Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userStatistical properties of metastable intermediates in DNA unzipping
111
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed following a power law, ranging from one base pair up to more than a hundred base pairs. We find that a large fraction of unzipping regions smaller than 10 bp are seldom detected because of the high compliance of the released single stranded DNA. We show how the compliance of a single nucleotide sets a limit value around 0.1 N/m for the stiffness of any local force probe aiming to discriminate one base pair at a time in DNA unzipping experiments.
rate research
Read More
The statistical properties of protein folding within the {phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of temperature is given for various levels of the nonlinearity of source and the strength of interaction between protein backbone and nonlinear source. It is found that the nonlinear source contributes constructively to the specific heat especially at higher temperature when it is weakly interacting with the protein backbone. This indicates increasing energy absorption as the intensity of nonlinear sources are getting greater. The simulation of protein folding dynamics within the model is also refined.
The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands.
We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p approx 500,$AA is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element, and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an $AT$-domain.
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the transport process. Using a two-dimensional stochastic model, we show that the dehybridization process proceeds by two distinct mechanisms; thermal denaturation in the limit of low driving voltage, and direct stripping in the high to moderate voltage regime. Additionally, we investigate the effects of introducing non-homologous defects into the DNA strand.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
