A New Analytical Scale DNA Affinity Binding Assay for Analyses of Specific Protein–DNA Interactions

2001 ◽  
Vol 299 (2) ◽  
pp. 203-210 ◽  
Author(s):  
N. Vinay Kumar ◽  
Lori R. Bernstein
Keyword(s):  
Binding Assay ◽  
Specific Protein ◽  
Affinity Binding ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Analytical Scale

scholarly journals Facilitation of DNA loop formation by protein–DNA non-specific interactions

Soft Matter ◽  
2019 ◽  
Vol 15 (26) ◽  
pp. 5255-5263 ◽  
Author(s):  
Jaeoh Shin ◽  
Anatoly B. Kolomeisky
Keyword(s):  
Specific Protein ◽  
Dna Looping ◽  
Specific Interactions ◽  
Loop Formation ◽  
Dna Interactions ◽  
Dna Loop ◽  
Protein Dna Interactions

DNA looping is facilitated by non-specific protein–DNA interactions.

scholarly journals Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

2018 ◽  
Author(s):  
Cheng Tan ◽  
Shoji Takada
Keyword(s):  
Structure Data ◽  
Dna Sequences ◽  
Complex Structure ◽  
Specific Protein ◽  
Coarse Grained ◽  
Binding Modes ◽  
Binding Assays ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Dynamics Simulations

ABSTRACTHow transcription factors (TFs) recognize their DNA sequences is often investigated complementarily by high-throughput protein binding assays and by structural biology experiments. The former quantifies the specificity of TF binding sites for numerous DNA sequences, often represented as the position-weight-matrix (PWM). The latter provides mechanistic insights into the interactions via the protein-DNA complex structures. However, these two types of data are not readily integrated. Here, we propose and test a new modeling method that incorporates the PWM with complex structure data. Based on pre-tuned coarse-grained models for proteins and DNAs, we model the specific protein-DNA interactions, PWMcos, in terms of an orientation-dependent potential function, which enables us to perform molecular dynamics simulations at unprecedentedly large scales. We show that the PWMcos model reproduces subtle specificity in the protein-DNA recognition. During the target search in genomic sequences, TF moves on highly rugged landscapes and occasionally flips on DNA depending on the sequence. The TATA-binding protein exhibits two remarkably distinct binding modes, of which frequencies differ between TATA-containing and TATA-less promoters. The PWMcos is general and can be applied to any protein-DNA interactions given their PWMs and complex structure data are available.

Sign in / Sign up

Export Citation Format

Share Document