| 1. |
- Carmona-Gutierrez, D., et al.
(author)
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Guidelines and recommendations on yeast cell death nomenclature
- 2018
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In: Microbial Cell. - : Shared Science Publishers OG. - 2311-2638. ; 5:1, s. 4-31
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Research review (peer-reviewed)abstract
- Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research.
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| 2. |
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| 3. |
- Choi, S. D., et al.
(author)
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Binding Mode of [Ruthenium(II) (1,10-Phenanthroline)2L]2+ with Poly(dT*dA-dT) Triplex. Ligand Size Effect on Third-Strand Stabilization
- 1997
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In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:1, s. 214-223
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Journal article (peer-reviewed)abstract
- The binding of homochiral [Ru(II)(1,10-phenanthroline)(2)L](2+) complexes {where L = 1,10-phenanthroline (phen), dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) or benzodipyrido[3,2-a:2',3'-c]phenazine (BDPPZ)} to poly(dT*dA-dT) triplex has been investigated by linear and circular dichroism and thermal denaturation. Analysis of the linear dichroism spectra indicates that the extended DPPZ and BDPPZ ligands lie approximately parallel to the base-pair and base-tripler planes consistent with intercalation which is also supported by strong hypochromism in the interligand absorption bands with either duplex or tripler. The spectral properties of any of the metal complex enantiomers were similar for binding to either duplex or tripler DNA, indicating that the third strand, which occupies the major groove of the template duplex, has little effect on the binding geometries and hence supports the hypothesis that the metal complexes all bind from the minor groove with the DPPZ and BDPPZ ligands intercalated but without intercalation in the case of [Ru(phen)(3)](2+). Third-strand stabilization depended on the nature of the third substituted phenanthroline chelate ligand but was not directly related to its size, with stabilizing power increasing in the order phen
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| 4. |
- Coates, C. G., et al.
(author)
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Picosecond time-resolved resonance Raman probing of the light-switch states of Ru(Phen)(2)dppz (2+)
- 2001
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 105:50, s. 12653-12664
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Journal article (peer-reviewed)abstract
- Picosecond time-resolved resonance Raman (picosecond-TR3) spectroscopy has been used to conduct an extensive photophysical characterization of the light- switch complex [Ru(phen)(2)dppz](2+) as a function of environment, in which studies have been carried out in aqueous and nonaqueous media and in DNA. The results are considered in rotation to a previous report describing environment-sensitive lowest triplet MLCT states. Vibrational marker features and enhancement patterns were used to determine the rapid progression (< 20 ps) between two triplet MLCT states in aqueous environment, followed by subnanosecond, nonradiative deactivation to the ground state. In nonaqueous environment, the long-lived, emissive triplet MLCT state is spectrally identified as the short-lived first triplet MLCT state observed in water, in agreement with the earlier proposed mechanism. The present data are shown to correlate well with previous nanosecond RR findings for the complex in each environment. Interestingly, a precursor state has been identified upon excitation in both nonaqueous solvent and in DNA, which precedes the triplet MLCT state, and the lifetime of which appears to be environment dependent. Observation of this state is discussed in relation to other recent femtosecond spectroscopic studies on this complex.
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| 5. |
- Ellouze, C., et al.
(author)
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Difference between active and inactive nucleotide cofactors in the effect of DNA binding and the helical structure of RecA filament
- 1999
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In: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 262:1, s. 88-94
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Journal article (peer-reviewed)abstract
- The RecA protein requires ATP or dATP for its coprotease and strand exchange activities. Other natural nucleotides, such as ADP, CTP, GTP, UTP and TTP, have little or no activation effect on RecA for these activities. We have investigated the activation mechanism, and the selectivity for ATP, by studying the effect of various nucleotides on the DNA binding and the helical structure of the RecA filament. The interaction with DNA was investigated via fluorescence measurements with a fluorescent DNA analog and fluorescein-labeled oligonucleotides, assisted by linear dichroism. Filament structure was investigated via small-angle neutron scattering. There is no simple correlation between filament elongation, DNA binding affinity of RecA, and DNA structure in the RecA complex. There may be multiple conformations of RecA, Both coprotease and strand exchange activities require formation of a rigid and well organized complex. The triphosphate nucleotides which do not activate RecA, destabilize the RecA-DNA complex, indicating that the chemical nature of the nucleotide nucleobase is very important for the stability of RecA-DNA complex. Higher stability of the RecA-DNA complex in the presence of adenosine 5'-O-3-thiotriphosphate or guanosine 5'-O-3-thiotriphosphate than ATP or GTP indicates that contact between the protein and the chemical group at the gamma position of the nucleotide also affects the stability of the RecA-DNA complex. This contact appears also important for the rigid organization of DNA because ADP strongly decreases the rigidity of the complex.
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| 6. |
- Ellouze, C., et al.
(author)
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Nucleotide Cofactor-Dependent Structural Change of Xenopus laevis Rad51 Protein Filament Detected by Small-Angle Neutron Scattering Measurements in Solution
- 1997
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In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:44, s. 13524-13529
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Journal article (peer-reviewed)abstract
- Rad51 protein, a eukaryotic homologue of RecA protein, forms a filamentous complex with DNA and catalyzes homologous recombination. We have analyzed the structure of Xenopus Rad51 protein (XRad51.1) in solution by small-angle neutron scattering (SANS). The measurements showed that XRad51.1 forms a helical filament independently of DNA. The sizes of the cross-sectional and helical pitch of the filament could be determined, respectively, from a Guinier plot and the position of the subsidiary maximum of SANS data. We observed that the helical structure is modified by nucleotide binding as in the case of RecA. Upon ATP binding under high-salt conditions (600 mM NaCl), the helical pitch of XRad51.1 filament was increased from 8 to 10 nm and the cross-sectional diameter decreased from 7 to 6 nm. The pitch sizes of XRad51.1 are similar to, though slightly larger than, those of RecA filament under corresponding conditions. A similar helical pitch size was observed by electron microscopy for budding yeast Rad51 [Ogawa, T., et al. (1993) Science 259, 1896-1899]. In contrast to the RecA filament, the structure of XRad51.1 filament with ADP is not significantly different from that with ATP. Thus, the hydrolysis of ATP to ADP does not modify the helical filament of XRad51.1. Together with our recent observation that ADP does not weaken the XRad51.1/DNA interaction, the effect of ATP hydrolysis on XRad51.1 nucleofilament should be very different from that on RecA.
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| 7. |
- Tuite, Eimer, 1966, et al.
(author)
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Effects of intercalators on complexation of RecA with duplex DNA
- 1995
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In: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 34:50, s. 16365-16374
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Journal article (peer-reviewed)abstract
- To elucidate the binding mode of recombination protein A (RecA) to double-stranded (ds) DNA, the effects on the RecA-DNA interaction of several mono- and bisintercalators of the acridine, phenanthridine, and cyanine classes have been investigated by linear dichroism spectroscopy. Simple monointercalators lacking side chains efficiently promoted the binding of RecA to dsDNA in the absence of nucleotide cofactor, which is otherwise required. Bisintercalators varied in their ability to induce RecA binding, while monointercalators with aminoalkyl side chains proved inefficient. Modification of DNA structure by the intercalator appears to be necessary for induction of RecA binding, but if the intercalator has a bulky minor-groove-binding side chain, it does not induce RecA binding. In detailed studies with acridines, neither the binding geometry of intercalators nor the structure of DNA was significantly modified upon binding of RecA without cofactor. Judged by circular dichroism, similar ReA conformational changes accompanied bis-9-aminoacridine- and ATPyS-induced RecA association with DNA. In the presence of ATPyS, the intercalators inhibited the rate of RecA binding to dsDNA and were extruded from DNA upon binding of RecA. This competitive aspect may suggest that intercalation of some amino acid residue(s) plays a role in nucleotide-induced RecA binding. The stoichiometry of the RecA-DNA-intercalator filament was determined; in the fully formed filament the base pair:intercalator ratio is 2, and the base pair:RecA ratio also 2. This contrasts with a base pair:RecA ratio of 3 in the ATPyS-induced filament, although in both cases the DNA experiences 50% extension.
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| 8. |
- Tuite, Eimer, 1966, et al.
(author)
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Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism
- 1997
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In: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 243:1-2, s. 482-492
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Journal article (peer-reviewed)abstract
- Linear and circular dichroic spectroscopies have been employed to investigate the effects of small DNA ligands on the interactions of two proteins which bind to the minor groove of DNA, viz. RecA protein from Escherichia coli and deoxyribonuclease I (bovine pancreas). Ligands representing three specific non-covalent binding modes were investigated: 4',6-diamidino-2-phenylindole and distamycin A (minor groove binders), methyl green (major groove binder), and methylene blue, ethidium bromide and ethidium dimer (intercalators). Linear dichroism was demonstrated to be an excellent detector, in real time, of DNA double-strand cleavage by deoxyribonuclease I. Ligands bound in all three modes interfered with the deoxyribonuclease I digestion of dsDNA, although the level of interference varied in a manner which could be related to the ligand binding site, the ligand charge appearing to be less important. In particular, the retardation of deoxyribonuclease I cleavage by the major groove binder methyl green demonstrates that accessibility to the minor groove can be affected by occupancy of the opposite groove. Binding of all three types of ligand also had marked effects on the interaction of RecA with dsDNA in the presence of non-hydrolyzable cofactor adenosine 5'-O-3-thiotriphosphate, decreasing the association rate to varying extents but with the strongest effects from ligands having some minor groove occupancy. Finally, each ligand was displaced from its DNA binding site upon completion of RecA association, again demonstrating that modification of either groove can affect the properties and behaviour of the other. The conclusions are discussed against the background of previous work on the use of small DNA ligands to probe DNA-protein interactions.
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