Control and observation of DNA nanodevices

The uniquely predictable and controllable binding mechanism of DNA strands has been exploited to construct a vast range of synthetic nanodevices, capable of autonomous motion and computation. This thesis proposes novel ideas for the control and observation of such devices. The first of these proposals hinges on introducing mismatched base pairs into toehold-mediated strand displacement – a fundamental primitive in most dynamic DNA devices and reaction networks. Previous findings that such mismatches can impede strand displacement are extended insofar as it is shown that this impediment is highly dependent on mismatch position. This discovery is examined in detail, both experimentally and through simulations created with a coarse-grained model of DNA. It is shown that this effect allows for kinetic control of strand displacement decoupled from reaction thermodynamics. The second proposal improves upon a previously presented strand displacement scheme, in which two strands perform displacement cooperatively. This scheme is extended to be cascadable, so that the output of one such reaction serves as input to the next. This scheme is implemented in reaction networks capable of performing fundamental calculations on directed graphs. The third proposal is exclusively concerned with a novel observation methodology. This method is based on single-molecule fluorescence microscopy, and uses quantum dots, a fluorescent type of semiconductor nanocrystal, as a label. These quantum dots display a set of characteristics particularly promising for single-molecule studies on the time- and length scales most commonly encountered in DNA nanotechnology. This method is shown to allow for highly precise measurements on static DNA devices. Preliminary data for the observation of a complex dynamic device is also presented.</p

Control and Observation of DNA Nanodevices

The uniquely predictable and controllable binding mechanism of DNA strands has been exploited to construct a vast range of synthetic nanodevices, capable of autonomous motion and computation. This thesis proposes novel ideas for the control and observation of such devices. The first of these proposals hinges on introducing mismatched base pairs into toehold-mediated strand displacement – a fundamental primitive in most dynamic DNA devices and reaction networks. Previous findings that such mismatches can impede strand displacement are extended insofar as it is shown that this impediment is highly dependent on mismatch position. This discovery is examined in detail, both experimentally and through simulations created with a coarse-grained model of DNA. It is shown that this effect allows for kinetic control of strand displacement decoupled from reaction thermodynamics. The second proposal improves upon a previously presented strand displacement scheme, in which two strands perform displacement cooperatively. This scheme is extended to be cascadable, so that the output of one such reaction serves as input to the next. This scheme is implemented in reaction networks capable of performing fundamental calculations on directed graphs. The third proposal is exclusively concerned with a novel observation methodology. This method is based on single-molecule fluorescence microscopy, and uses quantum dots, a fluorescent type of semiconductor nanocrystal, as a label. These quantum dots display a set of characteristics particularly promising for single-molecule studies on the time- and length scales most commonly encountered in DNA nanotechnology. This method is shown to allow for highly precise measurements on static DNA devices. Preliminary data for the observation of a complex dynamic device is also presented.This thesis is not currently available on ORA

Protéine C-réactive et facteurs de risques cardiovasculaires (étude des relations entre la pression pulsée centrale et périphérique et les marqueurs de l'inflammation chez des patients coronariens stables)

La pression pulsée est un facteur de risque de maladie coronaire. L'inflammation pourrait contribuer à expliquer cette relation. Le but de l'étude est d'évaluer l'influence du gradient de pression pulsée sur le taux de protéine C-réactive chez des patients à risque coronaire. La CRP ultrasensible et le gradient de pression pulsée aorto-fémoral ont été mesurés chez 85 patients adressés pour coronarographie. La perte du gradient de pression pulsée était associée à une augmentation de la CRP. Cette étude suggère que la valeur pronostic du gradient de pression pulsée pourrait en partie être médiée par un état micro inflammatoire.TOULOUSE3-BU Santé-Centrale (315552105) / SudocSudocFranceF

Intramolecular charge transfer with 4-fluorofluorazene and the flexible 4-fluoro-N-phenylpyrrole.

With 4-fluorofluorazene (FPP4F) and its flexible counterpart 4-fluoro-N-phenylpyrrole (PP4F) an intramolecular charge transfer (ICT) reaction occurs in the singlet excited state in sufficiently polar solvents. The ICT reaction begins to appear in tetrahydrofuran (E = 7.4) for FPP4F and in the more polar 1,2-dichloroethane (epsilon = 10.4) with PP4F, showing its presence by dual fluorescence from a locally excited (LE) and an ICT state. Only LE fluorescence is observed in less polar solvents such as n-hexane. The ICT reaction is more pronounced with FPP4F than for PP4F, due to the smaller energy gal) Delta E(S(1),S(2)) of the former molecule, in accordance with the PICT model. The occurrence of an ICT reaction is confirmed by the ICT dipole moments mu(e)(ICT) of 12 D (FPP4F) and 10 D (PP4F), clearly larger than mu(e)(LE) of similar to 4 D for FPP4F and PP4F. Isoemissive points are found in the fluorescence spectra of FPP4F and PP4F in acetonitrile (MeCN), ethyl cyanide (EtCN), and n-propyl cyanide (PrCN) as a function of temperature, confirming the two-state (LE and ICT) reaction mechanism. From plots of the logarithm of the ICT/LE fluorescence quantum yield ratio versus the reciprocal absolute temperature in these solvents, the ICT reaction enthalpies Delta H are determined, with larger -Delta H values for FPP4F than for PP4F: 19.2 as compared with 14.9 kJ/mol in MeCN, as an example. The picosecond fluorescence decay of PP4F at -45 degrees C becomes slower with decreasing solvent polarity, 5.1 ps (MeCN), 14 ps (EtCN), and 35 ps (PrCN), from which the LE -> ICT reaction rate constant is calculated, decreasing from 19 x 10(10) to 2.1 x 10(10) s(-1) between MeCN and PrCN. The femtosecond LE excited-state absorption spectra of FPP4F and PP4F do not undergo any time development in n-hexane (no ICT reaction), but show a fast ICT reaction in MeCN at 22 degrees C, with decay times of 1.1 ps (FPP4F) and 3.3 ps (PP4F). It is concluded that FPP4F and PP4F have a planar ICT state (PICT model), indicating that a perpendicular twist of the donor and acceptor subgroups in a donor/acceptor molecule is not a requirement for fast and efficient ICT. The molecular structures of FPP4F and PP4F obtained from X-ray crystal analysis reveal that the pyrrole group of PP4F is twisted over an angle theta = 25 degrees relative to the fluorophenyl moiety in the ground state, whereas as expected r-PP4F is practically planar (theta = 2 degrees). The pyrrole-phenyl bond length of FPP4F (140.7 pm) is shorter than that for PP4F (141.8 pm).Hungarian Science Foundation [76278

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)

Synopsis: In the crystal, actinomycin D intercalates between G-T wobble pairs of DNA involving the sequence d(TTAGTT); in solution, the dominant binding is between guanine and actinomycin. Abstract: The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution, and by molecular modeling. The crystal structures of the complex with 5'-TTAG[Br5U]T-3' provide interesting examples of MAD phasing, in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex; in the orthorhombic form there is one such complex in the asymmetric unit, in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of symmetry related molecule. The chromophore of the second actinomycin intercalates between BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A*T)*T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures with looping-out of unpaired bases. Although the available NOE-constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient for determining the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing