Atomic force microscopy captures the initiation of methyl-directed DNA mismatch repair

Josephs, Eric A.; Zheng, Tianli; Marszałek, Piotr E.

doi:10.1016/j.dnarep.2015.08.006

Cited by 12 publications

(14 citation statements)

References 66 publications

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“…DNA ligase resynthesizes the excised DNA segment, restoring covalent continuity in the repaired strand [29][30][31]. MutS-mediated loops in DNA have been observed using electron microscopy and AFM [28][29][30][31]. However, both methods did not allow for the investigation of the chemical structure and conformation of DNA.…”

Section: Introductionmentioning

confidence: 99%

Molecular Spectroscopic Markers of DNA Damage

Sofińska¹,

Wilkosz²,

Szymoński³

et al. 2020

Molecules

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Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage.

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Section: Introductionmentioning

confidence: 99%

Molecular Spectroscopic Markers of DNA Damage

Sofińska¹,

Wilkosz²,

Szymoński³

et al. 2020

Molecules

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“…Recently, Marszalek et al 69 used AFM to characterize the interaction of the complete MutS-MutL-MutH system with a mismatch. 69 From the high-resolution AFM images, they were able to identify the assembly and disassembly of the repair system.…”

Section: Afm Of Protein–dna Complexes: Static Afm Datamentioning

confidence: 99%

“…69 From the high-resolution AFM images, they were able to identify the assembly and disassembly of the repair system. Interestingly, they discovered that MutS acts as a scaffold to promote the assembly of MutL and MutH.…”

Section: Afm Of Protein–dna Complexes: Static Afm Datamentioning

confidence: 99%

Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy

Lyubchenko

Shlyakhtenko

2016

Crit Rev Eukaryot Gene Expr

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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.

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“…As a useful tool, AFM is increasingly being used to measure the interaction forces between samples and recognition events between proteins at the single molecule level. It is now also being used for measurement of interactions between antigen and antibody [ 21 , 22 ], misfolding of protein [ 23 , 24 , 25 ], and protein-DNA interactions [ 26 , 27 , 28 ].…”

Section: Introductionmentioning

confidence: 99%

Friction Determination by Atomic Force Microscopy in Field of Biochemical Science

Wang

2018

Micromachines

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Atomic force microscopy (AFM) is an analytical nanotechnology in friction determination between microscale and nanoscale surfaces. AFM has advantages in mechanical measurement, including high sensitivity, resolution, accuracy, and simplicity of operation. This paper will introduce the principles of mechanical measurement by using AFM and reviewing the progress of AFM methods in determining frictions in the field of biochemical science over the past decade. While three friction measurement assays—friction morphology, friction curve and friction process in experimental cases—are mainly introduced, important advances of technology, facilitating future development of AFM are also discussed. In addition to the principles and advances, the authors also give an overview of the shortcomings and restrictions of current AFM methods, and propose potential directions of AFM techniques by combining it with other well-established characterization techniques. AFM methods are expected to see an increase in development and attract wide attention in scientific research.

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Atomic force microscopy captures the initiation of methyl-directed DNA mismatch repair

Cited by 12 publications

References 66 publications

Molecular Spectroscopic Markers of DNA Damage

Molecular Spectroscopic Markers of DNA Damage

Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy

Friction Determination by Atomic Force Microscopy in Field of Biochemical Science

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