L. Finzi - Academia.edu (original) (raw)
Papers by L. Finzi
Proceedings of the National Academy of Sciences, 1990
Direct observation of large chiral domains in chloroplast thylakoid membranes by differential pol... more Direct observation of large chiral domains in chloroplast thylakoid membranes by differential polarization microscopy (photosynthesis/circular dichrosm/flinear dichroism/scattering)
Photosynthesis: from Light to Biosphere, 1995
Optical Methods for Ultrasensitive Detection and Analysis: Techniques and Applications, 1991
ABSTRACT Single molecules of DNA can be visualized in solution by epifluorescence microscopy, man... more ABSTRACT Single molecules of DNA can be visualized in solution by epifluorescence microscopy, manipulated and extended by a variety of mechanical, electrical and chemical means as described previously. This has been used to design experiments under an optical microscope, in which DNA molecules are extended by a known force, to determine the elastic response of the molecules, both in the presence and absence of ethidium bromide. It is found that at lower forces (smaller extensions) the molecules behave as entropic springs with a persistence length of 500 angstroms, and that at the ionic strengths used, the intercalation of ethidium bromide does not alter this persistence length, while it appears to elongate the contour length of the molecule by about 30%.
Review of Scientific Instruments, 1988
Based on the confocal scanning and differential polarization imaging technique, a computer-contro... more Based on the confocal scanning and differential polarization imaging technique, a computer-controlled confocal scanning differential polarization microscope has been built. This system possesses extensive image processing capability that provides digitized regular and/or differential polarization images. This microscope combines the advantages of the confocal design and the extended electronic sensitivity of polarization modulated instrumentation to achieve the measurement of an anisotropy
Macromolecules, 2012
Quantitative analysis of single molecule experiments show that adding either of two natural polya... more Quantitative analysis of single molecule experiments show that adding either of two natural polyamines, spermine or spermidine, produced more compact plectonemes in DNA in physiological concentrations of monovalent salt. They also promoted plectoneme formation at lower values of torsion in measurements of extension versus twist. Quantifying changes in the plectonemic DNA using some results from simple rod models suggested that exposure to polyamines reduced the radii and increased the densities of plectonemes. Thus, polyamines may limit the twist density by favoring writhe which maintains the B-form. Although polymerases may significantly stretch the double helix, denature DNA, and produce twist instead of writhe, natural polyamines stabilize base-pairing, limit twist to maintain the B-form, and promote supercoiling, which is conducive to replication and transcription and essential for DNA packaging.
Biophysical Journal, 2011
Biophysical Journal, 2015
Methods in enzymology, 2017
DNA is the carrier of genetic information and, as such, is at the center of most essential cellul... more DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available. It is an in vitro technique which allows investigation of DNA-protein interactions that change the effective length of a DNA tether. In this chapter, we will describe a recent strategy to multiplex TPM which substantially increases the throughput of TPM experiments, as well as a simulation to estimate the time resolution of experiments, such as transcriptional elongation assays, in which lengthy time averaging ...
Review of Scientific Instruments, 2002
A comparison of different calibration methods for optical tweezers with the differential interfer... more A comparison of different calibration methods for optical tweezers with the differential interference contrast (DIC) technique was performed to establish the uses and the advantages of each method. A detailed experimental and theoretical analysis of each method was performed with emphasis on the anisotropy involved in the DIC technique and the noise components in the detection. Finally, a time of
Biophysical Journal, 2014
Proceedings of the National Academy of Sciences of the United States of America, Jan 28, 2014
Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-... more Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling be...
Biophysical journal, 1995
Biological and Medical Physics, Biomedical Engineering, 2010
... L. Finzi () and D. Dunlap () Cell Biology Department, Emory University, 615 Michael St., At... more ... L. Finzi () and D. Dunlap () Cell Biology Department, Emory University, 615 Michael St., Atlanta, GA 30322, USA e-mail: lfinzi@physics.emory.edu Chapter 9 DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy ...
The Plant Cell, 2013
MADS domain transcription factors are key regulators of eukaryotic development. In plants, the ho... more MADS domain transcription factors are key regulators of eukaryotic development. In plants, the homeotic MIKC MADS factors that regulate floral organ identity have been studied in great detail. Based on genetic and protein-protein interaction studies, a floral quartet model was proposed that describes how these MADS domain proteins assemble into higher order complexes to regulate their target genes. However, despite the attractiveness of this model and its general acceptance in the literature, solid in vivo proof has never been provided. To gain deeper insight into the mechanisms of transcriptional regulation by MADS domain factors, we studied how SEEDSTICK (STK) and SEPALLATA3 (SEP3) directly regulate the expression of the reproductive meristem gene family transcription factor-encoding gene VERDANDI (VDD). Our data show that STK-SEP3 dimers can induce loop formation in the VDD promoter by binding to two nearby CC(A/T)6GG (CArG) boxes and that this is essential for promoter activity. Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model.
The Journal of Physical Chemistry B, 2006
The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bea... more The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping.
Proceedings of the National Academy of Sciences, 1990
Direct observation of large chiral domains in chloroplast thylakoid membranes by differential pol... more Direct observation of large chiral domains in chloroplast thylakoid membranes by differential polarization microscopy (photosynthesis/circular dichrosm/flinear dichroism/scattering)
Photosynthesis: from Light to Biosphere, 1995
Optical Methods for Ultrasensitive Detection and Analysis: Techniques and Applications, 1991
ABSTRACT Single molecules of DNA can be visualized in solution by epifluorescence microscopy, man... more ABSTRACT Single molecules of DNA can be visualized in solution by epifluorescence microscopy, manipulated and extended by a variety of mechanical, electrical and chemical means as described previously. This has been used to design experiments under an optical microscope, in which DNA molecules are extended by a known force, to determine the elastic response of the molecules, both in the presence and absence of ethidium bromide. It is found that at lower forces (smaller extensions) the molecules behave as entropic springs with a persistence length of 500 angstroms, and that at the ionic strengths used, the intercalation of ethidium bromide does not alter this persistence length, while it appears to elongate the contour length of the molecule by about 30%.
Review of Scientific Instruments, 1988
Based on the confocal scanning and differential polarization imaging technique, a computer-contro... more Based on the confocal scanning and differential polarization imaging technique, a computer-controlled confocal scanning differential polarization microscope has been built. This system possesses extensive image processing capability that provides digitized regular and/or differential polarization images. This microscope combines the advantages of the confocal design and the extended electronic sensitivity of polarization modulated instrumentation to achieve the measurement of an anisotropy
Macromolecules, 2012
Quantitative analysis of single molecule experiments show that adding either of two natural polya... more Quantitative analysis of single molecule experiments show that adding either of two natural polyamines, spermine or spermidine, produced more compact plectonemes in DNA in physiological concentrations of monovalent salt. They also promoted plectoneme formation at lower values of torsion in measurements of extension versus twist. Quantifying changes in the plectonemic DNA using some results from simple rod models suggested that exposure to polyamines reduced the radii and increased the densities of plectonemes. Thus, polyamines may limit the twist density by favoring writhe which maintains the B-form. Although polymerases may significantly stretch the double helix, denature DNA, and produce twist instead of writhe, natural polyamines stabilize base-pairing, limit twist to maintain the B-form, and promote supercoiling, which is conducive to replication and transcription and essential for DNA packaging.
Biophysical Journal, 2011
Biophysical Journal, 2015
Methods in enzymology, 2017
DNA is the carrier of genetic information and, as such, is at the center of most essential cellul... more DNA is the carrier of genetic information and, as such, is at the center of most essential cellular processes. To regulate its physiological function, specific proteins and motor enzymes constantly change conformational states with well-controlled dynamics. Twenty-five years ago, Schafer, Gelles, Sheetz, and Landick employed the tethered particle motion (TPM) technique for the first time to study transcription by RNA polymerase at the single-molecule level. TPM has since then remained one of the simplest, most affordable, and yet incisive single-molecule techniques available. It is an in vitro technique which allows investigation of DNA-protein interactions that change the effective length of a DNA tether. In this chapter, we will describe a recent strategy to multiplex TPM which substantially increases the throughput of TPM experiments, as well as a simulation to estimate the time resolution of experiments, such as transcriptional elongation assays, in which lengthy time averaging ...
Review of Scientific Instruments, 2002
A comparison of different calibration methods for optical tweezers with the differential interfer... more A comparison of different calibration methods for optical tweezers with the differential interference contrast (DIC) technique was performed to establish the uses and the advantages of each method. A detailed experimental and theoretical analysis of each method was performed with emphasis on the anisotropy involved in the DIC technique and the noise components in the detection. Finally, a time of
Biophysical Journal, 2014
Proceedings of the National Academy of Sciences of the United States of America, Jan 28, 2014
Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-... more Topoisomerases, polymerases, and the chirality introduced by the binding of histones or nucleoid-associated proteins affect DNA supercoiling in vivo. However, supercoiling is not just a by-product of DNA metabolism. Supercoiling is an indicator of cell health, it modifies the accessibility of chromatin, and coordinates the transcription of genes. This suggests that regulatory, protein-mediated loops in DNA may sense supercoiling of the genome in which they are embedded. The λ repressor (CI) maintains the quiescent (lysogenic) transcriptome of bacteriophage λ in infected Escherichia coli. CI-mediated looping prevents overexpression of the repressor protein to preserve sensitivity to conditions that trigger virulence (lysis). Experiments were performed to assess how well the CI-mediated DNA loop traps superhelicity and determine whether supercoiling enhances CI-mediated DNA looping. CI oligomers partitioned plasmids into topological domains and prevented the passage of supercoiling be...
Biophysical journal, 1995
Biological and Medical Physics, Biomedical Engineering, 2010
... L. Finzi () and D. Dunlap () Cell Biology Department, Emory University, 615 Michael St., At... more ... L. Finzi () and D. Dunlap () Cell Biology Department, Emory University, 615 Michael St., Atlanta, GA 30322, USA e-mail: lfinzi@physics.emory.edu Chapter 9 DNA Looping in Prophage Lambda: New Insight from Single-Molecule Microscopy ...
The Plant Cell, 2013
MADS domain transcription factors are key regulators of eukaryotic development. In plants, the ho... more MADS domain transcription factors are key regulators of eukaryotic development. In plants, the homeotic MIKC MADS factors that regulate floral organ identity have been studied in great detail. Based on genetic and protein-protein interaction studies, a floral quartet model was proposed that describes how these MADS domain proteins assemble into higher order complexes to regulate their target genes. However, despite the attractiveness of this model and its general acceptance in the literature, solid in vivo proof has never been provided. To gain deeper insight into the mechanisms of transcriptional regulation by MADS domain factors, we studied how SEEDSTICK (STK) and SEPALLATA3 (SEP3) directly regulate the expression of the reproductive meristem gene family transcription factor-encoding gene VERDANDI (VDD). Our data show that STK-SEP3 dimers can induce loop formation in the VDD promoter by binding to two nearby CC(A/T)6GG (CArG) boxes and that this is essential for promoter activity. Our in vivo data show that the size and position of this loop, determined by the choice of CArG element usage, is essential for correct expression. Our studies provide solid in vivo evidence for the floral quartet model.
The Journal of Physical Chemistry B, 2006
The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bea... more The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping.