Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

J Iwahara, AB Kolomeisky - Biophysical chemistry, 2021 - Elsevier
To perform their functions, transcription factors and DNA-repair/modifying enzymes
randomly search DNA in order to locate their specific targets on DNA. Discrete-state …

How pioneer transcription factors search for target sites on nucleosomal DNA

C Felipe, J Shin, AB Kolomeisky - The Journal of Physical …, 2022 - ACS Publications
All major biological processes start after protein molecules known as transcription factors
detect specific regulatory sequences on DNA and initiate genetic expression by associating …

Role of nucleosome sliding in the protein target search for covered DNA sites

A Mondal, AB Kolomeisky - The Journal of Physical Chemistry …, 2023 - ACS Publications
Associations of transcription factors (TFs) with specific sites on DNA initiate major cellular
processes. But DNA in eukaryotic cells is covered by nucleosomes which prevent TFs from …

Nucleosome breathing facilitates the search for hidden DNA sites by pioneer transcription factors

A Mondal, C Felipe, AB Kolomeisky - The Journal of Physical …, 2023 - ACS Publications
Transfer of genetic information starts with transcription factors (TFs) binding to specific sites
on DNA. But in living cells, DNA is mostly covered by nucleosomes. There are proteins …

DNA looping and DNA conformational fluctuations can accelerate protein target search

C Felipe, J Shin, AB Kolomeisky - The Journal of Physical …, 2021 - ACS Publications
Protein searching and binding to specific sites on DNA is a fundamentally important process
that marks the beginning of all major cellular transformations. While the dynamics of protein …

Why nucleosome breathing dynamics is asymmetric?

A Mondal, AB Kolomeisky - Biophysical Journal, 2024 - cell.com
In eukaryotic cells, DNA is bound to nucleosome particles, allowing for chromatin to be
efficiently confined in small cellular volumes. But these compact structures are not rigid, and …

Probing the Modulation in Facilitated Diffusion Guided by DNA-Protein Interactions in Target Search Processes

D Thonnekottu, D CHATTERJEE - Physical Chemistry Chemical …, 2024 - pubs.rsc.org
Many fundamental biophysical processes involving gene regulation and gene editing rely, at
the molecular level, on an intricate methodology of searching and locating the precise target …

Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights

B Punia, S Chaudhury - The Journal of Physical Chemistry B, 2022 - ACS Publications
The binding of proteins to their respective specific sites on the DNA through facilitated
diffusion serves as the initial step of various important biological processes. While this …

How to Find Targets That Are Always Hidden: Nucleosome-Covered DNA and Pioneer Transcription Factors

A Mondal, AB Kolomeisky - Target Search Problems, 2024 - Springer
Association of protein transcription factors (TFs) to specific DNA sites in promoter regions is
the fundamental event that initiates gene regulation. However eukaryotic DNA is mostly …

[PDF][PDF] Stochastic modeling of protein target search in different DNA topologies

CF dos Anjos - 2022 - repository.rice.edu
The target search process in DNA is the very first step for very fundamental biochemical and
biophysical steps that follow. Gene transcription and formation of protein-DNA structures are …