Interactions of H1 and H5 histones with polynucleotides of B- and Z-DNA conformations

Casilda V. Mura; B. David Stollar

doi:10.1021/bi00320a039

ALU non-B-DNA conformations, flipons, binary codes and evolution

Royal Society Open Science ◽

10.1098/rsos.200222 ◽

2020 ◽

Vol 7 (6) ◽

pp. 200222 ◽

Cited By ~ 2

Author(s):

Alan Herbert

Keyword(s):

Dna Damage ◽

Epigenetic Modification ◽

Rapid Change ◽

Sequence Motifs ◽

Alu Elements ◽

Evolutionary Innovation ◽

Alu Insertion ◽

Alu Sequence ◽

Dna Conformations ◽

Z Dna

ALUs contribute to genetic diversity by altering DNA's linear sequence through retrotransposition, recombination and repair. ALUs also have the potential to form alternative non-B-DNA conformations such as Z-DNA, triplexes and quadruplexes that alter the read-out of information from the genome. I suggest here these structures enable the rapid reprogramming of cellular pathways to offset DNA damage and regulate inflammation. The experimental data supporting this form of genetic encoding is presented. ALU sequence motifs that form non-B-DNA conformations under physiological conditions are called flipons. Flipons are binary switches. They are dissipative structures that trade energy for information. By efficiently targeting cellular machines to active genes, flipons expand the repertoire of RNAs compiled from a gene. Their action greatly increases the informational capacity of linearly encoded genomes. Flipons are programmable by epigenetic modification, synchronizing cellular events by altering both chromatin state and nucleosome phasing. Different classes of flipon exist. Z-flipons are based on Z-DNA and modify the transcripts compiled from a gene. T-flipons are based on triplexes and localize non-coding RNAs that direct the assembly of cellular machines. G-flipons are based on G-quadruplexes and sense DNA damage, then trigger the appropriate protective responses. Flipon conformation is dynamic, changing with context. When frozen in one state, flipons often cause disease. The propagation of flipons throughout the genome by ALU elements represents a novel evolutionary innovation that allows for rapid change. Each ALU insertion creates variability by extracting a different set of information from the neighbourhood in which it lands. By elaborating on already successful adaptations, the newly compiled transcripts work with the old to enhance survival. Systems that optimize flipon settings through learning can adapt faster than with other forms of evolution. They avoid the risk of relying on random and irreversible codon rewrites.

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The Effect of the B and Z DNA Conformations on the Introduction of Photodynamic Damage

BioScience ◽

10.2307/1309355 ◽

1983 ◽

Vol 33 (11) ◽

pp. 715-716

Author(s):

Ross S. Feldberg ◽

Caroline Brown ◽

Josephine A. Carew ◽

Judith L. Lucas

Keyword(s):

Dna Conformations ◽

Z Dna

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Base dynamics of local Z-DNA conformations as detected by electron paramagnetic resonance with spin-labeled deoxycytidine analogs

Biochemistry ◽

10.1021/bi00489a003 ◽

1990 ◽

Vol 29 (37) ◽

pp. 8522-8528 ◽

Cited By ~ 18

Author(s):

Oliver K. Strobel ◽

Robert S. Keyes ◽

Albert M. Bobst

Keyword(s):

Electron Paramagnetic Resonance ◽

Paramagnetic Resonance ◽

Dna Conformations ◽

Z Dna ◽

Electron Paramagnetic

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PROBING PHOTODYNAMIC DAMAGE IN NUCLEIC ACIDS WITH A DAMAGE-SPECIFIC DNA BINDING PROTEIN: A COMPARISON OF THE B and Z DNA CONFORMATIONS

Photochemistry and Photobiology ◽

10.1111/j.1751-1097.1983.tb04511.x ◽

1983 ◽

Vol 37 (5) ◽

pp. 521-524 ◽

Cited By ~ 7

Author(s):

Ross S. Feldberg ◽

Caroline Brown ◽

Josephine A. Carew ◽

Judith L. Lucas

Keyword(s):

Dna Binding ◽

Nucleic Acids ◽

Binding Protein ◽

Protein A ◽

Dna Binding Protein ◽

Dna Conformations ◽

Z Dna

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Microdosimetry of DNA conformations: relation between direct effect of 60Co gamma rays and topology of DNA geometrical models in the calculation of A-, B- and Z-DNA radiation-induced damage yields

Radiation and Environmental Biophysics ◽

10.1007/s00411-016-0644-7 ◽

2016 ◽

Vol 55 (2) ◽

pp. 243-254 ◽

Cited By ~ 1

Author(s):

Farid Semsarha ◽

Gholamreza Raisali ◽

Bahram Goliaei ◽

Hossein Khalafi

Keyword(s):

Direct Effect ◽

Gamma Rays ◽

And Topology ◽

Dna Conformations ◽

60Co Gamma ◽

Radiation Induced ◽

60Co Gamma Rays ◽

Z Dna

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An electron paramagnetic resonance probe to detect local Z-DNA conformations

Biochemical and Biophysical Research Communications ◽

10.1016/0006-291x(90)91027-p ◽

1990 ◽

Vol 166 (3) ◽

pp. 1435-1440 ◽

Cited By ~ 8

Author(s):

Oliver K. Strobel ◽

Robert S. Keyes ◽

Albert M. Bobst

Keyword(s):

Electron Paramagnetic Resonance ◽

Paramagnetic Resonance ◽

Dna Conformations ◽

Z Dna ◽

Electron Paramagnetic

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Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004714004684 ◽

2014 ◽

Vol 70 (7) ◽

pp. 1790-1800 ◽

Cited By ~ 18

Author(s):

Zhipu Luo ◽

Miroslawa Dauter ◽

Zbigniew Dauter

Keyword(s):

Data Sets ◽

Ultrahigh Resolution ◽

Dna Oligomers ◽

Structure Solution ◽

Dna Conformations ◽

Anomalous Signal ◽

Z Dna ◽

High Level ◽

Dna Dodecamer ◽

Phosphate Groups

A large number of Z-DNA hexamer duplex structures and a few oligomers of different lengths are available, but here the first crystal structure of the d(CGCGCGCGCGCG)2dodecameric duplex is presented. Two synchrotron data sets were collected; one was used to solve the structure by the single-wavelength anomalous dispersion (SAD) approach based on the anomalous signal of P atoms, the other set, extending to an ultrahigh resolution of 0.75 Å, served to refine the atomic model to anRfactor of 12.2% and anRfreeof 13.4%. The structure consists of parallel duplexes arranged into practically infinitely long helices packed in a hexagonal fashion, analogous to all other known structures of Z-DNA oligomers. However, the dodecamer molecule shows a high level of flexibility, especially of the backbone phosphate groups, with six out of 11 phosphates modeled in double orientations corresponding to the two previously observed Z-DNA conformations: ZI, with the phosphate groups inclined towards the inside of the helix, and ZII, with the phosphate groups rotated towards the outside of the helix.

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