Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing

Author(s):  
Andrew V. Anzalone ◽  
Xin D. Gao ◽  
Christopher J. Podracky ◽  
Andrew T. Nelson ◽  
Luke W. Koblan ◽  
...  
Keyword(s):  
Author(s):  
Regina Birchem

Spheroids of the green colonial alga Volvox consist of biflagellate Chlamydomonad-like cells embedded in a transparent sheath. The sheath, important as a substance through which metabolic materials, light, and the sexual inducer must pass to and from the cells, has been shown to have an ordered structure (1,2). It is composed of both protein and carbohydrate (3); studies of V. rousseletii indicate an outside layer of sulfated polysaccharides (4).Ultrastructural studies of the sheath material in developmental stages of V. carteri f. weismannia were undertaken employing variations in the standard fixation procedure, ruthenium red, diaminobenzidine, and high voltage electron microscopy. Sheath formation begins after the completion of cell division and inversion of the daughter spheroids. Golgi, rough ER, and plasma membrane are actively involved in phases of sheath synthesis (Fig. 1). Six layers of ultrastructurally differentiated sheath material have been identified.


Author(s):  
P.P.K. Smith

Grains of pigeonite, a calcium-poor silicate mineral of the pyroxene group, from the Whin Sill dolerite have been ion-thinned and examined by TEM. The pigeonite is strongly zoned chemically from the composition Wo8En64FS28 in the core to Wo13En34FS53 at the rim. Two phase transformations have occurred during the cooling of this pigeonite:- exsolution of augite, a more calcic pyroxene, and inversion of the pigeonite from the high- temperature C face-centred form to the low-temperature primitive form, with the formation of antiphase boundaries (APB's). Different sequences of these exsolution and inversion reactions, together with different nucleation mechanisms of the augite, have created three distinct microstructures depending on the position in the grain.In the core of the grains small platelets of augite about 0.02μm thick have farmed parallel to the (001) plane (Fig. 1). These are thought to have exsolved by homogeneous nucleation. Subsequently the inversion of the pigeonite has led to the creation of APB's.


Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.


Author(s):  
Barbara Trask ◽  
Susan Allen ◽  
Anne Bergmann ◽  
Mari Christensen ◽  
Anne Fertitta ◽  
...  

Using fluorescence in situ hybridization (FISH), the positions of DNA sequences can be discretely marked with a fluorescent spot. The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ≈0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.


Author(s):  
José L. Carrascosa ◽  
José M. Valpuesta ◽  
Hisao Fujisawa

The head to tail connector of bacteriophages plays a fundamental role in the assembly of viral heads and DNA packaging. In spite of the absence of sequence homology, the structure of connectors from different viruses (T4, Ø29, T3, P22, etc) share common morphological features, that are most clearly revealed in their three-dimensional structure. We have studied the three-dimensional reconstruction of the connector protein from phage T3 (gp 8) from tilted view of two dimensional crystals obtained from this protein after cloning and purification.DNA sequences including gene 8 from phage T3 were cloned, into Bam Hl-Eco Rl sites down stream of lambda promotor PL, in the expression vector pNT45 under the control of cI857. E R204 (pNT89) cells were incubated at 42°C for 2h, harvested and resuspended in 20 mM Tris HC1 (pH 7.4), 7mM 2 mercaptoethanol, ImM EDTA. The cells were lysed by freezing and thawing in the presence of lysozyme (lmg/ml) and ligthly sonicated. The low speed supernatant was precipitated by ammonium sulfate (60% saturated) and dissolved in the original buffer to be subjected to gel nitration through Sepharose 6B, followed by phosphocellulose colum (Pll) and DEAE cellulose colum (DE52). Purified gp8 appeared at 0.3M NaCl and formed crystals when its concentration increased above 1.5 mg/ml.


2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.


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