Analysis of scanning force microscopy images of protein-induced DNA bending using simulations

Dame, Remus T.; Mameren, Joost van; Luijsterburg, Martijn S.; Mysiak, M. E.; Janićijević, Ana; Pazdzior, Grzegorz; Vliet, Peter C. van der; Wyman, Claire; Wuite, Gijs J.L.

doi:10.1093/nar/gni073

Cited by 35 publications

(39 citation statements)

References 36 publications

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“…As a result of crosssectional analysis of the scIHF2 that bound with IHF box containing DNA, the three-dimensional geometry of scIHF2 was similarly shaped (height=1.15 nm, width= 15 nm) in the previous reports (Fig. 4c) [24,25].…”

Section: Evaluation Of Dna Binding and Bending Capability Of Scihf2 Usupporting

confidence: 66%

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DNA Binding and Bending Protein-Based DNA Actuator and its Practical Realization

et al. 2008

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In the life forms, the biomolecules such as DNA and protein are interacting with each other to maintain their life activity. Simultaneously, these biomolecules form DNA-protein complexes; as a result, the life forms can adjust to the external environment and continue its life activities. Therefore, using these characteristics of the DNA recognition ability of proteins, the novel molecular devices can be established. Here, we show the application of DNA binding and bending protein for design of the DNA actuator and its practical realization. The single polypeptide chain integrated host factor 2 (scIHF2), which is a DNA binding and bending protein, was used to bind to and/or bend the specific domains of DNA. Using this protein and designing the sequences of DNA, mechanical-functionalized DNAbased biomolecular device could be fabricated. Using these mechanisms, DNA binding and bending proteins have great potentials for establishing the DNA actuator for nanobiotechnology and nanotechnology applications.

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Section: Evaluation Of Dna Binding and Bending Capability Of Scihf2 Usupporting

confidence: 66%

“…Following the theory of DNA geometry, 100 bp of (n=10, approximately 34 nm) linker DNA was designed for fabrication of DNA actuator. This shortening of linker DNA was caused by wrapping around scIHF2 and bent, thus reversing the direction of the helix axis within the short length [24,25].…”

Section: Evaluation Of Dna Binding and Bending Capability Of Scihf2 Umentioning

confidence: 99%

DNA Binding and Bending Protein-Based DNA Actuator and its Practical Realization

et al. 2008

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“…Interestingly, recent findings demonstrated that an HU mutant acquired DNA condensation activity as a result of gaining the oligomerization activity (73). This proposed mechanism is clearly distinct from other DNA-associating proteins, such as HU (24), SMC (74), IHF (75) and FIS (76), which are proposed to function through a wrapping mechanism (48). …”

Section: Discussionmentioning

confidence: 81%

Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

Chan¹,

Wong²

2007

Nucleic Acids Research

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The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes.

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“…These methods have been exploited for different purposes, as the experimental validation of models for DNA adsorption and bending12456789 or the correlation of DNA shape and flexibility to melting10, ligand interactions111213, replication14, genomic packaging and transcription regulation1516. The wide applicability of DNA conformational studies demands simple experimental methods, characterized by a few processing steps for specimen preparation and minimum experimental bias on curvature and flexibility measurements.…”

mentioning

confidence: 99%

Symmetric curvature descriptors for label-free analysis of DNA

Buzio

Repetto

Giacopelli

et al. 2014

Sci Rep

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High-resolution microscopy techniques such as electron microscopy, scanning tunnelling microscopy and atomic force microscopy represent well-established, powerful tools for the structural characterization of adsorbed DNA molecules at the nanoscale. Notably, the analysis of DNA contours allows mapping intrinsic curvature and flexibility along the molecular backbone. This is particularly suited to address the impact of the base-pairs sequence on the local conformation of the strands and plays a pivotal role for investigations relating the inherent DNA shape and flexibility to other functional properties. Here, we introduce novel chain descriptors aimed to characterize the local intrinsic curvature and flexibility of adsorbed DNA molecules with unknown orientation. They consist of stochastic functions that couple the curvatures of two nanosized segments, symmetrically placed on the DNA contour. We show that the fine mapping of the ensemble-averaged functions along the molecular backbone generates characteristic patterns of variation that highlight all pairs of tracts with large intrinsic curvature or enhanced flexibility. We demonstrate the practical applicability of the method for DNA chains imaged by atomic force microscopy. Our approach paves the way for the label-free comparative analysis of duplexes, aimed to detect nanoscale conformational changes of physical or biological relevance in large sample numbers.

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Analysis of scanning force microscopy images of protein-induced DNA bending using simulations

Cited by 35 publications

References 36 publications

DNA Binding and Bending Protein-Based DNA Actuator and its Practical Realization

DNA Binding and Bending Protein-Based DNA Actuator and its Practical Realization

Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3

Symmetric curvature descriptors for label-free analysis of DNA

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