Direct measurement of DNA molecular length in solution using optical tweezers: detection of looping due to binding protein interactions

Sakata‐Sogawa, Kumiko; Kurachi, Masashi; Sogawa, Kazuhiro; Fujii‐Kuriyama, Yoshiaki; Tashiro, Hideo

doi:10.1007/s002490050110

Cited by 18 publications

(11 citation statements)

References 16 publications

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“…By self-association, Sp1 can join distant DNA segments, thereby causing the intervening DNA to loop. [12][13][14] Sp3, however, has been shown to function as both an activator and a repressor. 23 However, Merchiers et al 11 reported that Sp3 could act as activator of t-PA promoter activity, both by itself and in synergy with Sp1 in transfected Drosophila SL2 cells.…”

Section: Discussionmentioning

confidence: 99%

“…11 The C to T transition at Ϫ7351 in the t-PA enhancer alters a core nucleotide in a Sp1 binding motif. 4 Since Sp1 can promote long distant interactions by self-associating, [12][13][14] we have tested the hypothesis that this sequence variation has a direct effect on t-PA promoter-directed transcription. Here, we provide evidence that the t-PA Ϫ7351CϾT SNP is functional at the level of transcription.…”

Section: Introductionmentioning

confidence: 99%

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The t-PA -7351C>T enhancer polymorphism decreases Sp1 and Sp3 protein binding affinity and transcriptional responsiveness to retinoic acid

Wolf

Medcalf

Jern

2004

Blood

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We have previously identified a common polymorphism at the tissue-type plasminogen activator (t-PA) locus (؊7351C>T), located within a GC-box in the retinoic acid (RA) and steroid hormone responsive t-PA enhancer. The aim of the present study was to functionally characterize this t-PA variant. Electrophoretic mobility shift assays (EMSAs) using crude nuclear extracts from human endothelial, HeLa, and NT2 neuronal cells revealed a 10-fold greater protein binding affinity to the wild-

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The t-PA -7351C>T enhancer polymorphism decreases Sp1 and Sp3 protein binding affinity and transcriptional responsiveness to retinoic acid

Wolf

Medcalf

Jern

2004

Blood

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“…Typically, small particles in a liquid environment, like biological cells, or polystyrene microspheres, are trapped in the focus of a laser beam [1][2][3] . It has been used as a tool to manipulate biological material at cellular level, as well as to measure mechanical properties such as forces in femtoNewtons scale and stiffness or elasticity of membranes and single DNA macromolecule [4][5][6][7] . In the geometrical optics regime the optical force is generated by the momentum transfer due to refraction of the laser light at the boundaries of the particles that have a higher index of refraction than their surrounding medium and several different methods have been developed for trapping force strength calibration [8][9][10] .…”

Section: Introductionmentioning

confidence: 99%

Determination of fluid viscosity and femto Newton forces of Leishmania amazonensis using optical tweezers

et al. 2005

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The displacements of a polystyrene microsphere trapped by an optical tweezers (OT) can be used as a force transducer for mechanical measurements in life sciences such as the measurement of forces of living microorganisms or the viscosity of local fluids. The technique we used allowed us to measure forces on the 200 femto Newtons to 4 pico Newtons range of the protozoa Leishmania amazonensis, responsible for a serious tropical disease. These observations can be used to understand the infection mechanism and chemotaxis of these parasites. The same technique was used to measure viscosities of few microliters sample with agreement with known samples better than 5%. To calibrate the force as a function of the microsphere displacement we first dragged the microsphere in a fluid at known velcoity for a broad range of different optical and hydrodynamical parameters. The hydrodynamical model took into account the presence of two walls and the force depends on drag velocity, fluid viscosity and walls proximities, while the optical model in the geometric optics regime depends on the particle and fluid refractive indexes and laser power. To measure the high numerical (NA) aperture laser beam power after the objective we used an integration sphere to avoid the systematic errors of usual power meters for high NA beams. After this careful laser power measurement we obtained an almost 45 degrees straight line for the plot of the optical force (calculated by the particle horizontal displacement) versus hydrodynamic force (calculated by the drag velocity) under variation of all the parameters described below. This means that hydrodynamic models can be used to calibrate optical forces, as we have done for the parasite force measurement, or vice-versa, as we did for the viscosity measurements.

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“…The optical forces involved are very small, in the range of hundreds of femto to tens of pico Newtons, thus optical tweezers have also been used as a mechanical properties measuring tool for microscopic phenomena where the forces involved are in the same scale. Typically, it has been used to measure forces, stiffness or elasticities of membranes or single DNA macromolecule [4][5][6][7][8] . Force measurements are usually performed with restorative systems like springs.…”

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confidence: 99%

Ultrasensitive force spectroscopy measurement of single particle light scattering by the use of optical tweezers

et al. 2005

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Optical tweezers (OT) rely on the radiation pressure to trap and manipulate microscopic particles and living microorganisms. Because the optical forces vary from hundreds of femto to tens of pico Newtons, OT can be used as an ultra sensitive force measurement tool to study interactions involving very small forces. We use a double tweezers to perform ultra sensitive measurement of the force due to the scattering of light as a function of its wavelength, in other words, to perform a Force Spectroscopy. Our results show not only the Mie resonances but also a selective coupling to either the TE, TM or both microsphere modes using the light polarization and the beam positioning. Mie resonances have usually been observed by scattering measurements. Very few reports of levitation experiments observed these resonances directly through the force. The double tweezers system has the advantage and flexibility of a stable restorative force measurement system. The experimental results show excellent agreement with Gaussian shaped beam partial wave decomposition theory. The understanding of the optical scattering forces in dielectric microspheres under different incident beam conditions is important as they have been used as the natural force transducer for mechanical measurements. Our results show how careful one has to be when using optical force models for this purpose. The Mie resonances can change the force values by 30-50 %. Also the results clearly show how the usually assumed azimuthal symmetry in the horizontal plane no longer holds because the beam polarization breaks this symmetry.Optical tweezers rely on the radiation pressure to trap and manipulate microscopic particles 1-2 . The recent review by David Grier 3 shows its important use in many fields of research from physics to life sciences. The optical forces involved are very small, in the range of hundreds of femto to tens of pico Newtons, thus optical tweezers have also been used as a mechanical properties measuring tool for microscopic phenomena where the forces involved are in the same scale. Typically, it has been used to measure forces, stiffness or elasticities of membranes or single DNA macromolecule 4-8 . Force measurements are usually performed with restorative systems like springs. The optical tweezers, being one of the smallest force stable trap, can be itself used to characterize optical forces involved in scattering of particles. Its ultrasensitiveness can be useful for experimental characterization of hard to measure very low force fundamental phenomena. The understanding of the optical scattering forces in dielectric microspheres under different incident beam conditions is very important as they have been used as the natural transducer for force and other mechanical measurements. Our results show how careful one has to be when using optical force models for mechanical properties measurements.The optical force measurements were usually calibrated by the hydrodynamics force in microspheres at very low Reynolds number flow or through the Brownian ther...

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Direct measurement of DNA molecular length in solution using optical tweezers: detection of looping due to binding protein interactions

Cited by 18 publications

References 16 publications

The t-PA -7351C>T enhancer polymorphism decreases Sp1 and Sp3 protein binding affinity and transcriptional responsiveness to retinoic acid

The t-PA -7351C>T enhancer polymorphism decreases Sp1 and Sp3 protein binding affinity and transcriptional responsiveness to retinoic acid

Determination of fluid viscosity and femto Newton forces of Leishmania amazonensis using optical tweezers

Ultrasensitive force spectroscopy measurement of single particle light scattering by the use of optical tweezers

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