A protein-based electrochemical method for label-free characterization of sequence-specific protein–DNA interactions

2011 ◽  
Vol 56 (16) ◽  
pp. 5759-5765 ◽  
Author(s):  
Jinhai Xu ◽  
Xiaodie He ◽  
Liling Jin ◽  
Lan Jiang ◽  
Yifeng Zhou ◽  
...  
Keyword(s):  
Electrochemical Method ◽  
Specific Protein ◽  
Label Free ◽  
Dna Interactions ◽  
Protein Dna Interactions

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.

SURFACE PLASMON RESONANCE SPECTROSCOPY AND QUARTZ CRYSTAL MICROBALANCE STUDY OF PROTEIN-DNA INTERACTIONS IN HORMONE RECEPTOR BIOLOGY

COSMOS ◽  
2009 ◽  
Vol 05 (01) ◽  
pp. 79-95
Author(s):  
XIAODI SU
Keyword(s):  
Surface Plasmon Resonance ◽  
Surface Plasmon ◽  
Quartz Crystal Microbalance ◽  
Conformational Changes ◽  
Plasmon Resonance ◽  
Quartz Crystal ◽  
Resonance Spectroscopy ◽  
Dna Interactions ◽  
Protein Dna Interactions

Surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) are surface sensitive analytical techniques capable of real-time monitoring of biomolecular interactions. In this article we review our past work on the use of these two techniques for studying protein–DNA interactions, exemplified with estrogen receptors (ER) and their response elements (ERE). Various assay schemes have been developed for a comprehensive characterization of ER–ERE interactions in terms of sequence specificity, binding affinity, stoichiometry, ligand effects on binding dynamics and conformational changes in the proteins and DNA. These are all important characteristics underlining the mechanism of ER-mediated gene transcription. With these studies we have made the following demonstrations to describe the advantages of these two techniques, namely (i) SPR technique is superior and more versatile than conventional (electrophoretic mobility shift assay) EMSA for studying protein-DNA interactions; (ii) QCM is an alternative tool for studying conformational changes in protein–DNA complexes and (iii) combinational SPR and QCM analysis provides additional characterization of biomolecular films, e.g. film thickness, water content, and conformation rigidity etc.

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.

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