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 …
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
All major biological processes start after protein molecules known as transcription factors
detect specific regulatory sequences on DNA and initiate genetic expression by associating …
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 …
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
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 …
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
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 …
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 …
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 …
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 …
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 …
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 …
biophysical steps that follow. Gene transcription and formation of protein-DNA structures are …