Studying protein-DNA interactions using atomic force microscopy

EC Beckwitt, M Kong, B Van Houten - Seminars in cell & developmental …, 2018 - Elsevier
Atomic force microscopy (AFM) has made significant contributions to the study of protein-
DNA interactions by making it possible to topographically image biological samples. A …

Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex

Y Velmurugu, X Chen… - Proceedings of the …, 2016 - National Acad Sciences
DNA damage repair starts with the recognition of damaged sites from predominantly normal
DNA. In eukaryotes, diverse DNA lesions from environmental sources are recognized by the …

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide …

S Chakraborty, PJ Steinbach, D Paul, H Mu… - Nucleic Acids …, 2018 - academic.oup.com
Rad4/XPC recognizes diverse DNA lesions including ultraviolet-photolesions and
carcinogen-DNA adducts, initiating nucleotide excision repair. Studies have suggested that …

Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC

A Panigrahi, H Vemuri, M Aggarwal, K Pitta… - Nucleic Acids …, 2020 - academic.oup.com
The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent
genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC …

Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein

Y Velmurugu, P Vivas, M Connolly… - Nucleic acids …, 2018 - academic.oup.com
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate
potential binding sites prior to recognition have remained elusive for most systems. Here we …

Mapping the transition state for DNA bending by IHF

P Vivas, Y Velmurugu, SV Kuznetsov, PA Rice… - Journal of molecular …, 2012 - Elsevier
How DNA-bending proteins recognize their specific sites on DNA remains elusive,
particularly for proteins that use indirect readout, which relies on sequence-dependent …

“Flexible hinge” dynamics in mismatched DNA revealed by fluorescence correlation spectroscopy

TB Ten, V Zvoda, MK Sarangi, SV Kuznetsov… - Journal of Biological …, 2022 - Springer
Altered unwinding/bending fluctuations at DNA lesion sites are implicated as plausible
mechanisms for damage sensing by DNA-repair proteins. These dynamics are expected to …

[PDF][PDF] Exploring DNA Lesion Recognition Mechanisms for Cyclobutane Pyrimidine Dimers and 6-4 Photoproduct by Rad4

N Jakhar - 2023 - cdn.iiit.ac.in
Genome integrity is seriously threatened by UV radiation's ability to cause damage in DNA.
CPD and 6-4PP are two of the most frequent lesions brought on by Ultraviolet radiation …

Visualizing spontaneous DNA dynamics and its role in mismatch recognition by damage repair protein Rad4

S Chakraborty - 2018 - indigo.uic.edu
How DNA-binding proteins search for and identify their target sites buried amid a vast
excess of non-target sites remains a central question in biology. This study is aimed at …

Integration Host Factor (IHF)–DNA Interaction

Y Velmurugu, Y Velmurugu - Dynamics and Mechanism of DNA-Bending …, 2017 - Springer
Integration host factor (IHF) is a small hetero dimeric protein (~ 20 kDa), ubiquitous in
eubacteria. It binds to DNA in a sequence-specific manner and causes~ 35-bp long cognate …