in planar bilayers as a probe. We show ...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.107.120261
更新日期:2008-02-15 00:00:00
abstract::We have monitored the organization and dynamics of the hemolytic peptide melittin in membranes containing cholesterol by utilizing the intrinsic fluorescence properties of its functionally important sole tryptophan residue and circular dichroism spectroscopy. The significance of this study is based on the fact that th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.043596
更新日期:2004-10-01 00:00:00
abstract::The adsorption of hydrophobic ions such as tetraphenylborate to thin lipid membranes is known to saturate at approximately 0.1 ion/(nm)2. This saturation can be quantitatively explained by electrostatic repulsion between the ions if they are treated as discrete, mobile particles that adsorb within the lipid at least p...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(82)84489-5
更新日期:1982-07-01 00:00:00
abstract::The effects of temperature (3 degrees-26 degrees C) on the nonlinear components of the displacement current were measured in internally perfused, voltage clamped squid axons. Steps of potential were applied from a holding potential of -70mV (outside ground) to values from -130 to +70mV and either the current or its in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(78)85464-2
更新日期:1978-09-01 00:00:00
abstract::The yolk granule is the most abundant membrane-bound organelle present in sea urchin eggs and embryos. The major protein component of this organelle, toposome, accounts for approximately 50% of the total yolk protein and has been shown to be localized to the embryonic cell surface. Extensive characterization in severa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.089979
更新日期:2006-12-15 00:00:00