1,659 research outputs found
Effective charge and free energy of DNA inside an ion channel
Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin
channel in a lipid membrane driven by applied transmembrane voltage V was
extensively studied recently. While the bare charge of the ssDNA piece inside
the channel is approximately 12 (in units of electron charge) measurements of
different effective charges resulted in values between one and two. We explain
these challenging observations by a large self-energy of a charge in the narrow
water filled gap between ssDNA and channel walls, related to large difference
between dielectric constants of water and lipid, and calculate effective
charges of ssDNA. We start from the most fundamental stall charge , which
determines the force stalling DNA against the voltage V (L is
the length of the channel). We show that the stall charge is proportional
to the ion current blocked by DNA, which is small due to the self-energy
barrier. Large voltage V reduces the capture barrier which DNA molecule should
overcome in order to enter the channel by , where is the
effective capture charge. We expressed it through the stall charge . We
also relate the stall charge to two other effective charges measured for
ssDNA with a hairpin in the back end: the charge responsible for
reduction of the barrier for unzipping of the hairpin and the charge
responsible for DNA escape in the direction of hairpin against the voltage. At
small V we explain reduction of the capture barrier with the salt
concentration.Comment: Typos are correcte
Dynamics of a bubble formed in double stranded DNA
We study the fluctuational dynamics of a tagged base-pair in double stranded
DNA. We calculate the drift force which acts on the tagged base-pair using a
potential model that describes interactions at base pairs level and use it to
construct a Fokker-Planck equation.The calculated displacement autocorrelation
function is found to be in very good agreement with the experimental result of
Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the
entire time range of measurement. We calculate the most probable displacements
which predominately contribute to the autocorrelation function and the
half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let
DNA nanotweezers studied with a coarse-grained model of DNA
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces
the basic thermodynamics of short strands: duplex hybridization,
single-stranded stacking and hairpin formation, and also captures the essential
structural properties of DNA: the helical pitch, persistence length and
torsional stiffness of double-stranded molecules, as well as the comparative
flexibility of unstacked single strands. We apply the model to calculate the
detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple
machine driven by hybridization and strand displacement.Comment: 4 pages, 5 figure
Interaction of Tet Repressor with Operator DNA and with Tetracycline Studied by Infrared and Raman Spectroscopy
AbstractTet repressor (TetR) is involved in the most abundant mechanism of tetracycline (Tc) resistance of Gram-negative bacteria. Raman spectra were measured for the class D TetR protein, for an oligodeoxyribonucleotide with sequence corresponding to operator site O1, and for the TetR:oligonucleotide complex. TetR forms a complex with [Ni-Tc]+, which does not bind to operator DNA. Raman and infrared measurements indicate nearly identical conformations of TetR with and without [Ni-Tc]+. Differences between the experimental spectrum of the TetR:operator DNA complex and the computed sum of the component spectra provide direct spectroscopic evidence for changes in DNA backbone torsions and base stacking, rearrangement of protein backbone, and specific contacts between TetR residues and DNA bases. Complex formation is connected with intensity decrease at 1376cm−1 (participation of thymine methyl groups), intensity increase at 1467cm−1 (hydrogen bond formation at guanine N7), decreased intensity ratio I854/I823 (increased hydrophobicity of tyrosine environment), increased intensity at 1363cm−1 (increased hydrophobicity of tryptophan ring environment), differences in the range 670–833cm−1 (changes in B-DNA backbone torsions and base stacking), and decreased intensity of the amide I band (structural rearrangement of TetR backbone consistent with a reduction of the distance between the two binding helices)
Molecular Modeling of Nucleic Acid Structure: Energy and Sampling
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT ) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143698/1/cpnc0708.pd
Empirical corrections to the Amber RNA force field with Target Metadynamics
The computational study of conformational transitions in nucleic acids still faces many challenges. For example, in the case of single stranded RNA tetranucleotides, agreement between simulations and experiments is not satisfactory due to inaccuracies in the force fields commonly used in molecular dynamics simulations. We here use experimental data collected from high-resolution X-ray structures to attempt an improvement of the latest version of the AMBER force field. A modified metadynamics algorithm is used to calculate correcting potentials designed to enforce experimental distributions of backbone torsion angles. Replica-exchange simulations of tetranucleotides including these correcting potentials show significantly better agreement with independent solution experiments for the oligonucleotides containing pyrimidine bases. Although the proposed corrections do not seem to be portable to generic RNA systems, the simulations revealed the importance of the \u3b1 and \u3b6 backbone angles for the modulation of the RNA conformational ensemble. The correction protocol presented here suggests a systematic procedure for force-field refinement
Thermomechanics of DNA
A theory for thermomechanical behavior of homogeneous DNA at thermal
equilibrium predicts critical temperatures for denaturation under torque and
stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable
torque, and the overstretching transition as force-induced DNA melting.
Agreement with available single molecule manipulation experiments is excellent.Comment: 4 pages, 5 figures. Lette
Effect of shear force on the separation of double stranded DNA
Using the Langevin Dynamics simulation, we have studied the effects of the
shear force on the rupture of short double stranded DNA at different
temperatures. We show that the rupture force increases linearly with the chain
length and approaches to the asymptotic value in accordance with the
experiment. The qualitative nature of these curves almost remains same for
different temperatures but with a shift in the force. We observe three
different regimes in the extension of covalent bonds (back bone) under the
shear force.Comment: 4 pages, 4 figure
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