D. Fygenson - Academia.edu (original) (raw)
Papers by D. Fygenson
Proceedings of the National Academy of Sciences, 2004
Taxol and tau are two ligands that stabilize the microtubule (MT) lattice. Taxol is an anti-mitot... more Taxol and tau are two ligands that stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds β tubulin in the MT interior. Tau is a MT-associated protein that binds both α and β tubulin on the MT exterior. Both Taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts to bundle, stiffen, and space MTs. A structural study recently suggested that Taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces Taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau, yields the equilibrium dissociation constant of ≈2 μM, and determines the escape rate of Taxol through one pore to be 1.7 × 10 3 (M·s) –1 . Extension of the model yields a measure of Taxol cooperativity with a Hill coefficient of at least 15 when tau is present at a 1:1 molar ratio with tubulin.
The pandemic forced educators of instructional physics lab classes to rethink how labs are taught... more The pandemic forced educators of instructional physics lab classes to rethink how labs are taught. We targeted introductory modern physics labs for remotification. When exploring the photo-electric effect, diffraction and interference, gamma-ray absorption, atomic spectra, and the Franck-Hertz experiment, which all involve sophisticated equipment, students engage primarily by pressing buttons, turning knobs, and reading displays. We were able to adapt and motorize classroom equipment for nearly equivalent remote engagement at relatively low cost. This was possible using consumer-grade technology that has matured over the last 15 years, namely 3D printing, single-board computers, webcams, and open-source programming libraries. In this presentation, we will demonstrate how students view and control our apparatus through a website and discuss elements and principles that have been key for successful deployment and student learning. Such remotified experiments may have post-pandemic rel...
Mobility of taxol inside microtubules was investigated using fluorescence recovery after photoble... more Mobility of taxol inside microtubules was investigated using fluorescence recovery after photobleaching on flow-aligned bundles. Bundles were made of microtubules with either GMPCPP or GTP at the exchangeable site on the tubulin dimer. Recovery times were sensitive to bundle thickness and packing, indicating that taxol molecules are able to move laterally through the bundle. The density of open binding sites along a microtubule was varied by controlling the concentration of taxol in solution for GMPCPP samples. With [63 % sites occupied, recovery times were independent of taxol concentration and, therefore, inversely proportional to the microscopic dissociation rate, koff. It was found that 10 k GMPCPP off! kGTPoff; consistent with, but not fully accounting for, the difference in equilibrium constants for taxol on GMPCPP and GTP microtubules. With\63% sites occupied, recovery times decreased as;[Tax]"1/5 for both types of microtubules. We conclude that the diffusion of taxol in...
Nanoscale, Jan 5, 2017
We demonstrate a versatile process for assembling micron-scale filament architectures by controll... more We demonstrate a versatile process for assembling micron-scale filament architectures by controlling where DNA tile nanotubes nucleate on DNA origami assemblies. "Nunchucks," potential mechanical magnifiers of nanoscale dynamics consisting of two nanotubes connected by a dsDNA linker, form at yields sufficient for application and consistent with models.
Novel emitters consisting of silver nanoclusters that are bound to single-stranded DNA show great... more Novel emitters consisting of silver nanoclusters that are bound to single-stranded DNA show great promise as accurately positioned single photon sources that can interact coherently. Here, we present first results of a spectroscopic study.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 1995
The spontaneous nucleation of individual microtubules from tubulin dimers is observed directly un... more The spontaneous nucleation of individual microtubules from tubulin dimers is observed directly under conditions of marginal nucleation. The results are compared with measurements of bulk turbidity following a deep quench [W. A. Voter and H. P. Erickson, J. Biol. Chem. 259, 10 430 (1984)]. The size of the critical microtubule nucleus is 12+/-2 tubulin dimers in the two regimes, but
Genetics, 1998
This review summarizes mutagenesis studies, emphasizing the use of bacteriophage T4 mutator and a... more This review summarizes mutagenesis studies, emphasizing the use of bacteriophage T4 mutator and antimutator strains. Early genetic studies on T4 identified mutator and antimutator variants of DNA polymerase that, in turn, stimulated the development of model systems for the study of DNA polymerase fidelity in vitro. Later enzymatic studies using purified T4 mutator and antimutator polymerases were essential in elucidating mechanisms of base selection and exonuclease proofreading. In both cases, the base analogue 2-aminopurine (2AP) proved tremendously useful-first as a mutagen in vivo and then as a probe of DNA polymerase fidelity in vitro. Investigations into mechanisms of DNA polymerase fidelity inspired theoretical models that, in turn, called for kinetic and thermodynamic analyses. Thus, the field of DNA synthesis fidelity has grown from many directions: genetics, enzymology, kinetics, physical biochemistry, and thermodynamics, and today the interplay continues. The relative cont...
Both the anti-cancer drug taxol and the microtubule-associated protein tau suppress dynamics of m... more Both the anti-cancer drug taxol and the microtubule-associated protein tau suppress dynamics of microtubules (MT). We have observed taxol mobility with full-length 3-repeat tau, one of six tau isoforms, using fluorescence recovery after photobleaching (FRAP) on MTs and compare with earlier results on recombinant full-length adult 4-repeat tau. Taxol mobility becomes highly sensitive to taxol concentration in the presence of
ABSTRACT DNA nanotechnology, here in particular DNA origami, is based on self-assembly and can be... more ABSTRACT DNA nanotechnology, here in particular DNA origami, is based on self-assembly and can be used to construct arbitrary three-dimensional structures with nanometer precision. The dimensions of such DNA origami structures are typically on the order of a hundred nanometers or smaller. To achieve large-scale two-dimensional lattices that could be employed as scaffolds for crystalline arrangement of biomolecules and proteins, individual DNA origami tiles need to be assembled hierarchically. We work on the multimerization of DNA origami structures into extended one- and two- dimensional lattices that can cover areas of several square micrometers. This is achieved by complementary single stranded DNAs (sticky ends) at specific positions on the DNA origami objects that we intend to grow into periodic structures. We study the effect of varying multimerization conditions such as annealing temperatures, length of sticky ends and salt concentration on the quality and size of the resulting lattice.
The Analyst, 2015
We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C ... more We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C targets for single-color multiplexing by microfluidic capillary electrophoresis.
The Journal of Physical Chemistry C, 2009
The Journal of Physical Chemistry C, 2011
ABSTRACT We report UV excitation through the DNA bases as a universal pathway to visible emission... more ABSTRACT We report UV excitation through the DNA bases as a universal pathway to visible emission from DNA stabilized silver cluster fluorophores (AgDNAs). AgDNAs with peak emissions throughout the visible spectrum all exhibit two peaks in fluorescence excitation: a visible peak at a wavelength 50–150 nm shorter than the emission peak and a UV peak between 260 and 270 nm depending on the specifics of the DNA strand. UV excitation produces the same emission spectrum as visible excitation with 2–4 times greater intensity depending on the specific emitter. The excellent agreement between AgDNA excitation and absorption spectra, the similarity between AgDNA and bare DNA absorption spectra, and the ubiquity of UV excitation for all the AgDNAs studied strongly suggest that UV excitation proceeds via the DNA bases rather than by direct excitation of higher energy excited states of the Ag cluster. We explore the possibility that UV excitation can provide information about the type, number, and orientation of cluster-bound bases. As an efficient and universal means of exciting AgDNA fluorescence, UV excitation should prove useful in detailed studies of AgDNA photophysics and in identification and purification of the most stable AgDNA fluorophores.
Proceedings of the National Academy of Sciences, 2004
Taxol and tau are two ligands that stabilize the microtubule (MT) lattice. Taxol is an anti-mitot... more Taxol and tau are two ligands that stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds β tubulin in the MT interior. Tau is a MT-associated protein that binds both α and β tubulin on the MT exterior. Both Taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts to bundle, stiffen, and space MTs. A structural study recently suggested that Taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces Taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau, yields the equilibrium dissociation constant of ≈2 μM, and determines the escape rate of Taxol through one pore to be 1.7 × 10 3 (M·s) –1 . Extension of the model yields a measure of Taxol cooperativity with a Hill coefficient of at least 15 when tau is present at a 1:1 molar ratio with tubulin.
The pandemic forced educators of instructional physics lab classes to rethink how labs are taught... more The pandemic forced educators of instructional physics lab classes to rethink how labs are taught. We targeted introductory modern physics labs for remotification. When exploring the photo-electric effect, diffraction and interference, gamma-ray absorption, atomic spectra, and the Franck-Hertz experiment, which all involve sophisticated equipment, students engage primarily by pressing buttons, turning knobs, and reading displays. We were able to adapt and motorize classroom equipment for nearly equivalent remote engagement at relatively low cost. This was possible using consumer-grade technology that has matured over the last 15 years, namely 3D printing, single-board computers, webcams, and open-source programming libraries. In this presentation, we will demonstrate how students view and control our apparatus through a website and discuss elements and principles that have been key for successful deployment and student learning. Such remotified experiments may have post-pandemic rel...
Mobility of taxol inside microtubules was investigated using fluorescence recovery after photoble... more Mobility of taxol inside microtubules was investigated using fluorescence recovery after photobleaching on flow-aligned bundles. Bundles were made of microtubules with either GMPCPP or GTP at the exchangeable site on the tubulin dimer. Recovery times were sensitive to bundle thickness and packing, indicating that taxol molecules are able to move laterally through the bundle. The density of open binding sites along a microtubule was varied by controlling the concentration of taxol in solution for GMPCPP samples. With [63 % sites occupied, recovery times were independent of taxol concentration and, therefore, inversely proportional to the microscopic dissociation rate, koff. It was found that 10 k GMPCPP off! kGTPoff; consistent with, but not fully accounting for, the difference in equilibrium constants for taxol on GMPCPP and GTP microtubules. With\63% sites occupied, recovery times decreased as;[Tax]"1/5 for both types of microtubules. We conclude that the diffusion of taxol in...
Nanoscale, Jan 5, 2017
We demonstrate a versatile process for assembling micron-scale filament architectures by controll... more We demonstrate a versatile process for assembling micron-scale filament architectures by controlling where DNA tile nanotubes nucleate on DNA origami assemblies. "Nunchucks," potential mechanical magnifiers of nanoscale dynamics consisting of two nanotubes connected by a dsDNA linker, form at yields sufficient for application and consistent with models.
Novel emitters consisting of silver nanoclusters that are bound to single-stranded DNA show great... more Novel emitters consisting of silver nanoclusters that are bound to single-stranded DNA show great promise as accurately positioned single photon sources that can interact coherently. Here, we present first results of a spectroscopic study.
Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics, 1995
The spontaneous nucleation of individual microtubules from tubulin dimers is observed directly un... more The spontaneous nucleation of individual microtubules from tubulin dimers is observed directly under conditions of marginal nucleation. The results are compared with measurements of bulk turbidity following a deep quench [W. A. Voter and H. P. Erickson, J. Biol. Chem. 259, 10 430 (1984)]. The size of the critical microtubule nucleus is 12+/-2 tubulin dimers in the two regimes, but
Genetics, 1998
This review summarizes mutagenesis studies, emphasizing the use of bacteriophage T4 mutator and a... more This review summarizes mutagenesis studies, emphasizing the use of bacteriophage T4 mutator and antimutator strains. Early genetic studies on T4 identified mutator and antimutator variants of DNA polymerase that, in turn, stimulated the development of model systems for the study of DNA polymerase fidelity in vitro. Later enzymatic studies using purified T4 mutator and antimutator polymerases were essential in elucidating mechanisms of base selection and exonuclease proofreading. In both cases, the base analogue 2-aminopurine (2AP) proved tremendously useful-first as a mutagen in vivo and then as a probe of DNA polymerase fidelity in vitro. Investigations into mechanisms of DNA polymerase fidelity inspired theoretical models that, in turn, called for kinetic and thermodynamic analyses. Thus, the field of DNA synthesis fidelity has grown from many directions: genetics, enzymology, kinetics, physical biochemistry, and thermodynamics, and today the interplay continues. The relative cont...
Both the anti-cancer drug taxol and the microtubule-associated protein tau suppress dynamics of m... more Both the anti-cancer drug taxol and the microtubule-associated protein tau suppress dynamics of microtubules (MT). We have observed taxol mobility with full-length 3-repeat tau, one of six tau isoforms, using fluorescence recovery after photobleaching (FRAP) on MTs and compare with earlier results on recombinant full-length adult 4-repeat tau. Taxol mobility becomes highly sensitive to taxol concentration in the presence of
ABSTRACT DNA nanotechnology, here in particular DNA origami, is based on self-assembly and can be... more ABSTRACT DNA nanotechnology, here in particular DNA origami, is based on self-assembly and can be used to construct arbitrary three-dimensional structures with nanometer precision. The dimensions of such DNA origami structures are typically on the order of a hundred nanometers or smaller. To achieve large-scale two-dimensional lattices that could be employed as scaffolds for crystalline arrangement of biomolecules and proteins, individual DNA origami tiles need to be assembled hierarchically. We work on the multimerization of DNA origami structures into extended one- and two- dimensional lattices that can cover areas of several square micrometers. This is achieved by complementary single stranded DNAs (sticky ends) at specific positions on the DNA origami objects that we intend to grow into periodic structures. We study the effect of varying multimerization conditions such as annealing temperatures, length of sticky ends and salt concentration on the quality and size of the resulting lattice.
The Analyst, 2015
We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C ... more We tune the electrophoretic mobilities of silver nanocluster DNA probes for Hepatitis A, B and C targets for single-color multiplexing by microfluidic capillary electrophoresis.
The Journal of Physical Chemistry C, 2009
The Journal of Physical Chemistry C, 2011
ABSTRACT We report UV excitation through the DNA bases as a universal pathway to visible emission... more ABSTRACT We report UV excitation through the DNA bases as a universal pathway to visible emission from DNA stabilized silver cluster fluorophores (AgDNAs). AgDNAs with peak emissions throughout the visible spectrum all exhibit two peaks in fluorescence excitation: a visible peak at a wavelength 50–150 nm shorter than the emission peak and a UV peak between 260 and 270 nm depending on the specifics of the DNA strand. UV excitation produces the same emission spectrum as visible excitation with 2–4 times greater intensity depending on the specific emitter. The excellent agreement between AgDNA excitation and absorption spectra, the similarity between AgDNA and bare DNA absorption spectra, and the ubiquity of UV excitation for all the AgDNAs studied strongly suggest that UV excitation proceeds via the DNA bases rather than by direct excitation of higher energy excited states of the Ag cluster. We explore the possibility that UV excitation can provide information about the type, number, and orientation of cluster-bound bases. As an efficient and universal means of exciting AgDNA fluorescence, UV excitation should prove useful in detailed studies of AgDNA photophysics and in identification and purification of the most stable AgDNA fluorophores.