Ralf Seidel

Bio: Ralf Seidel is an academic researcher from Leipzig University. The author has contributed to research in topics: DNA & Helicase. The author has an hindex of 45, co-authored 130 publications receiving 5554 citations. Previous affiliations of Ralf Seidel include Max Planck Society & Delft University of Technology.

Nanoscale palladium metallization of DNA

Abstract: A magnetite colloid was prepared in alkaline solution according to the procedure published by Massart [11]. An aqueous solution containing 2.3 g (8.5 mmol) FeCl 3 ×6H 2 O in 4 mL H 2 O and 1.69 g (4.3 mmol) Fe(NH 4) 2 (SO 4) 2 in 1 mL of 2 M HCl, was added to 50 mL of 1 M (CH 3) 4 NOH×5H 2 O. The resulting black suspension was stirred for 1 h at room temperature and then sonicated in an ultrasonic bath for 1 h. The colloid was then centrifuged at 20 000 g for 1 h. The supernatant was decanted and the slurry resuspended in 20 mL water by sonication before being passed through a 0.2 mm pore cellulose nitrate membrane. A titanium dioxide sol was prepared by hydrolysis of titanium tetraiso-propoxide under a nitrogen atmosphere following the procedure described by O'Regan et al. [12]. 25 mL of titanium tetraisopropoxide was mixed with 4 mL of isopropanol in a dropping-funnel under a nitrogen atmosphere. This mixture was added slowly over a period of 5 min to 150 mL of vigorously stirred double-distilled, deionized water in a 250 mL three-neck flask equipped with heater, thermometer and stirrer. Ten minutes after the final alkoxide addition, 1 mL of 69 % HNO 3 was added. The white hydrolysis mixture was then stirred for 8 h at 80 C to remove the isopropanol, filtered through a 0.2 mm pore cellulose nitrate membrane, and sonicated for 1 h to produce a stable colloidal solution with a bluish-white coloration. Preparation of the Composites and Method of Calcination: Typically, a sample of the sliced copolymer gel (ca. 5 mm thick) was added to the colloidal sol and left for the desired period of time. The colloid-loaded gels were removed, washed with water and allowed to dry in air. Thermogravi-metric analysis (TGA) measurements were made using a NETZSCH STA 409EP machine. Samples were heated under air in an alumina crucible to a final temperature of 800 C at a rate of 5 K/min. Large samples of the miner-alized gels were calcined by heating to a temperature of 450 or 500 C in a Carbolite furnace (type ELF11/6) at a heating rate of 1 C min ±1. Analytical Methods: The morphology of the copolymer gel in the water-swollen state was examined using a Jeol 6310 SEM equipped with a cryo-stage and energy-dispersive X-ray (EDX). …

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes.

Abstract: Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component of the complex encodes target recognition by forming a site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the noncomplementary strand. Subsequently, the R-loop structure triggers DNA degradation. Although these reactions have been reconstituted, the exact mechanism of R-loop formation has not been fully resolved. Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynamics of torque-dependent R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems. We find that the protospacer adjacent motif (PAM) affects primarily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily R-loop stability. Furthermore, Cascade has higher torque stability than Cas9 by using a conformational locking step. Our data provide direct evidence for directional R-loop formation, starting from PAM recognition and expanding toward the distal protospacer end. Moreover, we introduce DNA supercoiling as a quantitative tool to explore the sequence requirements and promiscuities of orthogonal CRISPR-Cas systems in rapidly emerging gene-targeting applications.

Mechanical and structural properties of YOYO-1 complexed DNA

Abstract: YOYO-1 is a fluorescent dye widely used for probing the statistical–mechanical properties of DNA. However, currently contradicting data exist how YOYO-1 binding alters the DNA structure and rigidity. Here, we systematically address this problem using magnetic tweezers. Remarkably, we find that the persistence length of DNA remains constant independent of the amount of bound YOYO-1, which contrasts previous assumptions. While the ionic conditions can considerably alter the stability of YOYO-1 binding, the DNA bending rigidity seems not to be affected. We furthermore determine important structural parameters such as the binding site size, the elongation, as well as the untwisting angle per bound YOYO-1 molecule. We expect that our assay, in which all the parameters are determined within a single experiment, will be beneficial for a large range of other DNA binding drugs.

Synthesis of Platinum Cluster Chains on DNA Templates: Conditions for a Template-Controlled Cluster Growth

Abstract: We investigate the conditions which should be fulfilled to grow chains of nanosized noble metal clusters on DNA templates according to a selectively heterogeneous, template-controlled mechanism. A long incubation of double-stranded DNA molecules with Pt(II) complexes is necessary to obtain a template-directed formation of thin and uniform cluster chains after chemical reduction of the DNA/salt solution. Without this “activation” step, DNA acts as a nonspecific capping agent for the formed clusters and does not hinder the formation of random cluster aggregates. The effect of binding Pt(II) complexes to the DNA is investigated by UV−vis spectroscopy, electrophoresis experiments, and scanning force microscopy, revealing that the base stacking along the DNA molecule is significantly distorted but the double-stranded DNA configuration is retained. Citrate ions can be used as additional stabilizers for the heterogeneously grown metal clusters, leading to significantly more regular metal cluster chains. After a ...

Direct Mechanical Measurements Reveal the Material Properties of Three-Dimensional DNA Origami

Abstract: The application of three-dimensional DNA origami objects as rigid mechanical mediators or force sensing elements requires detailed knowledge about their complex mechanical properties. Using magnetic tweezers, we directly measure the bending and torsional rigidities of four- and six-helix bundles assembled by this technique. Compared to duplex DNA, we find the bending rigidities to be greatly increased while the torsional rigidities are only moderately augmented. We present a mechanical model explicitly including the crossovers between the individual helices in the origami structure that reproduces the experimentally observed behavior. Our results provide an important basis for the future application of 3D DNA origami in nanomechanics.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Shape‐Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics?

Abstract: Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.

The new frontier of genome engineering with CRISPR-Cas9

Abstract: The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.

Recent advances in the liquid-phase syntheses of inorganic nanoparticles.

Abstract: The development of novel materials is a fundamental focal point of chemical research; and this interest is mandated by advancements in all areas of industry and technology. A good example of the synergism between scientific discovery and technological development is the electronics industry, where discoveries of new semiconducting materials resulted in the evolution from vacuum tubes to diodes and transistors, and eventually to miniature chips. The progression of this technology led to the development * To whom correspondence should be addressed. B.L.C.: (504) 2801385 (phone); (504) 280-3185 (fax); bcushing@uno.edu (e-mail). C.J.O.: (504)280-6846(phone);(504)280-3185(fax);coconnor@uno.edu (e-mail). 3893 Chem. Rev. 2004, 104, 3893−3946