Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details

Naserian-Nik, AM; Tahani, Masoud; Karttunen, Mikko

doi:10.1039/c3ra23213a

Cited by 15 publications

(13 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Further stretching depends more on the sequence repetitions than on the number of hydrogen bonds. In addition to the previously observed influence of chemical modification of the DNA, 36 and simulation details, such as pulling speed 37,38 or initial pulling angle, 39 our study confirms that pulling speed plays important role. However, the most important factor is DNA length, which affords greater mechanical resistance to pulling, largely due to formation of higher order structures.…”

Section: Discussionsupporting

confidence: 85%

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

2018

View full text Add to dashboard Cite

The stability of DNA is crucial for the existence of most living organisms. Even a single DNA break can lead to serious problems, including cell death. In this work the position specificity of single strand breaks (SSB) and the stability of short DNA fragments of various lengths and sequence repetitions (d(AT), d(ATGC), d(GC), d(TTAGG), d(TTAGGG), and d(TTTAGGG) with SSBs and d(GC) with 2-60 repetitions without SSBs) were examined, by performing a series of steered molecular dynamics simulations using the coarse-grained NARES-2P force field. Our results show that the stability of DNA with a SSB strongly depends on the position of the break, and that the minimum length of DNA required for stability is sequence dependent. d(GC) with an SSB in position x was found to be less resistant to stretching than d(GC) without SSB, where x is the number of d(GC) repetitions. DNA sequences with longer repeated fragments (such as telomeres) exhibit greater stability in the presence of breaks positioned at the beginning of the chain, which could constitute a cellular defense mechanism against DNA damage.

show abstract

Section: Discussionsupporting

confidence: 85%

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

2018

View full text Add to dashboard Cite

show abstract

“…transcription, replication, slippage, rupture etc. [1][2][3][4][5][6][7][8][9][10][11][12][13]. Initially, it was thought that the interactions detected in SMFS experiments would be mostly of a mechanical nature and can be calculated by knowing the value of the applied force.…”

Section: Introductionmentioning

confidence: 99%

“…Initially, it was thought that the interactions detected in SMFS experiments would be mostly of a mechanical nature and can be calculated by knowing the value of the applied force. However, insights gathered from these experiments revealed that the measurement of molecular interactions depends not only on the magnitude of the applied force, but also on how and where the force is applied [3][4][5][6][7][8][9][10][11][12][13]. For example, Bockelmamm and coworkers [4,5] applied the force perpendicular to the helix direction (DNA unzipping) and measured the unzipping force ∼ 15 pN, whereas, Lee et al [6] studied the unbinding of double stranded DNA (dsDNA) by applying a force along the helix direction (rupture of DNA), and measured the rupture force, which is one order magnitude greater than the unzipping force.…”

Section: Introductionmentioning

confidence: 99%

Statistical mechanics of DNA rupture: Theory and simulations

Nath

Modi

Mishra

et al. 2013

The Journal of Chemical Physics

View full text Add to dashboard Cite

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the literature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.

show abstract

“…In recent years, AFM has been used for the study of biomolecules [11] and DNA molecules [12][13][14][15][16]. Ido used the NiCl 2 solution to modify the mica surface and measured the supercoil pitch of DNA molecules [17].…”

Section: Introductionmentioning

confidence: 99%

Imaging of DNA molecules by atomic force microscope

Guo

Wang

et al. 2017

2017 IEEE International Conference on Manipulation, Manufacturing and Measurement on the Nanoscale (3m-Nano)

View full text Add to dashboard Cite

This paper explores suitable conditions for the imaging of DNA molecules by atomic force microscope (AFM). As a typical biological macro-molecule, DNA with genetic information has attracted extensive attention, which is an important research subject in biomedicine. In this work, 3-Aminopropyl Triethyl Silane (APTES), Ni 2+ and Mg 2+ were used to modify the surface of mica substrate, and DNA molecules were adhered to the mica surface through the physical interaction of charges. The DNA molecules were imaged using an AFM under both air conditions and liquid conditions. By analyzing the images of DNA molecules obtained in the experiments, it was found that the mica surface modified with Ni 2+ had the best imaging quality under the liquid condition. This work will be useful for the study of high quality AFM imaging of DNA molecules, and the manipulation of DNA molecules by AFM mechanical forces.

show abstract

Pulling of double-stranded DNA by atomic force microscopy: a simulation in atomistic details

Cited by 15 publications

References 85 publications

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

Computational Studies of the Mechanical Stability for Single-Strand Break DNA

Statistical mechanics of DNA rupture: Theory and simulations

Imaging of DNA molecules by atomic force microscope

Contact Info

Product

Resources

About