Related Experiment Video
Updated: Aug 14, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
Identification of conserved structural features at sequentially degenerate locations in transcription factor binding
Heather E Burden1, Zhiping Weng
1Bioinformatics Program, Boston University, Boston, MA 02215, USA. hburden@bu.edu
Unlabelled:
Many locations within transcription factor binding sites are not sequentially conserved and appear to be degenerate. We hypothesize that some of these positions contain essential structural codes that are recognized by the transcription factors that bind to them. The structural codes can be defined by base-pair step parameters that describe the relative displacement and orientation of two adjacent base pairs in a nucleic acid structure. We have developed a method, Identification of Conserved Structural Features (ICSF), which uses base-pair step parameters obtained from a collection of high-resolution DNA crystal structures to discover structural conservation that exists in the sequentially degenerate areas within a binding site and produce profiles of the structural features along the entire site. We have focused our study on the transcription factor binding sites in the JASPAR database and have found that one-third (P-value > or = 0.05) of the binding sites contain sequentially degenerate locations with highly conserved structural features as described by the base-pair step parameters. These results will help us to gain a better understanding of the process by which transcription factors recognize their binding sites and possibly lead to an improvement in our ability to find these sites in genomic sequences.
Availability:
ICSF is freely available to academic users at http://zlab.bu.edu/ICSF .
Supplementary Information:
http://zlab.bu.edu/ICSF .
More Related Videos
09:17Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
Published on: March 1, 2022
12:29Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
Published on: April 16, 2018
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Binding of Transcription Regulators
Cooperative Binding of Transcription Regulators
Cis-regulatory Sequences
Cis-regulatory Sequences