Stabilization of double-stranded DNA molecule by nonhistone peptidic effector from calf thymus

1976 ◽  
Vol 3 (1) ◽  
pp. 55-64 ◽  
Author(s):  
G. L. Gianfranceschi ◽  
D. Amici ◽  
L. Guglielmi
Keyword(s):  
Dna Molecule ◽  
Double Stranded Dna ◽  
Calf Thymus

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

1985 ◽  
Vol 43 ◽  
pp. 522-523
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Tertiary Structure ◽  
Dna Complexes ◽  
Tertiary Structures ◽  
Self Assembling ◽  
Double Stranded Dna ◽  
Calf Thymus ◽  
Dna Organization ◽  
Condensed Dna ◽  
Dna Size

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.

scholarly journals p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

2020 ◽  
Vol 16 ◽  
pp. 337-350
Author(s):  
Panagiotis S Gritzapis ◽  
Panayiotis C Varras ◽  
Nikolaos-Panagiotis Andreou ◽  
Katerina R Katsani ◽  
Konstantinos Dafnopoulos ◽  
...  
Keyword(s):  
Energy State ◽  
Theoretical Studies ◽  
Triplet Energy ◽  
Imine Group ◽  
Sar Studies ◽  
Double Stranded Dna ◽  
Structure Activity ◽  
Calf Thymus ◽  
Carbamate Group ◽  
Synthetic Nucleases

A number of p-pyridinyl oxime carbamate derivatives were prepared upon the reaction of the corresponding oximes with isocyanates. These novel compounds reacted photochemically in the presence of supercoiled plasmid DNA. Structure–activity relationship (SAR) studies revealed that the substituent on the imine group was not affecting the extend of the DNA damage, whereas the substituent of the carbamate group was critical, with the halogenated derivatives to be able to cause extensive single and double stranded DNA cleavages, acting as “synthetic nucleases”, independently of oxygen and pH. Calf thymus–DNA affinity studies showed a good-to-excellent affinity of selected both active and non-active derivatives. Preliminary theoretical studies were performed, in an effort to explain the reasons why some derivatives cause photocleavage and some others not, which were experimentally verified using triplet state activators and quenchers. These theoretical studies seem to allow the prediction of the activity of derivatives able to pass intersystem crossing to their triplet energy state and thus create radicals able to damage DNA. With this study, it is shown that oxime carbamate derivatives have the potential to act as novel effective photobase generating DNA-photocleavers, and are proposed as new leads for “on demand” biotechnological applications in drug discovery and medicine.

scholarly journals High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast

2017 ◽  
Author(s):  
Yi Yin ◽  
Margaret Dominska ◽  
Eunice Yim ◽  
Thomas D. Petes
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Mitotic Recombination ◽  
Template Switching ◽  
Wild Type ◽  
Dna Breaks ◽  
Repair Synthesis ◽  
Heteroduplex Dna ◽  
Dna Molecule ◽  
Double Stranded Dna

AbstractDouble-stranded DNA breaks (DSBs) can be generated by both endogenous and exogenous agents. In diploid yeast strains, such breaks are usually repaired by homologous recombination (HR), and a number of different HR pathways have been described. An early step for all HR pathways is formation of a heteroduplex, in which a single-strand from the broken DNA molecule pairs with a strand derived from an intact DNA molecule. If the two strands of DNA are not identical, within the heteroduplex DNA (hetDNA), there will be mismatches. In a wild-type strain, these mismatches are removed by the mismatch repair (MMR) system. In strains lacking MMR, the mismatches persist and can be detected by a variety of genetic and physical techniques. Most previous studies involving hetDNA formed during mitotic recombination have been restricted to a single locus with DSBs induced at a defined position by a site-specific endonuclease. In addition, in most of these studies, recombination between repeated genes was examined; in such studies, the sequence homologies were usually less than 5 kb. In the present study, we present a global mapping of hetDNA formed in a UV-treated MMR-defective mlh1 strain. Although about two-thirds of the recombination events were associated with hetDNA with a continuous array of unrepaired mismatches, in about one-third of the events, we found regions of unrepaired mismatches flanking regions without mismatches. We suggest that these discontinuous hetDNAs involve template switching during repair synthesis, repair of a double-stranded DNA gap, and/or Mlh1-independent MMR. Many of our observed events are not explicable by the simplest form of the double-strand break repair (DSBR) model of recombination. We also studied hetDNA associated with spontaneous recombination events selected on chromosomes IV and V in a wild-type strain. The interval on chromosome IV contained a hotspot for spontaneous crossovers generated by an inverted pair of transposable elements (HS4). We showed that HS4-induced recombination events are associated with the formation of very large (>30 kb) double-stranded DNA gaps.

Exploration of Spin-Dependent Thermoelectricity in the Chiral Double-Stranded DNA Molecule Coupled to Ferromagnetic Leads

2019 ◽  
Vol 12 (2) ◽  
Author(s):  
Lei-Lei Nian ◽  
Long Bai ◽  
Wenting Yu ◽  
Jun Tang ◽  
Huichao Li ◽  
...  
Keyword(s):  
Dna Molecule ◽  
Double Stranded Dna

Strategies for error reduction in high-magnification stereoscopic measurements based on error equation calculations

1983 ◽  
Vol 41 ◽  
pp. 704-705
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
In Vitro Model ◽  
Freeze Fracture ◽  
Calf Thymus Dna ◽  
High Magnification ◽  
Double Stranded Dna ◽  
Error Magnitude ◽  
Calf Thymus ◽  
Dna Organization ◽  
Vitro Model

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.

Transfection with extracellularly UV-damaged DNA induces human and rat cells to express a mutator phenotype towards parvovirus H-1

1984 ◽  
Vol 4 (2) ◽  
pp. 324-328
Author(s):  
C Dinsart ◽  
J J Cornelis ◽  
B Klein ◽  
A J van der Eb ◽  
J Rommelaere
Keyword(s):  
Mammalian Cells ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Dna Virus ◽  
Double Stranded Dna ◽  
Mutator Activity ◽  
Calf Thymus ◽  
Circular Dnas ◽  
Uv Lesions ◽  
Damaged Dna

Human and rat cells transfected with UV-irradiated linear double-stranded DNA from calf thymus displayed a mutator activity. This phenotype was identified by growing a lytic thermosensitive single-stranded DNA virus (parvovirus H-1) in those cells and determining viral reversion frequencies. Likewise, exogenous UV-irradiated closed circular DNAs, either double-stranded (simian virus 40) or single-stranded (phi X174), enhanced the ability of recipient cells to mutate parvovirus H-1. The magnitude of mutator activity expression increased along with the number of UV lesions present in the inoculated DNA up to a saturation level. Unirradiated DNA displayed little inducing capacity, irrespective of whether it was single or double stranded. Deprivation of a functional replication origin did not impede UV-irradiated simian virus 40 DNA from providing rat and human cells with a mutator function. Our data suggest that in mammalian cells a trans-acting mutagenic signal might be generated from UV-irradiated DNA without the necessity for damaged DNA to replicate.

scholarly journals Light-scattering studies on deoxyribonucleic acid flexibility. The solution properties of a small circular deoxyribonucleic acid molecule

1972 ◽  
Vol 130 (4) ◽  
pp. 1019-1028 ◽  
Author(s):  
Douglas J. Jolly ◽  
Ailsa M. Campbell
Keyword(s):  
Light Scattering ◽  
Deoxyribonucleic Acid ◽  
Persistence Length ◽  
Resolving Power ◽  
Experimental Investigations ◽  
Volume Factor ◽  
Circular Dna ◽  
Dna Molecule ◽  
Double Stranded Dna ◽  
Infected Cells

Previous investigations on the persistence length of DNA in solution have revealed large discrepancies between hydrodynamic results and those from light-scattering techniques which have potentially a greater resolving power. The information obtained from experiments on a small circular DNA molecule has resolved these discrepancies. The non-superhelical circular double-stranded DNA molecule from bacteriophage [unk]X174-infected cells is small enough to permit accurate light-scattering extrapolations, and its solutions have negligible anisotropy. The persistence length obtained from experimental investigations on this molecule is comparable with that obtained by hydrodynamic techniques, even with variation of the excluded-volume factor.

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