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Journal articles on the topic 'DNA bubbles'

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Published: 4 June 2021
Last updated: 4 February 2022

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1

Makasheva, Kristina A., Anton V. Endutkin, and Dmitry O. Zharkov. "Requirements for DNA bubble structure for efficient cleavage by helix–two-turn–helix DNA glycosylases." Mutagenesis 35, no. 1 (2019): 119–28. http://dx.doi.org/10.1093/mutage/gez047.

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Abstract Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix–two-turn–helix (H2TH) structural superfamily, remove oxidised purines and pyrimidines, respectively. Interestingly, the human H2TH family glycosylases, NEIL1, NEIL2 and NEIL3, have been reported to prefer oxidative lesions in DNA bubbles or single-stranded DNA. It had been hypothesised that NEIL2 might be involved in the repair of lesions in transcription bubbles; however, bubble-like structures may appear in other cellular contexts such as displacement loops (D-loops) associated with transcription, recombination or telomere maintenance. The activities of bacterial Fpg and Nei on bubble substrates were not addressed. Also, it is not known whether H2TH enzymes process bubbles containing the third DNA or RNA strand, and how the bubble length and position of the lesion within a bubble affect the excision. We have investigated the removal of 8-oxoguanine (8-oxoG) and 5,6-dihydrouracil (DHU) by Escherichia coli Fpg and Nei and human NEIL1 and NEIL2 from single-strand oligonucleotides, perfect duplexes, bubbles with different numbers of unpaired bases (6–30), bubbles containing the lesion in different positions and D-loops with the third strand made of DNA or RNA. Fpg, NEIL1 and NEIL2 efficiently excised lesions located within bubbles, with NEIL1 and NEIL2 being specific for DHU, and Fpg removing both 8-oxoG and DHU. Nei, in contrast, was significantly active only on DHU located in double-stranded DNA. Fpg and NEIL1 also tolerated the presence of the third strand of either DNA or RNA in D-loops if the lesion was in the single-stranded part, and Fpg, Nei and NEIL1 excised lesions from the double-stranded DNA part of D-loops. The presence of an additional unpaired 5′-tail of DNA or RNA did not affect the activity. No significant position preference for lesions in a 12-mer bubble was found. Overall, the activities of Fpg, NEIL1 and NEIL2 on these non-canonical substrates are consistent with the possibility that these enzymes may participate in the repair in structures arising during transcription or homologous recombination.
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2

Severin, N., W. Zhuang, C. Ecker, A. A. Kalachev, I. M. Sokolov, and J. P. Rabe. "Blowing DNA Bubbles." Nano Letters 6, no. 11 (2006): 2561–66. http://dx.doi.org/10.1021/nl061989b.

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3

Gonzalez, Rodrigo, Yan Zeng, Vassili Ivanov, and Giovanni Zocchi. "Bubbles in DNA melting." Journal of Physics: Condensed Matter 21, no. 3 (2008): 034102. http://dx.doi.org/10.1088/0953-8984/21/3/034102.

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4

Grinevich, A. A., A. A. Ryasik, and L. V. Yakushevich. "Trajectories of DNA bubbles." Chaos, Solitons & Fractals 75 (June 2015): 62–75. http://dx.doi.org/10.1016/j.chaos.2015.02.009.

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5

Hariadi, Rizal F., Erik Winfree, and Bernard Yurke. "Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics." Proceedings of the National Academy of Sciences 112, no. 45 (2015): E6086—E6095. http://dx.doi.org/10.1073/pnas.1424673112.

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Quantifying the mechanical forces produced by fluid flows within the ocean is critical to understanding the ocean’s environmental phenomena. Such forces may have been instrumental in the origin of life by driving a primitive form of self-replication through fragmentation. Among the intense sources of hydrodynamic shear encountered in the ocean are breaking waves and the bursting bubbles produced by such waves. On a microscopic scale, one expects the surface-tension–driven flows produced during bubble rupture to exhibit particularly high velocity gradients due to the small size scales and masses involved. However, little work has examined the strength of shear flow rates in commonly encountered ocean conditions. By using DNA nanotubes as a novel fluid flow sensor, we investigate the elongational rates generated in bursting films within aqueous bubble foams using both laboratory buffer and ocean water. To characterize the elongational rate distribution associated with a bursting bubble, we introduce the concept of a fragmentation volume and measure its form as a function of elongational flow rate. We find that substantial volumes experience surprisingly large flow rates: during the bursting of a bubble having an air volume of 10 mm3, elongational rates at least as large as ϵ˙=1.0×108 s−1 are generated in a fragmentation volume of ∼2×10−6μL. The determination of the elongational strain rate distribution is essential for assessing how effectively fluid motion within bursting bubbles at the ocean surface can shear microscopic particles and microorganisms, and could have driven the self-replication of a protobiont.
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6

Wu, Weimin, Naiqian Cheng, Lindsay Black, Hendrik Dietz, and Alasdair Steven. "Biphasic Packing of DNA and Internal Proteins in Bacteriophage T4 Heads Revealed by Bubblegram Imaging." Viruses 12, no. 11 (2020): 1282. http://dx.doi.org/10.3390/v12111282.

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The virions of tailed bacteriophages and the evolutionarily related herpesviruses contain, in addition to highly condensed DNA, substantial quantities of internal proteins. These proteins (“ejection proteins”) have roles in scaffolding, maturational proteolysis, and cell-to-cell delivery. Whereas capsids are amenable to analysis at high resolution by cryo-electron microscopy, internal proteins have proved difficult to localize. In this study, we investigated the distribution of internal proteins in T4 by bubblegram imaging. Prior work has shown that at suitably high electron doses, radiation damage generates bubbles of hydrogen gas in nucleoprotein specimens. Using DNA origami as a test specimen, we show that DNA does not bubble under these conditions; it follows that bubbles represent markers for proteins. The interior of the prolate T4 head, ~1000 Å long by ~750 Å wide, has a bubble-free zone that is ~100–110 Å thick, underlying the capsid shell from which proteins are excluded by highly ordered DNA. Inside this zone, which is plausibly occupied by ~4 layers of coaxial spool, bubbles are generated at random locations in a disordered ensemble of internal proteins and the remainder of the genome.
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7

Zeng, Yan, and Giovanni Zocchi. "Mismatches and Bubbles in DNA." Biophysical Journal 90, no. 12 (2006): 4522–29. http://dx.doi.org/10.1529/biophysj.105.069591.

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8

van Erp, T. S., S. Cuesta-López, and M. Peyrard. "Bubbles and denaturation in DNA." European Physical Journal E 20, no. 4 (2006): 421–34. http://dx.doi.org/10.1140/epje/i2006-10032-2.

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9

Hennig, D., J. F. R. Archilla, and J. M. Romero. "Modelling the thermal evolution of enzyme-created bubbles in DNA." Journal of The Royal Society Interface 2, no. 2 (2005): 89–95. http://dx.doi.org/10.1098/rsif.2004.0024.

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The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach, we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that, in fact, from certain local structural distortions, there originate oscillating localized patterns, that is, radial and torsional breathers, which are associated with localized H-bond deformations, reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim, the underlying nonlinear oscillator network of the DNA duplex is brought into contact with a heat bath using the Nosé–Hoover method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for non-zero temperature, the H-bond breathers move coherently along the double chain, whereas at T =0 standing radial and torsional breathers result.
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10

Liang, C., and S. A. Gerbi. "Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method." Molecular and Cellular Biology 14, no. 2 (1994): 1520–29. http://dx.doi.org/10.1128/mcb.14.2.1520.

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The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.
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11

Liang, C., and S. A. Gerbi. "Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method." Molecular and Cellular Biology 14, no. 2 (1994): 1520–29. http://dx.doi.org/10.1128/mcb.14.2.1520-1529.1994.

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The replication origin region for DNA amplification in Sciara coprophila DNA puff II/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90 degrees to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.
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12

Kim, Sook Ho, Hae Jun Jung, Il-Buem Lee, Nam-Kyung Lee, and Seok-Cheol Hong. "Sequence-dependent cost for Z-form shapes the torsion-driven B–Z transition via close interplay of Z-DNA and DNA bubble." Nucleic Acids Research 49, no. 7 (2021): 3651–60. http://dx.doi.org/10.1093/nar/gkab153.

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Abstract Despite recent genome-wide investigations of functional DNA elements, the mechanistic details about their actions remain elusive. One intriguing possibility is that DNA sequences with special patterns play biological roles, adopting non-B-DNA conformations. Here we investigated dynamics of thymine-guanine (TG) repeats, microsatellite sequences and recurrently found in promoters, as well as cytosine–guanine (CG) repeats, best-known Z-DNA forming sequence, in the aspect of Z-DNA formation. We measured the energy barriers of the B–Z transition with those repeats and discovered the sequence-dependent penalty for Z-DNA generates distinctive thermodynamic and kinetic features in the torque-induced transition. Due to the higher torsional stress required for Z-form in TG repeats, a bubble could be induced more easily, suppressing Z-DNA induction, but facilitate the B–Z interconversion kinetically at the transition midpoint. Thus, the Z-form by TG repeats has advantages as a torsion buffer and bubble selector while the Z-form by CG repeats likely behaves as torsion absorber. Our statistical physics model supports quantitatively the populations of Z-DNA and reveals the pivotal roles of bubbles in state dynamics. All taken together, a quantitative picture for the transition was deduced within the close interplay among bubbles, plectonemes and Z-DNA.
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13

Dhar, S. K., N. R. Choudhury, V. Mittal, A. Bhattacharya, and S. Bhattacharya. "Replication initiates at multiple dispersed sites in the ribosomal DNA plasmid of the protozoan parasite Entamoeba histolytica." Molecular and Cellular Biology 16, no. 5 (1996): 2314–24. http://dx.doi.org/10.1128/mcb.16.5.2314.

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In the protozoan parasite Entamoeba histolytica (which causes amoebiasis in humans), the rRNA genes (rDNA) in the nucleus are carried on an extrachromosomal circular plasmid. For strain HM-1:IMSS, the size of the rDNA plasmid is 24.5 kb, and 200 copies per genome are present. Each circle contains two rRNA transcription units as inverted repeats separated by upstream and downstream spacers. We have studied the replication of this molecule by neutral/neutral two-dimensional gel electrophoresis and by electron microscopy. All restriction fragments analyzed by two-dimensional gel electrophoresis gave signals corresponding to simple Y's and bubbles. This showed that replication initiated in this plasmid at multiple, dispersed locations spread throughout the plasmid. On the basis of the intensity of the bubble arcs, initiations from the rRNA transcription units seemed to occur more frequently than those from intergenic spacers. Multiple, dispersed initiation sites were also seen in the rDNA plasmid of strain HK-9 when it was analyzed by two-dimensional gel electrophoresis. Electron microscopic visualization of replicating plasmid molecules in strain HM-1:IMISS showed multiple replication bubbles in the same molecule. The location of bubbles on the rDNA circle was mapped by digesting with PvuI or BsaHI, which linearize the molecule, and with SacII, which cuts the circle twice. The distance of the bubbles from one end of the molecule was measured by electron microscopy. The data corroborated those from two-dimensional gels and showed that replication bubbles were distributed throughout the molecule and that they appeared more frequently in rRNA transcription units. The same interpretation was drawn from electron microscopic analysis of the HK-9 plasmid. Direct demonstration of more than one bubble in the same molecule is clear evidence that replication of this plasmid initiates at multiple sites. Potential replication origins are distributed throughout the plasmid. Such a mechanism is not known to operate in any naturally occurring prokaryotic or eukaryotic plasmid.
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14

Kapri, Rajeev, and Somendra M. Bhattacharjee. "Bubbles in DNA by random force." Physica A: Statistical Mechanics and its Applications 384, no. 1 (2007): 10–14. http://dx.doi.org/10.1016/j.physa.2007.04.108.

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15

Grinevich, Andrey A., Artem A. Ryasik, and Ludmila V. Yakushevich. "130 Modeling the DNA bubbles dynamics." Journal of Biomolecular Structure and Dynamics 33, sup1 (2015): 84. http://dx.doi.org/10.1080/07391102.2015.1032763.

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16

Zrimec, Jan, and Ales Lapanje. "Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability." IEEE/ACM Transactions on Computational Biology and Bioinformatics 12, no. 5 (2015): 1137–45. http://dx.doi.org/10.1109/tcbb.2015.2396057.

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17

Brennen, Christopher Earls. "Cavitation in medicine." Interface Focus 5, no. 5 (2015): 20150022. http://dx.doi.org/10.1098/rsfs.2015.0022.

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We generally think of bubbles as benign and harmless and yet they can manifest the most remarkable range of physical effects. Some of those effects are the stuff of our everyday experience as in the tinkling of a brook or the sounds of breaking waves at the beach. But even these mundane effects are examples of the ability of bubbles to gather, focus and radiate energy (acoustic energy in the above examples). In other contexts that focusing of energy can lead to serious technological problems as when cavitation bubbles eat great holes through ships' propeller blades or cause a threat to the integrity of the spillways at the Hoover Dam. In liquid-propelled rocket engines, bubbles pose a danger to the stability of the propulsion system, and in artificial heart valves they can cause serious damage to the red blood cells. In perhaps the most extraordinary example of energy focusing, collapsing cavitation bubbles can emit not only sound, but also light with black body radiation temperatures equal to that of the sun (Brennen 1995 Cavitation and bubble dynamics ). But, harnessed carefully, this almost unique ability to focus energy can also be put to remarkably constructive use. Cavitation bubbles are now used in a remarkable range of surgical and medical procedures, for example to emulsify tissue (most commonly in cataract surgery or in lithotripsy procedures for the reduction of kidney and gall stones) or to manipulate the DNA in individual cells. By creating cavitation bubbles non-invasively thereby depositing and focusing energy non-intrusively, one can generate minute incisions or target cancer cells. This paper will begin by briefly reviewing the history of cavitation phenomena and will end with a vision of the new horizons for the amazing cavitation bubble.
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18

Adamcik, Jozef, Jae-Hyung Jeon, Konrad J. Karczewski, Ralf Metzler, and Giovanni Dietler. "Quantifying supercoiling-induced denaturation bubbles in DNA." Soft Matter 8, no. 33 (2012): 8651. http://dx.doi.org/10.1039/c2sm26089a.

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19

Kalosakas, G., K. Ø. Rasmussen, and A. R. Bishop. "Nonlinear excitations in DNA: polarons and bubbles." Synthetic Metals 141, no. 1-2 (2004): 93–97. http://dx.doi.org/10.1016/j.synthmet.2003.08.020.

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20

Larijani, Mani, Alexander P. Petrov, Oxana Kolenchenko, Maribel Berru, Sergey N. Krylov, and Alberto Martin. "AID Associates with Single-Stranded DNA with High Affinity and a Long Complex Half-Life in a Sequence-Independent Manner." Molecular and Cellular Biology 27, no. 1 (2006): 20–30. http://dx.doi.org/10.1128/mcb.00824-06.

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ABSTRACT Activation-induced cytidine deaminase (AID) initiates secondary antibody diversification processes by deaminating cytidines on single-stranded DNA. AID preferentially mutates cytidines preceded by W(A/T)R(A/G) dinucleotides, a sequence specificity that is evolutionarily conserved from bony fish to humans. To uncover the biochemical mechanism of AID, we compared the catalytic and binding kinetics of AID on WRC (a hot-spot motif, where W equals A or T and R equals A or G) and non-WRC motifs. We show that although purified AID preferentially deaminates WRC over non-WRC motifs to the same degree observed in vivo, it exhibits similar binding affinities to either motif, indicating that its sequence specificity is not due to preferential binding of WRC motifs. AID preferentially deaminates bubble substrates of five to seven nucleotides rather than larger bubbles and preferentially binds to bubble-type rather than to single-stranded DNA substrates, suggesting that the natural targets of AID are either transcription bubbles or stem-loop structures. Importantly, AID displays remarkably high affinity for single-stranded DNA as indicated by the low dissociation constants and long half-life of complex dissociation that are typical of transcription factors and single-stranded DNA binding protein. These findings suggest that AID may persist on immunoglobulin and other target sequences after deamination, possibly acting as a scaffolding protein to recruit other factors.
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21

Shigaev, A. S., I. V. Lihachev, and V. D. Lakhno. "DNA Model with Non-Local Inter-Site Interaction in Collisional Thermostat." Mathematical Biology and Bioinformatics 15, no. 2 (2020): 129–37. http://dx.doi.org/10.17537/2020.15.129.

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A modified Peyrard-Bishop-Dauxios model with non-local nature of the inter-site potential was studied in a collisional thermostat with a Maxwell velocity distribution of short-lived virtual particles at a temperature of 310 K. Introduction of non-locality to the inter-site potential was found to reduce significantly the equilibrium constants for the denaturation bubble formation reaction. This property improves the agreement of calculated data with experiments. The effect is especially pronounced for large bubbles. The end effects in the new version of the model are investigated. The significant contribution of entropy and the important role of the processes of transfer and localization of mechanical energy at the end sections of DNA are shown.
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22

Hwa, T., E. Marinari, K. Sneppen, and L. h. Tang. "Localization of denaturation bubbles in random DNA sequences." Proceedings of the National Academy of Sciences 100, no. 8 (2003): 4411–16. http://dx.doi.org/10.1073/pnas.0736291100.

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23

Smelkova, Natalia V., and James A. Borowiec. "Synthetic DNA Replication Bubbles Bound and Unwound with Twofold Symmetry by a Simian Virus 40 T-Antigen Double Hexamer." Journal of Virology 72, no. 11 (1998): 8676–81. http://dx.doi.org/10.1128/jvi.72.11.8676-8681.1998.

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ABSTRACT Dimerization of simian virus 40 T-antigen hexamers (TAgH) into double hexamers (TAgDH) on model DNA replication forks has been found to greatly stimulate T-antigen DNA helicase activity. To explore the interaction of TAgDH with DNA during unwinding, we examined the binding of TAgDH to synthetic DNA replication bubbles. Tests of replication bubble substrates containing different single-stranded DNA (ssDNA) lengths indicated that efficient formation of a TAgDH requires ≥40 nucleotides (nt) of ssDNA. DNase I probing of a substrate containing a 60-nt ssDNA bubble complexed with a TAgDH revealed that T antigen bound the substrate with twofold symmetry. The strongest protection was observed over the 5′ junction on each strand, with 5 bp of duplex DNA and ∼17 nt of adjacent ssDNA protected from nuclease cleavage. Stimulation of the T-antigen DNA helicase activity by an increase in ATP concentration caused the protection to extend in the 5′ direction into the duplex region, while resulting in no significant changes to the 3′ edge of strongest protection. Our data indicate that each TAgH encircles one ssDNA strand, with a different strand bound at each junction. The process of DNA unwinding results in each TAgH interacting with a greater length of DNA than was initially bound, suggesting the generation of a more highly processive helicase complex.
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24

Dasanna, Anil Kumar, Nicolas Destainville, John Palmeri, and Manoel Manghi. "Strand diffusion-limited closure of denaturation bubbles in DNA." EPL (Europhysics Letters) 98, no. 3 (2012): 38002. http://dx.doi.org/10.1209/0295-5075/98/38002.

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25

Yuan, Chongli, Elizabeth Rhoades, Xiong Wen Lou, and Lynden A. Archer. "Spontaneous sharp bending of DNA: role of melting bubbles." Nucleic Acids Research 34, no. 16 (2006): 4554–60. http://dx.doi.org/10.1093/nar/gkl394.

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26

Vallée, Nicolas, Sandrine Gaillard, André Peinnequin, Jean-Jacques Risso, and Jean-Eric Blatteau. "Evidence of cell damages caused by circulating bubbles: high level of free mitochondrial DNA in plasma of rats." Journal of Applied Physiology 115, no. 10 (2013): 1526–32. http://dx.doi.org/10.1152/japplphysiol.00025.2013.

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Bubble formation can occur in the vascular system after diving, leading to decompression sickness (DCS). DCS signs and symptoms range from minor to death. Too often, patients are admitted to a hyperbaric center with atypical symptoms, as bubbles cannot be detected anymore. In the absence of a relevant biomarker for humans, the therapeutic management remains difficult. As circulating DNA was found in the blood of healthy humans and animals, our study was made to correlate the extracellular mitochondrial DNA (mDNA) concentration with the occurrence of clinical DCS symptoms resulting from initial bubble-induced damages. Therefore, 109 rats were subjected to decompression from a simulated 90-m sea water dive, after which, 78 rats survived (71.6%). Among the survivors, 15.6% exhibited typical DCS symptoms (DCS group), whereas the remaining 56% showed no detectable symptoms (noDCS group). Here, we report that the symptomatic rats displayed both a circulating mDNA level (DNADCS → 2.99 ± 2.62) and a bubble grade (median Spencer score = 3) higher than rats from the noDCS group (DNAnoDCS → 1.49 ± 1.27; Spencer score = 1). These higher levels could be correlated with the platelet and leukocyte consumption induced by the pathogenic decompression. Rats with no detectable bubble had lower circulating mDNA than those with higher bubble scores. We determined that in rats, a level of circulating mDNA >1.91 was highly predictive of DCS with a positive-predictive value of 87.3% and an odds ratio of 4.57. Thus circulating mDNA could become a relevant biomarker to diagnose DCS and should be investigated further to confirm its potential application in humans.
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27

Larijani, Mani, and Alberto Martin. "Single-Stranded DNA Structure and Positional Context of the Target Cytidine Determine the Enzymatic Efficiency of AID." Molecular and Cellular Biology 27, no. 23 (2007): 8038–48. http://dx.doi.org/10.1128/mcb.01046-07.

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ABSTRACT Activation-induced cytidine deaminase (AID) initiates antibody diversification processes by deaminating immunoglobulin sequences. Since transcription of target genes is required for deamination in vivo and AID exclusively mutates single-stranded DNA (ssDNA) in vitro, AID has been postulated to mutate transcription bubbles. However, since ssDNA generated by transcription can assume multiple structures, it is unknown which of these are targeted in vivo. Here we examine the enzymatic and binding properties of AID for different DNA structures. We report that AID has minimal activity on stem-loop structures and preferentially deaminates five-nucleotide bubbles. We compared AID activity on cytidines placed at various distances from the single-stranded/double-stranded DNA junction of bubble substrates and found that the optimal target consists of a single-stranded NWRCN motif. We also show that high-affinity binding is required for but does not necessarily lead to efficient deamination. Using nucleotide analogues, we show that AID's WRC preference (W = A or T; R = A or G) involves the recognition of a purine in the R position and that the carbonyl or amino side chains of guanosine negatively influence specificity at the W position. Our results indicate that AID is likely to target short-tract regions of ssDNA produced by transcription elongation and that it requires a fully single-stranded WRC motif.
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28

Ambjörnsson, Tobias, and Ralf Metzler. "Binding dynamics of single-stranded DNA binding proteins to fluctuating bubbles in breathing DNA." Journal of Physics: Condensed Matter 17, no. 20 (2005): S1841—S1869. http://dx.doi.org/10.1088/0953-8984/17/20/013.

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29

Mitchell, J. S., C. A. Laughton, and Sarah A. Harris. "Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA." Nucleic Acids Research 39, no. 9 (2011): 3928–38. http://dx.doi.org/10.1093/nar/gkq1312.

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30

Sicard, François, Nicolas Destainville, and Manoel Manghi. "DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates." Journal of Chemical Physics 142, no. 3 (2015): 034903. http://dx.doi.org/10.1063/1.4905668.

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31

Burnham, Daniel R., Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, and Cees Dekker. "Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively." Nucleic Acids Research 45, no. 8 (2017): 4687–95. http://dx.doi.org/10.1093/nar/gkx147.

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32

Ross, Jason P., Isao Suetake, Shoji Tajima, and Peter L. Molloy. "Recombinant mammalian DNA methyltransferase activity on model transcriptional gene silencing short RNA–DNA heteroduplex substrates." Biochemical Journal 432, no. 2 (2010): 323–32. http://dx.doi.org/10.1042/bj20100579.

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The biochemical mechanism of short RNA-induced TGS (transcriptional gene silencing) in mammals is unknown. Two competing models exist; one suggesting that the short RNA interacts with a nascent transcribed RNA strand (RNA–RNA model) and the other implying that short RNA forms a heteroduplex with DNA from the unwound double helix, an R-loop structure (RNA–DNA model). Likewise, the requirement for DNA methylation to enact TGS is still controversial. In vitro assays using purified recombinant murine Dnmt (DNA methyltransferase) 1-dN (where dN indicates an N-terminal truncation), 3a and 3b enzymes and annealed oligonucleotides were designed to question whether Dnmts methylate DNA in a RNA–DNA heteroduplex context and whether a RNA–DNA heteroduplex R-loop is a good substrate for Dnmts. Specifically, model synthetic oligonucleotides were used to examine methylation of single-stranded oligonucleotides, annealed oligonucleotide duplexes, RNA–DNA heteroduplexes, DNA bubbles and R-loops. Dnmt methylation activity on the model substrates was quantified with initial velocity assays, novel ARORA (annealed RNA and DNA oligonucleotide-based methylation-sensitive restriction enzyme analysis), tBS (tagged-bisulfite sequencing) and the quantitative PCR-based method MethylQuant. We found that RNA–DNA heteroduplexes and R-loops are poor substrates for methylation by both the maintenance (Dnmt1) and de novo (Dnmt3a and Dnmt3b) Dnmts. These results suggest the proposed RNA/DNA model of TGS in mammals is unlikely. Analysis of tagged-bisulfite genomic sequencing led to the unexpected observation that Dnmt1-dN can methylate cytosines in a non-CpG context in DNA bubbles. This may have relevance in DNA replication and silencing of transcriptionally active loci in vivo.
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33

Jeon, Jae-Hyung, and Wokyung Sung. "How Topological Constraints Facilitate Growth and Stability of Bubbles in DNA." Biophysical Journal 95, no. 8 (2008): 3600–3605. http://dx.doi.org/10.1529/biophysj.108.132258.

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34

THEODORAKOPOULOS, NIKOS. "BUBBLES, CLUSTERS AND DENATURATION IN GENOMIC DNA: MODELING, PARAMETRIZATION, EFFICIENT COMPUTATION." Journal of Nonlinear Mathematical Physics 18, sup2 (2011): 429–47. http://dx.doi.org/10.1142/s1402925111001611.

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35

McCauley, Micah J., Ioulia Rouzina, and Mark C. Williams. "Bubbles, Free Ends and the Kinetics of Force-Induced DNA Melting." Biophysical Journal 102, no. 3 (2012): 176a. http://dx.doi.org/10.1016/j.bpj.2011.11.957.

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36

Якушевич, Л. В., та L. V. Yakushevich. "Траектории кинков ДНК в последовательностях, содержащих кодирующие области генов". Mathematical Biology and Bioinformatics 12, № 1 (2017): 1–13. http://dx.doi.org/10.17537/2017.12.1.

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Coding regions (CDS) being an integral part of any gene sequence, play an important role in the process of transcription. One of the tasks associated with the CDS regions, consists in the modeling of the passage of transcription bubbles named also open states or DNA kinks through the coding regions. In this paper, we present a simple and convenient approach to the modeling of the passage. It includes the calculation of the energy profile of the sequence and reducing the initial task to the modeling of the movement of a quasi particle in the field with this energy profile. To illustrate the method, we present the results of the calculations of the trajectories of the DNA kinks moving in the sequence of gene coding interferon alpha 17 (IFNA17) that consists of the three regions: the coding region and the two regions with unknown functional properties. To analyze the kink dynamics, we apply approximation where the DNA parameters are being averaged separately over each of the three regions. In the absences of dissipation, the total kink energy is constant. At the same time the kink velocity is constant only inside each of the regions. In the presence of dissipation, the total kink energy decreases. It is shown that the greater the total initial energy of the kink, the faster the energy decrease. It is suggested that the proposed approach could be useful in finding the ways to govern the movement of transcription bubbles at the first stage of the process of transcription.
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37

King, G. A., P. Gross, U. Bockelmann, M. Modesti, G. J. L. Wuite, and E. J. G. Peterman. "Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy." Proceedings of the National Academy of Sciences 110, no. 10 (2013): 3859–64. http://dx.doi.org/10.1073/pnas.1213676110.

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38

King, Graeme A., Peter Gross, Ulrich Bockelmann, Mauro Modesti, Gijs J. L. Wuite, and Erwin J. G. Peterman. "Revealing the Competition between Peeled-Ssdna, Melting Bubbles and S-DNA during DNA Overstretching using Fluorescence Microscopy." Biophysical Journal 104, no. 2 (2013): 262a. http://dx.doi.org/10.1016/j.bpj.2012.11.1472.

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39

Kobayashi, Takehiko, Theo Rein, and Melvin L. DePamphilis. "Identification of Primary Initiation Sites for DNA Replication in the Hamster Dihydrofolate Reductase Gene Initiation Zone." Molecular and Cellular Biology 18, no. 6 (1998): 3266–77. http://dx.doi.org/10.1128/mcb.18.6.3266.

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ABSTRACT Mammalian replication origins appear paradoxical. While some studies conclude that initiation occurs bidirectionally from specific loci, others conclude that initiation occurs at many sites distributed throughout large DNA regions. To clarify this issue, the relative number of early replication bubbles was determined at 26 sites in a 110-kb locus containing the dihydrofolate reductase (DHFR)-encoding gene in CHO cells; 19 sites were located within an 11-kb sequence containing ori-β. The ratio of ∼0.8-kb nascent DNA strands to nonreplicated DNA at each site was quantified by competitive PCR. Nascent DNA was defined either as DNA that was labeled by incorporation of bromodeoxyuridine in vivo or as RNA-primed DNA that was resistant to λ-exonuclease. Two primary initiation sites were identified within the 12-kb region, where two-dimensional gel electrophoresis previously detected a high frequency of replication bubbles. A sharp peak of nascent DNA occurred at the ori-β origin of bidirectional replication where initiation events were 12 times more frequent than at distal sequences. A second peak occurred 5 kb downstream at a previously unrecognized origin (ori-β′). Thus, the DHFR gene initiation zone contains at least three primary initiation sites (ori-β, ori-β′, and ori-γ), suggesting that initiation zones in mammals, like those in fission yeast, consist of multiple replication origins.
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40

Kawazu, Takeshi, Kazumi Hakamada, Yusuke Oda, Jun Miyake, Kazuo Maruyama, and Takeshi Nagasaki. "Ultrasound-mediated Transfection with Liposomal Bubbles Delivers Plasmid DNA Directly into Nucleus." Chemistry Letters 40, no. 3 (2011): 298–99. http://dx.doi.org/10.1246/cl.2011.298.

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41

Hennig, D. "Formation and propagation of oscillating bubbles in DNA initiated by structural distortions." European Physical Journal B - Condensed Matter 37, no. 3 (2003): 391–97. http://dx.doi.org/10.1140/epjb/e2004-00071-7.

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42

Kalejta, R. F., H. B. Lin, P. A. Dijkwel, and J. L. Hamlin. "Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques." Molecular and Cellular Biology 16, no. 9 (1996): 4923–31. http://dx.doi.org/10.1128/mcb.16.9.4923.

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Using neutral/neutral and neutral/alkaline two-dimensional (2-D) gel techniques, we previously obtained evidence that initiation can occur at any of a large number of sites distributed throughout a broad initiation zone in the dihydrofolate reductase (DHFR) domain of Chinese hamster ovary (CHO) cells. However, other techniques have suggested a much more circumscribed mode of initiation in this locus. This dichotomy has raised the issue whether the patterns of replicating DNA on 2-D gels have been misinterpreted and, in some cases, may represent such noncanonical replication intermediates as broken bubbles or microbubbles. In an accompanying study (R. F. Kalejta and J. L. Hamlin, Mol. Cell. Biol. 16:4915-4922, 1996), we have shown that broken bubbles migrate to unique positions in three different gel systems and therefore are not likely to be confused with classic replication intermediates. Here, we have applied a broken bubble assay developed from that study to an analysis of the amplified DHFR locus in CHO cells. This assay gives information about the number and positions of initiation sites within a fragment. In addition, we have analyzed the DHFR locus by a novel stop-and-go-alkaline gel technique that measures the size of nascent strands at all positions along each arc in a neutral/neutral 2-D gel. Results of these analyses support the view that the 2-D gel patterns previously assigned to classic, intact replication bubbles and single-forked structures indeed correspond to these entities. Furthermore, potential nascent-strand start sites appear to be distributed at very frequent intervals along the template in the intergenic region in the DHFR domain.
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43

Lin, Jinzhong, Yulong Shen, Jinfeng Ni, and Qunxin She. "A type III-A CRISPR–Cas system mediates co-transcriptional DNA cleavage at the transcriptional bubbles in close proximity to active effectors." Nucleic Acids Research 49, no. 13 (2021): 7628–43. http://dx.doi.org/10.1093/nar/gkab590.

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Abstract Many type III CRISPR–Cas systems rely on the cyclic oligoadenylate (cOA) signaling pathway to exert immunization. However, LdCsm, a type III-A lactobacilli immune system mediates efficient plasmid clearance in spite of lacking cOA signaling. Thus, the system provides a good model for detailed characterization of the RNA-activated DNase in vitro and in vivo. We found ATP functions as a ligand to enhance the LdCsm ssDNase, and the ATP enhancement is essential for in vivo plasmid clearance. In vitro assays demonstrated LdCsm cleaved transcriptional bubbles at any positions in non-template strand, suggesting that DNA cleavage may occur for transcribing DNA. Destiny of target plasmid versus nontarget plasmid in Escherichia coli cells was investigated, and this revealed that the LdCsm effectors mediated co-transcriptional DNA cleavage to both target and nontarget plasmids, suggesting LdCsm effectors can mediate DNA cleavage to any transcriptional bubbles in close proximity upon activation. Subcellular locations of active LdCsm effectors were then manipulated by differential expression of LdCsm and CTR, and the data supported the hypothesis. Strikingly, stepwise induction experiments indicated allowing diffusion of LdCsm effector led to massive chromosomal DNA degradation, suggesting this unique IIIA system can facilitate infection abortion to eliminate virus-infected cells.
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44

Zhang, X., H. Chen, S. Le, I. Rouzina, P. S. Doyle, and J. Yan. "Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry." Proceedings of the National Academy of Sciences 110, no. 10 (2013): 3865–70. http://dx.doi.org/10.1073/pnas.1213740110.

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45

Kamath-Loeb, Ashwini S., Jiang-Cheng Shen, Michael W. Schmitt та Lawrence A. Loeb. "The Werner Syndrome Exonuclease Facilitates DNA Degradation and High Fidelity DNA Polymerization by Human DNA Polymerase δ". Journal of Biological Chemistry 287, № 15 (2012): 12480–90. http://dx.doi.org/10.1074/jbc.m111.332577.

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DNA Polymerase δ (Pol δ) and the Werner syndrome protein, WRN, are involved in maintaining cellular genomic stability. Pol δ synthesizes the lagging strand during replication of genomic DNA and also functions in the synthesis steps of DNA repair and recombination. WRN is a member of the RecQ helicase family, loss of which results in the premature aging and cancer-prone disorder, Werner syndrome. Both Pol δ and WRN encode 3′ → 5′ DNA exonuclease activities. Pol δ exonuclease removes 3′-terminal mismatched nucleotides incorporated during replication to ensure high fidelity DNA synthesis. WRN exonuclease degrades DNA containing alternate secondary structures to prevent formation and enable resolution of stalled replication forks. We now observe that similarly to WRN, Pol δ degrades alternate DNA structures including bubbles, four-way junctions, and D-loops. Moreover, WRN and Pol δ form a complex with enhanced ability to hydrolyze these structures. We also present evidence that WRN can proofread for Pol δ; WRN excises 3′-terminal mismatches to enable primer extension by Pol δ. Consistent with ourin vitroobservations, we show that WRN contributes to the maintenance of DNA synthesis fidelityin vivo. Cells expressing limiting amounts (∼10% of normal) of WRN have elevated mutation frequencies compared with wild-type cells. Together, our data highlight the importance of WRN exonuclease activity and its cooperativity with Pol δ in preserving genome stability, which is compromised by the loss of WRN in Werner syndrome.
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46

Heck, M. M., and A. C. Spradling. "Multiple replication origins are used during Drosophila chorion gene amplification." Journal of Cell Biology 110, no. 4 (1990): 903–14. http://dx.doi.org/10.1083/jcb.110.4.903.

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DNA from Drosophila egg chambers undergoing chorion gene amplification was analyzed using the two-dimensional gel technique of Brewer and Fangman. At stage 10, 34% of DNA molecules from the maximally amplified region of the third chromosome chorion gene cluster contained replication forks or bubbles. These nonlinear forms were intermediates in the process of amplification; they were confined to follicle cells, and were found only within the replicating region during the time of amplification. Multiple origins gave rise to these intermediates, since three separate regions of the third chromosome chorion locus contained replication bubbles. However, initiation was nonrandom; the majority of initiations appeared to occur near the Bgl II site located between the s18 and s15 chorion genes. The P[S6.9] chorion transposon also contained abundant replication intermediates in follicle cells from a transformed line. Initiation within P[S6.9] occurred near two previously defined cis-regulatory elements, one near the same Bgl II site (in the AER-d region) and one near the ACE3 element.
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47

Szambowska, Anna, Ingrid Tessmer, Petri Kursula, et al. "DNA binding properties of human Cdc45 suggest a function as molecular wedge for DNA unwinding." Nucleic Acids Research 42, no. 4 (2013): 2308–19. http://dx.doi.org/10.1093/nar/gkt1217.

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Abstract The cell division cycle protein 45 (Cdc45) represents an essential replication factor that, together with the Mcm2-7 complex and the four subunits of GINS, forms the replicative DNA helicase in eukaryotes. Recombinant human Cdc45 (hCdc45) was structurally characterized and its DNA-binding properties were determined. Synchrotron radiation circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering and atomic force microscopy revealed that hCdc45 exists as an alpha-helical monomer and possesses a structure similar to its bacterial homolog RecJ. hCdc45 bound long (113-mer or 80-mer) single-stranded DNA fragments with a higher affinity than shorter ones (34-mer). hCdc45 displayed a preference for 3′ protruding strands and bound tightly to single-strand/double-strand DNA junctions, such as those presented by Y-shaped DNA, bubbles and displacement loops, all of which appear transiently during the initiation of DNA replication. Collectively, our findings suggest that hCdc45 not only binds to but also slides on DNA with a 3′–5′ polarity and, thereby acts as a molecular ‘wedge’ to initiate DNA strand displacement.
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48

Rieloff, Ellen, Sandra C. C. Nunes, Alberto A. C. C. Pais, and Marie Skepö. "Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study." ACS Omega 2, no. 5 (2017): 1915–21. http://dx.doi.org/10.1021/acsomega.7b00323.

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49

Wu, Weimin, William W. Newcomb, Naiqian Cheng, Anastasia Aksyuk, Dennis C. Winkler, and Alasdair C. Steven. "Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging." Journal of Virology 90, no. 10 (2016): 5176–86. http://dx.doi.org/10.1128/jvi.03224-15.

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ABSTRACTThe herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids—which develop into infectious virions—are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled.IMPORTANCEIn addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
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50

A., Abraham. "INTRODUCING IN VITRO EXPERIMENTS OF OXYGEN BUBBLES SHOCKWAVES TRIGGERING INTRACELLULAR LIPIDS LUMINESCENCE: IMPLICATIONS IN CANCER ETIOLOGY." International Journal of Research -GRANTHAALAYAH 7, no. 4 (2019): 355–64. http://dx.doi.org/10.29121/granthaalayah.v7.i4.2019.921.

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Background
 The main purpose of this manuscript is to introduce a mechanism supporting a previously hypothesized factor in cancer origin, where endogenous energy emission during cell respiration was identified as additional factor in cancer origin. Recent published reports identify the pressure profile of shockwaves as causing lipid droplets membrane deformation. Lipid metabolism has been highlighted to have a key role in cancer metabolism, and metastasis; for example, several publications have suggested targeting lipid metabolism of cancer cells as a strategy to control metastasis. New studies have revealed that lipid layers are responsible for the storage and discharge of static electricity. This manuscript introduces shockwaves from oxygen bubbles bursts as a mechanism causing intracellular lipids discharge or static electricity. The effect causes shape changes of lipid droplets up to a light emission stage.
 Materials and Methods
 Cheek cells intracellular material, including DNA strands and lipid droplets were precipitated in a test tube by following written instructions on DNA precipitation published online by The University of Michigan. The DNA precipitate was transferred onto a clean glass slide and covered by a similar one and dubbed a sandwich (SDW). A slide assembly was developed where the effect of oxygen bubbles cavitation-induced shockwaves on the trapped DNA precipitate and lipid droplets were recorded. Microphotographs and video recordings were stored in a computer via a video-microscope.
 Results
 Lipid droplets exposed to prolonged shockwaves energy were documented to undergo recurrent expanding architectural deformation up to a final contracting phase where light was emitted. 
 Conclusions
 Intracellular lipid droplets are ubiquitously present in cells; and recent research has shown their expanded roles in cellular signaling in both mitotic and non-mitotic cells. In cancer, one highlighted key role is the potential of lipid metabolism in metastatic colonization. Data introduced in this manuscript demonstrates a direct consequence of ROS (H2O2) decomposition (via oxygen bubbles bursts) as a trigger for lipid intracellular droplets emission of light radiation, thus supporting a previously proposed biophysical mechanism in cancer origin.
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