Dna Dynamics

In this work, the retarding influence of a gel on the rotational motion of a macromolecule is investigated within the framework of the Effective Medium (EM) model. This is an extension of an earlier study that considered the effect of a gel on the translational motion of a macromolecule [Allison, S. et al. J. Phys. Chem. B 2008, 112, 5858-5866]. The macromolecule is modeled as an array of non-overlapping spherical beads with no restriction placed on their size or configuration. Specific applications include the rotational motion of right circular cylinders and wormlike chains modeled as strings of identical touching beads. The procedure is then used to examine the electric birefringence decay of a 622 base pair DNA fragment in an agarose gel. At low gel concentration (M  0.010 gm/mL), good agreement between theory and experiment is achieved if the persistence length of DNA is taken to be 65 nm and the gel fiber radius of agarose is taken to be 2.5 nm. At higher gel concentrations, the EM model substantially underestimates the rotational relaxation time of DNA and this can be attributed to the onset of direct interactions that become significant when the effective particle size becomes comparable to the mean gel fiber spacing.

The conformational flexibility of the DNA double helix is of great interest because of its potential role in protein recognition, packaging into chromosomes, formation of photodefects, and interaction with drugs. Theory finds that DNA is very flexible; however, there is a scarcity of experimental results that examine intrinsic properties of the DNA bases for the inherent flexibility in solution. We have studied the dynamics of poly(dA)-poly(dT) and (dA)20n(dT)20 in a 50 mM cacodylate, 0.1 M NaCI, pH 7 buffer by using the time-correlated picosecond fluorescence anisotropy of thymine selectively excited at 293 nm. For both nucleic acids, a large-amplitude biphasic decrease in the anisotropy is observed that has a very fast, large-amplitude component on the picosecond time scale and a slower, smaller-amplitude component on the nanosecond time scale. These modes are sensitive to sucrose concentration, and are greatly attenuated at 77% sucrose by volume. This observation suggests that motions of the bases make a significant contribution to the observed fluorescence depolarization (in the absence of sucrose). Measurements on the single-stranded systems poly(dT) and (dT)20 reveal a much smaller amplitude of the very fast depolarization mode. These observations are consistent with a mechanism that involves concerted motions in the interior of the double-stranded systems.

We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC) 2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na + Cl − or K + Cl −. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 s) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ∼80% of the DNA curvature present in experimentally solved structures.

We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC) 2 ) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na + Cl -or K + Cl -. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 s) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

The complete unzipping of DNA double helix by small size gold nanoparticles having weakly positive surface charge has been monitored using ensemble and single molecule fluorescence resonance energy transfer (smFRET) techniques. We believe, as the gold nanoparticles have positive charge on the surface, the DNA and nanoparticles were pulled together to form two single strands. The positively charged ligands on the nanoparticles attached to the DNA, and the hydrophobic ligands of the nanoparticles became tangled with each other, pulling the nanoparticles into clusters. At the same time, the nanoparticles pulled the DNA apart. The conformational changes followed by unzipping have been investigated for long DNA (calf thymus DNA) as well as for short DNA (∼40 base pair) using ensemble methods like circular dichroism (CD) spectroscopy, fluorescence intercalation assay, viscometric method, and single molecule FRET imaging. This observation not only reveals a new aspect in the field of nano-...

The use of software developed for the simulation of injection molding is evaluated through a case study of a micro-injection molded micro-pump component. The purpose of this evaluation is to determine if commercially available injection molding simulation software developed for macro-injection molding provides sufficient support to the development of micro-injection molded components. It is concluded from this experience that the software provides sufficient support to reduce the development cycle by minimizing the amount of process optimization required with physical samples.

Complementary oligonucleotides with 5' overhanging deoxyguanosine or deoxycytidine stretches, respectively, of the general form 5'-d(GGGCAARAAC)-5'-d(C-CCGTTYTTG), where R represents the bases adenine (A), hypoxanthine (base of inosine nucleoside, I), purine (M),

At TpA steps in DNA, the adenine base experiences exceptionally large amplitude (20°-50°) and slow (10 ms-1 µs) motion [Kennedy et al. (1993) Biochemistry 32, 8022-8035] which has been correlated with transitions between multiple conformational states [Lefevre et al. (1985) FEBS Lett. 190, 37-40]. The base dynamics can be detected in one-dimensional 1 H NMR spectra as excess line width of the aromatic proton resonances. The magnitude of the excess line width is temperature dependent and reaches a maximum at some temperature. In order to better understand the origin of the dynamics, we have studied the effect of N 6-methylation of the TpA adenine on both the line widths and its local structure. Here, solution-state 500 and 750 MHz 1 H NMR data collected on [d(CGAGGTTTAAACCTCG)] 2 show that the excess line width of theTpA adenine-H2 is diminished when the TpA adenine is N 6-methylated and that the line width no longer experiences a maximum as the temperature is varied. The resonances sharpen upon methylation because the amplitude of base motion is restricted due to steric effects and due to other structural changes at the TpA site. Additionally, both the TpA adenine-H8 and the exchangeable imino resonance of thymine at the TpA step were also found to have excess line width that is diminished upon N 6-methylation. In order to elucidate the structural features responsible for TpA base dynamics, solution-state NMR structures of [d(CGAGGTTTAAACCTCG)] 2 and its A9 N 6-methylated derivative were determined at 750 MHz. Comparison of the structures shows that poor base stacking at the TpA step may contribute to, or be the origin of, its base dynamics.

Satellite DNA variability follows a pattern of concerted evolution through homogenization of new variants by genomic turnover mechanisms and variant fixation by chromosome redistribution into new combinations with the sexual process. Bacillus taxa share the same Bag320 satellite family and their reproduction ranges from strict bisexuality (B. grandii) to automictic (B. atticus) and apomictic (B. whitei = rossius/ grandii; B. lynceorum = rossius/grandii/atticus) unisexuality. Thelytokous reproduction clearly allows uncoupling of homogenization from fixation. Both trends and absolute values of satellite variability were analyzed in all Bacillus taxa but B. rossius, on 906 sequenced monomers at all level of comparisons: intraspecimen, intrapopulation, interpopulation, intersubspecies, and interspecies. For unisexuals, allozymic and mitochondrial clones were also taken into account. Different reproductive modes (sexual/parthenogenetic) appear to explain observed variability trends, supp...

In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and dispersion. We state that a dispersion coefficient P and a coefficient of nonlinearity Q , existing in nonlinear Schrödinger equation, are mutually dependent and show how function and can be obtained. Also, we show how all this can be used to find a possible interval for the parameter describing helicoidal structure of DNA.

We study DNA dynamics relying on the plane-base rotator model for DNA. It is shown that this dynamics can be represented by kink and antikink solitons. We demonstrate that two velocities are relevant and these are the velocities of both a double and a single stranded DNA. A key question is which one is bigger as this is related to a value of the ratio of two parameters describing the hydrogen and the covalent interactions in DNA. If the velocity of double stranded DNA is larger than one of the single stranded chain then the two ferromagnetic strands are coupled antiferromagnetically. Otherwise, the two DNA strands are coupled ferromagnetically. We discuss possible experiments based on micromanipulation techniques that should be carried out to determine these velocities and the solitonic width.

We present a systematic study of the long-timescale dynamics of the Drew-Dickerson dodecamer (DDD: d(CGCGAATTGCGC) 2) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt to 2 M Na + Cl − or K + Cl −. The sensitivity of the simulations to the use of different solvent and ion models is analyzed in detail using multi-microsecond simulations. Finally, an extended (10 s) simulation is used to characterize slow and infrequent conformational changes in DDD, leading to the identification of previously uncharacterized conformational states of this duplex which can explain biologically relevant conformational transitions. With a total of more than 43 s of unrestrained molecular dynamics simulation, this study is the most extensive investigation of the dynamics of the most prototypical DNA duplex.

We study DNA dynamics relying on the plane-base rotator model for DNA. It is shown that this dynamics can be represented by kink and antikink solitons. We demonstrate that two velocities are relevant and these are the velocities of both a double and a single stranded DNA. A key question is which one is bigger as this is related to a value of the ratio of two parameters describing the hydrogen and the covalent interactions in DNA. If the velocity of double stranded DNA is larger than one of the single stranded chain then the two ferromagnetic strands are coupled antiferromagnetically. Otherwise, the two DNA strands are coupled ferromagnetically. We discuss possible experiments based on micromanipulation techniques that should be carried out to determine these velocities and the solitonic width.

In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and dispersion. We state that a dispersion coefficient P and a coefficient of nonlinearity Q , existing in nonlinear Schrödinger equation, are mutually dependent and show how function and can be obtained. Also, we show how all this can be used to find a possible interval for the parameter describing helicoidal structure of DNA.