scispace - formally typeset
Search or ask a question
Topic

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.


Papers
More filters
Journal ArticleDOI
TL;DR: Structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations and the application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration.
Abstract: This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.

38 citations

Journal ArticleDOI
TL;DR: The DnaFabric project was used to generate two DNA fibre models corresponding to two DNA compaction levels representing the hetero and the euchromatin, and the relative difference of the DNA damage computed in the two fibres for the same number of projectiles was found to be constant.

38 citations

Journal ArticleDOI
TL;DR: By applying a modified “molecular combing” technique and imaging in air with atomic force microscope, DNA molecules were aligned on a mica surface which was chemically modified with a small organic molecule, (3-aminopropyl)-triethanoxysilane.
Abstract: Manipulating DNA molecules to form molecular patterns on a nanometer scale is a subject with wide prospects By applying a modified “molecular combing” technique and imaging in air with atomic force microscope, we aligned DNA molecules on a mica surface which was chemically modified with a small organic molecule, (3-aminopropyl)-triethanoxysilane Two-dimensional patterns of DNA molecules were also constructed

37 citations

Book
07 Jul 2012
TL;DR: The model is the first in which an explicit stacking transition is present in single strands, and also the only coarse-grained model to date to capture both hairpin formation within a single strand and duplex formation between strands.
Abstract: In this thesis I present a novel coarse-grained model of deoxyribonucleic acid (DNA). The model represents single-stranded DNA as a chain of rigid nucleotides, and includes potentials to represent chain connectivity, excluded volume, hydrogen-bonding and base stacking interactions. The parameterization of these interactions is justified by comparing the model's representation of a range of physical phenomena to experimental data. In particular, the geometrical structure and elastic moduli of duplex DNA, and the flexibility of single-stranded DNA, are shown to be physically reasonable. Additionally, the thermodynamics of single-stranded stacking, duplex hybridization, hairpin formation and more complex motifs are shown to agree well with experimental data. The model is optimized for capturing the thermodynamic and mechanical changes associated with duplex formation from single strands. Considerable attention is therefore given to ensuring that single-stranded DNA behaves physically, an approach which differs from previous attempts to model DNA. As a result, the model is the first in which an explicit stacking transition is present in single strands, and also the only coarse-grained model to date to capture both hairpin formation within a single strand and duplex formation between strands. The scope of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice -- the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology. The simulations suggest that branch migration during toehold-mediated strand displacement -- a central feature of many nanomachines -- does not have a flat free-energy profile, as is generally assumed. This finding may help to explain the observed dependence of displacement rate on toehold length. Finally, the operation of a two-footed DNA walker on a single-stranded DNA track is considered. The model suggests that several aspects of the walker will reduce its efficiency, including a tendency to bind to an undesired site on the track. Several design modifications are suggested to improve the operation of the walker.

36 citations

Journal ArticleDOI
TL;DR: It is demonstrated that fluorescently-labeled multihelical DNA tiles can be used as a model platform to systematically investigate multivalent DNA hybridization and the stability and cooperativity of a network of DNA sticky-end associations could lead to greater control over hierarchical nanostructure formation and algorithmic self-assembly.

36 citations

Network Information
Related Topics (5)
DNA
107.1K papers, 4.7M citations
76% related
Protein structure
42.3K papers, 3M citations
76% related
Ab initio
57.3K papers, 1.6M citations
73% related
Binding site
48.1K papers, 2.5M citations
72% related
DNA replication
30.1K papers, 1.5M citations
72% related
Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20216
20208
20194
201810
201712
201617