Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair.

Abstract:

:We characterized the effect of the first basepair on the conformational dynamics of the fluorescent dye Cy3 attached to the 5' end of double-stranded DNA using gaussian-mixture adaptive umbrella sampling simulations. In the simulations, the sampling of all five dihedral angles along the linker was enhanced, so that both stacked and unstacked states were sampled. The affinity of Cy3 for a T·A basepair (with the dye attached to T) was found to be significantly less than for the other basepairs. This was verified experimentally by measuring the activation energies for cis-trans isomerization of the dye. The simulation and experimental results indicate the existence of partially unstacked conformations amenable to photoisomerization. The simulations also showed that stacking of Cy3 straightens the DNA while stabilizing the first basepair. Our findings indicate that fluorescence is modulated by Cy3-DNA interactions in a sequence-dependent manner.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Spiriti J,Binder JK,Levitus M,van der Vaart A

doi

10.1016/j.bpj.2011.01.014

subject

Has Abstract

pub_date

2011-02-16 00:00:00

pages

1049-57

issue

4

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(11)00060-9

journal_volume

100

pub_type

杂志文章
  • The mechanochemistry of molecular motors.

    abstract::A theory of molecular motors is presented that explains how the energy released in single chemical reactions can generate mechanical motion and force. In the simplest case the fluctuating movements of a motor enzyme are well described by a diffusion process on a two-dimensional potential energy surface, where one dime...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76615-X

    authors: Keller D,Bustamante C

    更新日期:2000-02-01 00:00:00

  • Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA.

    abstract::We perform single-molecule spatial tracking measurements of a DNA repair protein, the C-terminal domain of Ada (C-Ada) from Escherichia coli, moving on DNA extended by flow. The trajectories of single proteins labeled with a fluorophore are constructed. We analyze single-protein dwell times on DNA for different flow r...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2008.11.021

    authors: Lin Y,Zhao T,Jian X,Farooqui Z,Qu X,He C,Dinner AR,Scherer NF

    更新日期:2009-03-04 00:00:00

  • Change in membrane elastic modulus on activation of glucose transport system of brush border membrane vesicles studied by osmotic swelling and dynamic light scattering.

    abstract::The cell membrane having a transport system is inferred to be flexible when its function is being activated. For the brush border membrane vesicles prepared from rat small intestine, which have the co-transport system of Na+ and glucose, the membrane elasticity was measured as a function of the d-glucose concentration...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(88)83130-8

    authors: Miyamoto S,Maeda T,Fujime S

    更新日期:1988-04-01 00:00:00

  • Slow and incomplete inactivations of voltage-gated channels dominate encoding in synthetic neurons.

    abstract::Electrically excitable channels were expressed in Chinese hamster ovary cells using a vaccinia virus vector system. In cells expressing rat brain IIA Na+ channels only, brief pulses (< 1 ms) of depolarizing current resulted in action potentials with a prolonged (0.5-3 s) depolarizing plateau; this plateau was caused b...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81153-6

    authors: Hsu H,Huang E,Yang XC,Karschin A,Labarca C,Figl A,Ho B,Davidson N,Lester HA

    更新日期:1993-09-01 00:00:00

  • Genome Dashboards: Framework and Examples.

    abstract::Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the re...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.02.018

    authors: Li Z,Sun R,Bishop TC

    更新日期:2020-05-05 00:00:00

  • D-enantiomers take a close look at the functioning of a cardiac cationic L-amino acid transporter.

    abstract::Cationic amino acid transporters are highly selective for L-enantiomers such as L-arginine (L-Arg). Because of this stereoselectivity, little is known about the interaction of these transporters with D-isomers. To study whether these compounds can provide information on the molecular mechanism of transport, inward cur...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.09.025

    authors: Zhou J,Peluffo RD

    更新日期:2010-11-17 00:00:00

  • Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength.

    abstract::Current far-field fluorescence nanoscopes provide subdiffraction resolution by exploiting a mechanism of fluorescence inhibition. This mechanism is implemented such that features closer than the diffraction limit emit separately when simultaneously exposed to excitation light. A basic mechanism for such transient fluo...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2010.08.012

    authors: Testa I,Wurm CA,Medda R,Rothermel E,von Middendorf C,Fölling J,Jakobs S,Schönle A,Hell SW,Eggeling C

    更新日期:2010-10-20 00:00:00

  • Energy landscape of the prion protein helix 1 probed by metadynamics and NMR.

    abstract::The characterization of the structural dynamics of proteins, including those that present a substantial degree of disorder, is currently a major scientific challenge. These dynamics are biologically relevant and govern the majority of functional and pathological processes. We exploited a combination of enhanced molecu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.12.003

    authors: Camilloni C,Schaal D,Schweimer K,Schwarzinger S,De Simone A

    更新日期:2012-01-04 00:00:00

  • Bistability of cell-matrix adhesions resulting from nonlinear receptor-ligand dynamics.

    abstract::Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters results from positive feedback mediated by structural rather than biochemical proces...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.090209

    authors: Erdmann T,Schwarz US

    更新日期:2006-09-15 00:00:00

  • Ionic blockade of the rat connexin40 gap junction channel by large tetraalkylammonium ions.

    abstract::The rat connexin40 gap junction channel is permeable to monovalent cations including tetramethylammonium and tetraethylammonium ions. Larger tetraalkyammonium (TAA(+)) ions beginning with tetrabutylammonium (TBA(+)) reduced KCl junctional currents disproportionately. Ionic blockade by tetrapentylammonium (TPeA(+)) and...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)75960-7

    authors: Musa H,Gough JD,Lees WJ,Veenstra RD

    更新日期:2001-12-01 00:00:00

  • Effects of hydrostatic pressure on lipid bilayer membranes. II. Activation and reaction volumes of carrier mediated ion transport.

    abstract::Measurements of voltage relaxations following brief charge-pulses applied to lipid bilayers have been performed at different hydrostatic pressures in the presence of the neutral carriers cyclo (D-Val-L-Pro-L-Val-D-Pro)3(PV) and valinomycin. From double-exponential relaxations observed in membranes containing PV-K+ com...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83443-9

    authors: Benz R,Conti F

    更新日期:1986-07-01 00:00:00

  • Fusion Pore Expansion and Contraction during Catecholamine Release from Endocrine Cells.

    abstract::Amperometry recording reveals the exocytosis of catecholamine from individual vesicles as a sequential process, typically beginning slowly with a prespike foot, accelerating sharply to initiate a spike, reaching a peak, and then decaying. This complex sequence reflects the interplay between diffusion, flux through a f...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.06.001

    authors: Jackson MB,Hsiao YT,Chang CW

    更新日期:2020-07-07 00:00:00

  • Folding, misfolding, and amyloid protofibril formation of WW domain FBP28.

    abstract::We study the folding mechanism of a triple beta-strand WW domain from the Formin binding protein 28 (FBP28) at atomic resolution with explicit water model using replica exchange molecular dynamics computer simulations. Extended sampling over a wide range of temperatures to obtain the free energy, enthalpy, and entropy...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.105.076406

    authors: Mu Y,Nordenskiöld L,Tam JP

    更新日期:2006-06-01 00:00:00

  • A slow component of gating current in crayfish giant axons resembles inactivation charge movement.

    abstract::Recent experimental evidence from a number of preparations indicates that sodium channel inactivation may be intrinsically voltage sensitive. Intrinsically voltage sensitive inactivation should produce a charge movement. Crayfish giant axons provide a unique opportunity to reexamine the slower components of gating cur...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(83)84434-8

    authors: Swenson RP Jr

    更新日期:1983-03-01 00:00:00

  • Structural locus of the pH gate in the Kir1.1 inward rectifier channel.

    abstract::The closed-state crystal structure of prokaryotic inward rectifier, KirBac1.1, has implicated four inner helical phenylalanines near the cytoplasmic side as a possible locus of the channel gate. In the present study, we investigate whether this structural feature corresponds to the physiological pH gate of the renal i...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.051474

    authors: Sackin H,Nanazashvili M,Palmer LG,Krambis M,Walters DE

    更新日期:2005-04-01 00:00:00

  • Ion effects on gating of the Ca(2+)-activated K+ channel correlate with occupancy of the pore.

    abstract::We studied the effects of permeant ions on the gating of the large conductance Ca(2+)-activated K+ channel from rat skeletal muscle. Rb+ blockade of inward K+ current caused an increase in the open probability as though Rb+ occupancy of the pore interferes with channel closing. In support of this hypothesis, we direct...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(92)81869-6

    authors: Demo SD,Yellen G

    更新日期:1992-03-01 00:00:00

  • Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: a general mechanism for proton release in bacteriorhodopsin.

    abstract::The pKa values of ionizable groups that lie between the active site region of bacteriorhodopsin (bR) and the extracellular surface of the protein are reported. Glu-204 is found to have an elevated pKa in the resting state of bR, suggesting that it corresponds to the proton-releasing group in bR. Its elevated pKa is pr...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79320-7

    authors: Sampogna RV,Honig B

    更新日期:1996-09-01 00:00:00

  • Packaging double-helical DNA into viral capsids: structures, forces, and energetics.

    abstract::Small, icosahedral double-stranded DNA bacteriophage pack their genomes tightly into preformed protein capsids using an ATP-driven motor. Coarse-grain molecular-mechanics models provide a detailed picture of DNA packaging in bacteriophage, revealing how conformation depends on capsid size and shape, and the presence o...

    journal_title:Biophysical journal

    pub_type: 杂志文章,评审

    doi:10.1529/biophysj.108.131797

    authors: Petrov AS,Harvey SC

    更新日期:2008-07-01 00:00:00

  • Gating currents from Kv7 channels carrying neuronal hyperexcitability mutations in the voltage-sensing domain.

    abstract::Changes in voltage-dependent gating represent a common pathogenetic mechanism for genetically inherited channelopathies, such as benign familial neonatal seizures or peripheral nerve hyperexcitability caused by mutations in neuronal K(v)7.2 channels. Mutation-induced changes in channel voltage dependence are most ofte...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.02.004

    authors: Miceli F,Vargas E,Bezanilla F,Taglialatela M

    更新日期:2012-03-21 00:00:00

  • Open-Boundary Molecular Dynamics of a DNA Molecule in a Hybrid Explicit/Implicit Salt Solution.

    abstract::The composition and electrolyte concentration of the aqueous bathing environment have important consequences for many biological processes and can profoundly affect the behavior of biomolecules. Nevertheless, because of computational limitations, many molecular simulations of biophysical systems can be performed only ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.02.042

    authors: Zavadlav J,Sablić J,Podgornik R,Praprotnik M

    更新日期:2018-05-22 00:00:00

  • Ratchetlike properties of in vitro microtubule translocation by a Chlamydomonas inner-arm dynein species c in the presence of flow.

    abstract::To investigate the force generation properties of Chlamydomonas axonemal inner-arm dyneins in response to external force, we analyzed microtubule gliding on dynein-coated surfaces under shear flow. When inner-arm dynein c was used, microtubule translocation in the downstream direction accelerated with increasing flow ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.07.010

    authors: Kikushima K,Kamiya R

    更新日期:2009-09-16 00:00:00

  • A point mutation in domain 4-segment 6 of the skeletal muscle sodium channel produces an atypical inactivation state.

    abstract::We compared wild-type rat skeletal muscle NaChs (micro1) and a mutant NaCh (Y1586K) that has a single amino acid substitution, lysine (K) for tyrosine (Y), at position 1586 in the S6 transmembrane segment of domain 4. In Y1586K, macroscopic current decay is faster, the V(1/2) of the activation curve is shifted in the ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76635-5

    authors: O'Reilly JP,Wang SY,Wang GK

    更新日期:2000-02-01 00:00:00

  • Stability and robustness of an organelle number control system: modeling and measuring homeostatic regulation of centriole abundance.

    abstract::Control of organelle abundance is a fundamental unsolved problem in cell biology. Mechanisms for number control have been proposed in which organelle assembly is actively increased or decreased to compensate for deviations from a set-point, but such phenomena have not been experimentally verified. In this report we ex...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.107052

    authors: Marshall WF

    更新日期:2007-09-01 00:00:00

  • Blind test of physics-based prediction of protein structures.

    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

    authors: Shell MS,Ozkan SB,Voelz V,Wu GA,Dill KA

    更新日期:2009-02-01 00:00:00

  • Cooperativity in F-actin: chemical modifications of actin monomers affect the functional interactions of myosin with unmodified monomers in the same actin filament.

    abstract::We have chemically modified a fraction of the monomers in actin filaments, and then measured the effects on the functional interaction of myosin with unmodified monomers within the same filament. Two modifications were used: (a) covalent attachment of various amounts of myosin subfragment-1 (S1) with the bifunctional ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81057-9

    authors: Prochniewicz E,Katayama E,Yanagida T,Thomas DD

    更新日期:1993-07-01 00:00:00

  • Monomer diffusion into polymer domains in sickle hemoglobin.

    abstract::The gelation of sickle hemoglobin includes the formation of spherulitic arrays of polymers, known as polymer domains, which are an intrinsic result of the polymer formation mechanism. We have observed the diffusion of monomers into domains as they form, which substantially increases the total concentration of hemoglob...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(90)82449-8

    authors: Cho MR,Ferrone FA

    更新日期:1990-10-01 00:00:00

  • Carcinoma and SV40-transfected normal ovarian surface epithelial cell comparison by nonphotochemical hole burning.

    abstract::Results are presented of nonphotochemical-hole-burning experiments on the mitochondrial specific dye rhodamine 800 incubated with two human ovarian surface epithelial cell lines: OSE(tsT)-14 normal cells and OV167 carcinoma cells. This dye is selective for the plasma and inner membranes of the mitochondria, as shown b...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74945-5

    authors: Walsh RJ,Reinot T,Hayes JM,Kalli KR,Hartmann LC,Small GJ

    更新日期:2003-02-01 00:00:00

  • Low-resolution reconstruction of a synthetic DNA holliday junction.

    abstract::We have studied the low-resolution solution conformation of a Holliday (or four-way) DNA junction by using small-angle x-ray scattering, sedimentation velocity, and computational modeling techniques. The scattering data were analyzed in two independent ways: firstly, by rigid-body modeling of the scattering data using...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(04)74355-6

    authors: Nöllmann M,Stark WM,Byron O

    更新日期:2004-05-01 00:00:00

  • On kinetics of phage adsorption.

    abstract::Adsorption of lambda-phage on sensitive bacteria Escherichia coli is a classical problem but not all issues have been resolved. One of the outstanding problems is the rate of adsorption, which in some cases appears to exceed the theoretical limit imposed by the law of random diffusion. We revisit this problem by condu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.102962

    authors: Moldovan R,Chapman-McQuiston E,Wu XL

    更新日期:2007-07-01 00:00:00

  • Detachment of agglutinin-bonded red blood cells. III. Mechanical analysis for large contact areas.

    abstract::An experimental method and analysis are introduced which provide direct quantitation of the strength of adhesive contact for large agglutinin-bonded regions between macroscopically smooth membrane capsules (e.g., red blood cells). The approach yields intrinsic properties for separation of adherent regions independent ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(91)82298-6

    authors: Berk D,Evans E

    更新日期:1991-04-01 00:00:00