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Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.


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Journal ArticleDOI
TL;DR: Computational insight reveals that the observed structure and dynamics of entangled λ-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with the experimental observation.
Abstract: Intrinsic dynamics of DNA plays a crucial role in DNA protein interactions and has been emphasized as a possible key component for in vivo chromatin organization. We have prepared an entangled DNA microtube above the overlap concentration by exploiting the complementary cohesive ends of lambda-phage DNA, which is confirmed by atomic force microscopy and agarose gel electrophoresis. Photon correlation spectroscopy further confirmed that the entangled solutions are found to exhibit the classical hydrodynamics of a single chain segment on length scales smaller than the hydrodynamic length scale of single lambda-phage DNA molecule. We also observed that in 41.6% (gm water/gm DNA) hydrated state, lambda-phage DNA exhibits a dynamic transition temperature (T-dt) at 187 K and a crossover temperature (T-c) at 246 K. Computational insight reveals that the observed structure and dynamics of entangled lambda-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with our experimental observation.

5 citations

Posted Content
TL;DR: Simulation is used to investigate the accuracy of estimation of both the selection parameter $omega and branch lengths in cases where the underlying DNA process is heterogeneous but $\omega$ is constant, and it is found that both $\omegas$ and branch length can be mis-estimated in these scenarios.
Abstract: Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed that when evolution occurs under a heterogeneous process it is important to consider the property of model closure, because non-closed models can give biased estimates of evolutionary processes. The existing codon models that account for the genetic code are not closed; to establish this it is enough to show that they are not linear (meaning that the sum of two codon rate matrices in the model is not a matrix in the model). This raises the concern that a single codon model fit to a heterogeneous process might mis-estimate both the effect of selection and branch lengths. Codon models are typically constructed by choosing an underlying DNA model (e.g., HKY) that acts identically and independently at each codon position, and then applying the genetic code via the parameter $\omega$ to modify the rate of transitions between codons that code for different amino acids. Here we use simulation to investigate the accuracy of estimation of both the selection parameter $\omega$ and branch lengths in cases where the underlying DNA process is heterogeneous but $\omega$ is constant. We find that both $\omega$ and branch lengths can be mis-estimated in these scenarios. Errors in $\omega$ were usually less than 2% but could be as high as 17%. We also assessed if choosing different underlying DNA models had any affect on accuracy, in particular we assessed if using closed DNA models gave any advantage. However, a DNA model being closed does not imply that the codon model constructed from it is closed, and in general we found that using closed DNA models did not decrease errors in the estimation of $\omega$.

5 citations

Proceedings ArticleDOI
30 Apr 2003
TL;DR: The chief aims are to elucidate the mechanism by which DNA replication is controlled in cells and to seek novel strategies for controlling molecular scale processes and the function of nanodevices.
Abstract: The advent of techniques to detect and manipulate individual molecules has revealed that mechanical tension on a DNA polymer can control both the speed and direction of the DNA polymerase (DNAp) motor. Reconciling the interpretation of these single molecule experiments with crystal structural data has been the focus of our previous work. In more recent work, we are developing a more broadly applicable conceptual framework to describe how tension on a DNA polymer can produce both the "tuning" and "switching" phenomena observed in DNA polymerase motors. The chief aims are to elucidate the mechanism by which DNA replication is controlled in cells and to seek novel strategies for controlling molecular scale processes and the function of nanodevices.

5 citations

Journal ArticleDOI
TL;DR: A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described and suggestions are given to enhance the basic helical frame to show the shapes and sizes of the nitrogenous base rings, 3′ and 5′ chain termini, and base pair hydrogen bonding.
Abstract: Since the first DNA model was created ≈50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance the basic helical frame to show the shapes and sizes of the nitrogenous base rings, 3′ and 5′ chain termini, and base pair hydrogen bonding. Students can incorporate random or real gene sequence data into their models. One example of a gene sequence, for the protein oxytocin, is given. Left-handed Z-DNA, as well as right-handed A-DNA and B-DNA models can be constructed. Aimed for use in high school science classes, it takes 2–3 hours to complete DNA models with 30 labeled base pairs. Photos of oxytocin models are included. The size of this sturdy model is appropriate for visually-impaired students to feel the helical shape and read the genetic code in Braille. This model is i...

4 citations

Journal ArticleDOI
TL;DR: In this article, a coarse-grained model of DNA-functionalized particles is presented, which provides explicit DNA representation and complementary interactions between Watson-Crick base pairs, which lead to the formation of singlestranded hairpin and double-stranded DNA.
Abstract: DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA- functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

4 citations

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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20216
20208
20194
201810
201712
201617