Torus Circumference and Thickness Parameters From a Linear DNA Size Series Suggest How Toruses Self-Assemble

Author(s):  
George C. Ruben ◽  
Kenneth A. Marx

Certain double stranded DNA bacteriophage and viruses are thought to have their DNA organized into large torus shaped structures. Morphologically, these poorly understood biological DNA tertiary structures resemble spermidine-condensed DNA complexes formed in vitro in the total absence of other macromolecules normally synthesized by the pathogens for the purpose of their own DNA packaging. Therefore, we have studied the tertiary structure of these self-assembling torus shaped spermidine- DNA complexes in a series of reports. Using freeze-etch, low Pt-C metal (10-15Å) replicas, we have visualized the microscopic DNA organization of both calf Thymus( CT) and linear 0X-174 RFII DNA toruses. In these structures DNA is circumferentially wound, continuously, around the torus into a semi-crystalline, hexagonal packed array of parallel DNA helix sections.

Author(s):  
George C. Ruben ◽  
Kenneth A. Marx

Torus shaped spermidine-DNA structures formed in vitro are thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. For this reason we have used freeze-etch low Pt-C metal replica TEM to visualize toruses formed from a variety of condensed DNAs. Both Calf Thymus DNA and circular and linear ϕX-174 RFII DNA freeze-etch TEM and biochemical data support a circumferential DNA winding model for hydrated spermidine-condensed DNA toruses. Heretofore, we utilized stereoscopic measurements from tilt views of thin replicas (60-90 Å) of toruses to yield information about the DNA topology and thickness of these objects. In a companion paper in these proceedings we examine the precision of such stereoscopic measurements on tilt micrographs of a torus. In our attempts to visualize DNA toruses we have noted that deep-etched toruses are generally suspended above the surface by virtue of a residual attachment to the ice.


Author(s):  
George C. Ruben ◽  
Kenneth A. Marx

We have used freeze-fracture TEM to visualize toroidal shaped spermidine Calf Thymus DNA complexes. DNA collapsed into these complexes represents an in vitro model system for the packaging of double stranded DNA in bacteriophage and virus heads. Both freeze fracture TEM and biochemical data support a circumferential DNA winding model for DNA organization in the hydrated torus. To better understand this microscopic DNA organization we made stereoscopic measurements of surface DNA topology in high-resolution eucentric tilt views of freeze-etch, single direction shadowed, low Pt-C metal (9Å) replicas. Here we calculate and discuss the error magnitude associated with these modern high-magnification stereoscopic measurements. Freeze fracture TEM was performed on spermidine-condensed Calf Thymus DNA samples as previously described. Micrographs (105 x with a JEM 100 CX) were printed at 2.5 x 105 for measurement with a floating-mark stereometer (SB 190 Mirror Stereoscope, Cartographic Eng. Ltd.). Figure 1 shows the DNA torus we made measurements on.


Author(s):  
George C. Ruben ◽  
Kenneth A. Marx

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.


1981 ◽  
Vol 195 (1) ◽  
pp. 171-176 ◽  
Author(s):  
V Giancotti ◽  
S Cosimi ◽  
P D Cary ◽  
C Crane-Robinson ◽  
G Geraci

The separation and purification of histone H1 from the sperm of the sea-urchin Sphaerechinus granularis is described. Physical studies were used to compare this histone H1 molecule with H1 histones from other species. C.d. and 270 MHz n.m.r. spectroscopy indicate that, despite significant compositional differences from other sea-urchin sperm H1 histones, their secondary and tertiary structures are very similar. A large difference in helicity was, however, found between S. granularis histone H1 and calf thymus histone H1, and their n.m.r. and fluorescence spectra also differ considerably. It is concluded that secondary structure and tertiary structure have not been conserved in the evolution of the H1 histone family.


2018 ◽  
Vol 475 (17) ◽  
pp. 2727-2748
Author(s):  
Patrycja Sosińska-Zawierucha ◽  
Piotr Zawierucha ◽  
Andrzej Bręborowicz ◽  
Jan Barciszewski

Based on experimental and bioinformatic approaches, we present the first empirically established complete secondary structure of human BC200 RNA. BC200 RNA is a brain-specific non-messenger RNA with a confirmed regulatory role in dendritic translation in neurons. Although the involvement of human BC200 RNA in various types of tumour and Alzheimer's disease has been repeatedly confirmed, the exact secondary structure remains not fully elucidated. To determine the secondary structure of BC200 RNA in vitro, we performed partial hydrolysis with sequence-specific nucleases and lead-induced cleavage. We also examined the availabilities of putative single-stranded regions and base-pairing interactions via specific DNAzymes and RNase H assay. To determine the complete spatial folding of BC200 RNA, we used experimental data as constraints in structure prediction programs and performed a comparison of results obtained by several algorithms using different criteria. Based on the experimental-derived secondary structure of BC200 RNA, we also predicted the tertiary structure of BC200 RNA. The presented combination of experimental and bioinformatic approaches not only enabled the determination of the most reliable secondary and tertiary structures of human BC200 RNA (largely in agreement with the previous phylogenetic model), but also verified the compatibility and potential disadvantages of utilizing in silico structure prediction programs.


2019 ◽  
Vol 117 (1) ◽  
pp. 308-316 ◽  
Author(s):  
Maonan Wang ◽  
Yun Chen ◽  
Weijuan Cai ◽  
Huan Feng ◽  
Tianyu Du ◽  
...  

Cancer remains one of the most challenging diseases to treat. For accurate cancer diagnosis and targeted therapy, it is important to assess the localization of the affected area of cancers. The general approaches for cancer diagnostics include pathological assessments and imaging. However, these methods only generally assess the tumor area. In this study, by taking advantage of the unique microenvironment of cancers, we effectively utilize in situ self-assembled biosynthetic fluorescent gold nanocluster-DNA (GNC-DNA) complexes to facilitate safe and targeted cancer theranostics. In in vitro and in vivo tumor models, our self-assembling biosynthetic approach allowed for precise bioimaging and inhibited cancer growth after one injection of DNA and gold precursors. These results demonstrate that in situ bioresponsive self-assembling GNC-PTEN (phosphatase and tensin homolog) complexes could be an effective noninvasive technique for accurate cancer bioimaging and treatment, thus providing a safe and promising cancer theranostics platform for cancer therapy.


Diabetes ◽  
1996 ◽  
Vol 45 (9) ◽  
pp. 1197-1203 ◽  
Author(s):  
J. Saldeen ◽  
D. T. Curiel ◽  
D. L. Eizirik ◽  
A. Andersson ◽  
E. Strandell ◽  
...  

2020 ◽  
Vol 17 (2) ◽  
pp. 125-132
Author(s):  
Marjanu Hikmah Elias ◽  
Noraziah Nordin ◽  
Nazefah Abdul Hamid

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.


1992 ◽  
Vol 267 (1) ◽  
pp. 331-338
Author(s):  
A J Griffith ◽  
P R Blier ◽  
T Mimori ◽  
J A Hardin
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