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


: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.


Biophys J


Biophysical journal


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




Has Abstract


2011-02-16 00:00:00














  • Modulation of vesicle adhesion and spreading kinetics by hyaluronan cushions.

    abstract::The adhesion of giant unilamellar phospholipid vesicles to planar substrates coated with extracellular matrix mimetic cushions of hyaluronan is studied using quantitative reflection interference contrast microscopy. The absolute height of the vesicle membrane at the vicinity of the substrate is measured by considering...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Limozin L,Sengupta K

    更新日期:2007-11-01 00:00:00

  • Compressibilities and volume fluctuations of archaeal tetraether liposomes.

    abstract::Bipolar tetraether lipids (BTLs) are abundant in crenarchaeota, which thrive in both thermophilic and nonthermophilic environments, with wide-ranging growth temperatures (4-108°C). BTL liposomes can serve as membrane models to explore the role of BTLs in the thermal stability of the plasma membrane of crenarchaeota. I...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Chong PL,Sulc M,Winter R

    更新日期:2010-11-17 00:00:00

  • Sodium channels: ionic model of slow inactivation and state-dependent drug binding.

    abstract::Inactivation is a fundamental property of voltage-gated ion channels. Fast inactivation of Na(+) channels involves channel block by the III-IV cytoplasmic interdomain linker. The mechanisms of nonfast types of inactivation (intermediate, slow, and ultraslow) are unclear, although the ionic environment and P-loops rear...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tikhonov DB,Zhorov BS

    更新日期:2007-09-01 00:00:00

  • STICCS reveals matrix-dependent adhesion slipping and gripping in migrating cells.

    abstract::Two-color spatio-temporal image cross-correlation spectroscopy (STICCS) is a new, to our knowledge, image analysis method that calculates space-time autocorrelation and cross-correlation functions from fluorescence intensity fluctuations. STICCS generates cellular flow and diffusion maps that reveal interactions and c...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Toplak T,Pandzic E,Chen L,Vicente-Manzanares M,Horwitz AR,Wiseman PW

    更新日期:2012-10-17 00:00:00

  • On phasing the small-angle x-ray diffraction pattern from nerve myelin.

    abstract::Using a method they developed, Stamatoff and Krimm (1976) have phased swelling data from nerve myelin. Although most phases agree with those I determined previously, there are a few differences. In this letter the two different phasings, theirs and my own, are used to compute the corresponding electron-density profile...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Blaurock AE

    更新日期:1979-04-01 00:00:00

  • Molecular models need to be tested: the case of a solar flares discoidal HDL model.

    abstract::In the absence of atomic structures of high-density lipoproteins in their lipid-bound states, many molecular models have been produced based on experimental data. Using molecular dynamics, we show that a recently proposed "solar-flares" model of discoidal high-density lipoprotein is implausible. Our simulations show a...

    journal_title:Biophysical journal

    pub_type: 信件


    authors: Shih AY,Sligar SG,Schulten K

    更新日期:2008-06-01 00:00:00

  • Regulation of nerve terminal calcium channel selectivity by a weak acid site.

    abstract::The effects of low pH, and of alkaline earth cations, were examined on calcium uptake by pinched-off nerve terminals (synaptosomes). This uptake appears to be mediated by voltage-sensitive Ca channels (J. Physiol. 247:617, 1975). Ca uptake was measured in low (5 mM) or high (77 mM) potassium media. The extra uptake pr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Nachshen DA,Blaustein MP

    更新日期:1979-05-01 00:00:00

  • Effects of bath resistance on action potentials in the squid giant axon: myocardial implications.

    abstract::This study presents a simplified version of the quasi-one-dimensional theory (Wu, J., E. A. Johnson, and J. M. Kootsey. 1996. A quasi-one-dimensional theory for anisotropic propagation of excitation in cardiac muscle. Biophys. J. 71:2427-2439) with two components of the extracellular current, along and perpendicular t...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wu J,Wikswo JP Jr

    更新日期:1997-11-01 00:00:00

  • In situ determination of structure and fluctuations of coexisting fluid membrane domains.

    abstract::Biophysical understanding of membrane domains requires accurate knowledge of their structural details and elasticity. We report on a global small angle x-ray scattering data analysis technique for coexisting liquid-ordered (Lo) and liquid-disordered (Ld) domains in fully hydrated multilamellar vesicles. This enabled t...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Heftberger P,Kollmitzer B,Rieder AA,Amenitsch H,Pabst G

    更新日期:2015-02-17 00:00:00

  • Proton transport through influenza A virus M2 protein reconstituted in vesicles.

    abstract::Influenza A virus M2 protein is known to form acid-activated, proton-selective, amantadine-sensitive channels. We directly measured proton uptake in vesicles containing reconstituted M2 by monitoring external pH after addition of valinomycin to vesicles with 100-fold-diluted external [K(+)]. External pH typically incr...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Moffat JC,Vijayvergiya V,Gao PF,Cross TA,Woodbury DJ,Busath DD

    更新日期:2008-01-15 00:00:00

  • Forces applied by cilia measured on explants from mucociliary tissue.

    abstract::Forces applied by intact mucus-propelling cilia were measured for the first time that we know of using a combined atomic force microscopy (AFM) and electrooptic system. The AFM probe was dipped into a field of beating cilia and its time-dependent deflection was recorded as it was struck by the cilia while the electroo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Teff Z,Priel Z,Gheber LA

    更新日期:2007-03-01 00:00:00

  • Blocking dynamics of the SMR transporter EmrE impairs efflux activity.

    abstract::EmrE is a small multidrug resistance transporter that has been well studied as a model for secondary active transport. Because transport requires the protein to convert between at least two states open to opposite sides of the membrane, it is expected that blocking these conformational transitions will prevent transpo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Dutta S,Morrison EA,Henzler-Wildman KA

    更新日期:2014-08-05 00:00:00

  • Calcium regulation of an actin spring.

    abstract::Calcium is essential for many biological processes involved in cellular motility. However, the pathway by which calcium influences motility, in processes such as muscle contraction and neuronal growth, is often indirect and complex. We establish a simple and direct mechanochemical link that shows how calcium quantitat...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tam BK,Shin JH,Pfeiffer E,Matsudaira P,Mahadevan L

    更新日期:2009-08-19 00:00:00

  • Kinetics and thermodynamics of association of a phospholipid derivative with lipid bilayers in liquid-disordered and liquid-ordered phases.

    abstract::We have measured the rates of insertion into, desorption from, and spontaneous interlayer translocation (flip-flop) in liquid-disordered and liquid-ordered phase lipid bilayer membranes, of the fluorescent phospholipid derivative NBD-dimyristoylphosphatidyl ethanolamine. This study made use of a recently described met...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Abreu MS,Moreno MJ,Vaz WL

    更新日期:2004-07-01 00:00:00

  • PGE(2) activation of apical membrane Cl(-) channels in A6 epithelia: impedance analysis.

    abstract::Measurements of transepithelial electrical impedance of continuously short-circuited A6 epithelia were made at audio frequencies (0.244 Hz to 10.45 kHz) to investigate the time course and extent to which prostaglandin E(2) (PGE(2)) modulates Cl(-) transport and apical membrane capacitance in this cell-cultured model e...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Păunescu TG,Helman SI

    更新日期:2001-08-01 00:00:00

  • The functional form of angular forces around transition metal ions in biomolecules.

    abstract::A method for generating angular forces around sigma-bonded transition metal ions is generalized to treat pi-bonded configurations. The theoretical approach is based on an analysis of ligand-field and small-cluster Hamiltonians based on the moments of the electron state distribution. The functional forms that are obtai...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Carlsson AE,Zapata S

    更新日期:2001-07-01 00:00:00

  • Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins.

    abstract::Quantitative characterization of protein interactions under physiological conditions is vital for systems biology. Fluorescence photobleaching/activation experiments of GFP-tagged proteins are frequently used for this purpose, but robust analysis methods to extract physicochemical parameters from such data are lacking...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Beaudouin J,Mora-Bermúdez F,Klee T,Daigle N,Ellenberg J

    更新日期:2006-03-15 00:00:00

  • The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations.

    abstract::Solid-state NMR study shows that the 22-residue K3 peptide (Ser(20)-Lys(41)) from beta(2)-microglobulin (beta(2)m) adopts a beta-strand-loop-beta-strand conformation in its fibril state. Residue Pro(32) has a trans conformation in the fibril state of the peptide, while it adopts a cis conformation in the native state ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Liang C,Derreumaux P,Mousseau N,Wei G

    更新日期:2008-07-01 00:00:00

  • Assembly-associated structural changes of bacteriophage T7 capsids. Detection by use of a protein-specific probe.

    abstract::To detect changes in capsid structure that occur when a preassembled bacteriophage T7 capsid both packages and cleaves to mature-size longer (concatameric) DNA, the kinetics and thermodynamics are determined here for the binding of the protein-specific probe, 1,1'-bi(4-anilino)naphthalene-5,5'-di-sulfonic acid (bis-AN...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Khan SA,Griess GA,Serwer P

    更新日期:1992-11-01 00:00:00

  • Actin modifies Ca2+ block of epithelial Na+ channels in planar lipid bilayers.

    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


    authors: Berdiev BK,Latorre R,Benos DJ,Ismailov II

    更新日期:2001-05-01 00:00:00

  • Receptor displacement in the cell membrane by hydrodynamic force amplification through nanoparticles.

    abstract::We introduce an intrinsically multiplexed and easy to implement method to apply an external force to a biomolecule and thus probe its interaction with a second biomolecule or, more generally, its environment (for example, the cell membrane). We take advantage of the hydrodynamic interaction with a controlled fluid flo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Türkcan S,Richly MU,Bouzigues CI,Allain JM,Alexandrou A

    更新日期:2013-07-02 00:00:00

  • The height of biomolecules measured with the atomic force microscope depends on electrostatic interactions.

    abstract::In biological applications of atomic force microscopy, the different surface properties of the biological sample and its support become apparent. Observed height differences between the biomolecule and its supporting surface are thus not only of structural origin, but also depend on the different sample-tip and suppor...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Müller DJ,Engel A

    更新日期:1997-09-01 00:00:00

  • Direct observation of poloxamer 188 insertion into lipid monolayers.

    abstract::P188, a triblock copolymer of the form poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) helps seal electroporated cell membranes, arresting the leakage of intracellular materials from the damaged cells. To explore the nature of the interaction between P188 and cell membranes, we have constructed a model...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Maskarinec SA,Hannig J,Lee RC,Lee KY

    更新日期:2002-03-01 00:00:00

  • Discrimination of cardiac subcellular creatine kinase fluxes by NMR spectroscopy: a new method of analysis.

    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


    authors: Joubert F,Hoerter JA,Mazet JL

    更新日期:2001-12-01 00:00:00

  • Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations.

    abstract::We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacolo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Khandelia H,Witzke S,Mouritsen OG

    更新日期:2010-12-15 00:00:00

  • Analytical calculation of intracellular calcium wave characteristics.

    abstract::We present a theoretical analysis of intracellular calcium waves propagated by calcium feedback at the inositol 1,4,5-trisphosphate (IP3) receptor. The model includes essential features of calcium excitability, but is still analytically tractable. Formulas are derived for the wave speed, amplitude, and width. The calc...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Kupferman R,Mitra PP,Hohenberg PC,Wang SS

    更新日期:1997-06-01 00:00:00

  • Asymmetrical membranes and surface tension.

    abstract::The (31)P-nuclear magnetic resonance chemical shift of phosphatidic acid in a membrane is sensitive to the lipid head group packing and can report qualitatively on membrane lateral compression near the aqueous interface. We have used high-resolution (31)P-nuclear magnetic resonance to evaluate the lateral compression ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Traïkia M,Warschawski DE,Lambert O,Rigaud JL,Devaux PF

    更新日期:2002-09-01 00:00:00

  • Electric-Induced Reversal of Morphogenesis in Hydra.

    abstract::Morphogenesis involves the dynamic interplay of biochemical, mechanical, and electrical processes. Here, we ask to what extent can the course of morphogenesis be modulated and controlled by an external electric field? We show that at a critical amplitude, an external electric field can halt morphogenesis in Hydra rege...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Braun E,Ori H

    更新日期:2019-10-15 00:00:00

  • Deformation and flow of red blood cells in a synthetic lattice: evidence for an active cytoskeleton.

    abstract::We introduce the use of microfabrication techniques to construct on a silicon wafer a synthetic capillary bed with 2.5- to 4-micron (mu)-wide channels. Establishment of a fluid pressure gradient allowed us to observe simultaneously using optical microscopy hundreds of cells flowing through the bed at physiological spe...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Brody JP,Han Y,Austin RH,Bitensky M

    更新日期:1995-06-01 00:00:00

  • Deuterium-Enhanced Raman Spectroscopy for Histidine pKa Determination in a pH-Responsive Hydrogel.

    abstract::We report here a method for the determination of the pKa of histidine in complex or heterogeneous systems amenable to neither solid-state nor solution NMR spectroscopy. Careful synthesis of a fluorenylmethyloxycarbonyl- and trityl-protected, C2-deuterated histidine produces a vibrational-probe-equipped amino acid that...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Braun GA,Pogostin BH,Pucetaite M,Londergan CH,Åkerfeldt KS

    更新日期:2020-11-03 00:00:00