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61.
  • Doglia, S. M., et al. (författare)
  • QUINACRINE - SPECTROSCOPIC PROPERTIES AND INTERACTIONS WITH POLYNUCLEOTIDES
  • 1993
  • Ingår i: Biopolymers. - : Wiley. - 0006-3525 .- 1097-0282. ; 33:9, s. 1431-1442
  • Tidskriftsartikel (refereegranskat)abstract
    • The acridine dye quinacrine and its interactions with calf thymus DNA, poly(dA-dT).poly(dA-dT), and poly(dG-dC).poly(dG-dC) were studied by light absorption, linear dichroism, and fluorescence spectroscopy. The transition moments of quinacrine give rise to absorption bands polarized along the short axis (400-480-nm band), and the long axis (345-nm and 290-nm bands) of the molecule, respectively. Linear dichroism studies show that quinacrine intercalates into calf thymus DNA as well as into the polynucleotides, displaying fairly homogeneous binding to poly (dA-dT).poly(dA-dT), but more than one type of intercalation site for calf thymus DNA and poly(dG-dC).poly(dG-dC). Fluorescence spectroscopy shows that for free quinacrine the pK = 8.1 between the mono- and diprotonated states also remains unchanged in the excited state. Quinacrine bound to calf thymus DNA and polynucleotides exhibits light absorption typical for the intercalated diprotonated form. The fluorescence enhancement of quinacrine bound to poly (dA-dT).poly(dA-dT) may be due to shielding from water interactions involving transient H-bond formation. The fluorescence quenching in poly (dG-dC).poly (dG-dC) may be due to excited state electron transfer from guanine to quinacrine. (C) 1993 John Wiley & Sons, Inc.
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62.
  • Egholm, M., et al. (författare)
  • PNA HYBRIDIZES TO COMPLEMENTARY OLIGONUCLEOTIDES OBEYING THE WATSON-CRICK HYDROGEN-BONDING RULES
  • 1993
  • Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 365:6446, s. 566-568
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA ANALOGUES are currently being intensely investigated owing to their potential as gene-targeted drugs1-3. Furthermore, their properties and interaction with DNA and RNA could provide a better understanding of the structural features of natural DNA that determine its unique chemical, biological and genetic properties3,4. We recently designed a DNA analogue, PNA, in which the backbone is structurally homomorphous with the deoxyribose backbone and consists of N-(2-aminoethyl)glycine units to which the nucleobases are attached5-9. We showed that PNA oligomers containing solely thymine and cytosine can hybridize to complementary oligonucleotides, presumably by forming Watson-Crick-Hoogsteen (PNA)2-DNA triplexes, which are much more stable than the corresponding DNA-DNA duplexes5-7, and bind to double-stranded DNA by strand displacement5,8. We report here that PNA containing all four natural nucleobases hybridizes to complementary oligonucleotides obeying the Watson-Crick base-pairing rules, and thus is a true DNA mimic in terms of base-pair recognition.
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63.
  • Ellouze, C., et al. (författare)
  • Difference between active and inactive nucleotide cofactors in the effect of DNA binding and the helical structure of RecA filament
  • 1999
  • Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 262:1, s. 88-94
  • Tidskriftsartikel (refereegranskat)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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64.
  • Ellouze, C., et al. (författare)
  • Dissociation of non-complementary second DNA strand from RecA filament without ATP hydrolysis: mechanism of the search for homologous DNA
  • 1997
  • Ingår i: Journal of Biochemistry. - 0021-924X. ; 121:6, s. 1070-1075
  • Tidskriftsartikel (refereegranskat)abstract
    • RecA protein catalyzes the DNA annealing and mimics the DNA strand exchange reaction in vitro in the presence of ATP or its non-hydrolyzable analog, adenosine 5'-O-3-thiotriphosphate (ATP gamma S). For these activities RecA coordinates two DNA molecules [Takahashi, M. and Norden, B. (1994) Adv. Biophys, 30, 1-35]. In order to get a better understanding of how RecA performs the search for sequence complementarity or homology between two DNA molecules, the association and dissociation kinetics oa second DNA molecule to and from RecA in the presence of ATP gamma S have been investigated, The kinetics were monitored by fluorescence measurements of partly etheno-modified poly(dA) assisted by linear dichroism measurements of the flow-oriented complex. The association of the second DNA is fast;, regardless of whether the sequence is complementary or not. Bg contrast, the dissociation kinetics is strongly dependent on sequence complementarity, If the second DNA is complementary to the first, dissociation is extremely slow, whilst that of non-complementary second DNA is fast, In no case does the first DNA leave the RecA fiber, Our findings indicate that the dissociation step is important in the search for homology by RecA.
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65.
  • Ellouze, C., et al. (författare)
  • Evidence for Elongation of the Helical Pitch of the RecA Filament Upon ATP and ADP Binding Using Small-Angle Neutron Scattering
  • 1995
  • Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 233:2, s. 579-583
  • Tidskriftsartikel (refereegranskat)abstract
    • Structural changes of the RecA filament upon binding of cofactors have been investigated by small-angle neutron scattering. Both ATP and ADP increased the helical pitch of the RecA homopolymer, which is observed to be 7 nm in the absence of any cofactor. The binding of ATP altered the pitch to 9 nm, whereas the binding of ADP only produced a pitch of 8.2 nm. The pitch determined for the RecA complex with the ATP analog adenosine 5'-[gamma-thio]triphosphate was similar to that found with ATP. Thus, at least three, somewhat different, RecA helical filamentous structures may form in solution. The binding of DNA to RecA did not alter the pitch significantly, indicating that the cofactor binding is the determining factor for the size of the helical pitch of the RecA filament. We also found that elongation of the helical pitch is a necessary, but not a sufficient condition, for the coprotease activity of RecA. The presence of acetate or glutamate ions is also required. The pitch of the ADP . RecA filament is in agreement with that found in the crystal structure. This correlation indicates that this structure corresponds to that of the ADP . RecA filament in solution, although this is not the species active in recombination.
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66.
  • Ellouze, C., et al. (författare)
  • Nucleotide Cofactor-Dependent Structural Change of Xenopus laevis Rad51 Protein Filament Detected by Small-Angle Neutron Scattering Measurements in Solution
  • 1997
  • Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 36:44, s. 13524-13529
  • Tidskriftsartikel (refereegranskat)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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67.
  • Engman, Cecilia, 1974, et al. (författare)
  • DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
  • 2004
  • Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 32:17, s. 5087-95
  • Tidskriftsartikel (refereegranskat)abstract
    • The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.
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68.
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