cgDNAweb

cgDNAweb provides interactive visualization and prediction of sequence-dependent ground state configurations of double-stranded DNA using the cgDNA coarse-grain rigid-base model to determine minimum free-energy shapes and fluctuation properties for sequences from a few base pairs to several hundred base pairs.

Key Features:

• Interactive Visualization: Visualization of sequence-dependent ground state configurations of double-stranded DNA.
• Sequence-Dependent Analysis: Analysis of sequence-dependent equilibrium statistical-mechanical properties relevant to protein binding sites, nucleosome positioning, and phased A-tracts.
• Ground State Prediction: Prediction of minimum free-energy shapes for arbitrary DNA sequences (few bp to several hundred bp) using the cgDNA coarse-grain rigid-base model.
• Comparison of Sequences: Comparison of ground state shapes and sequence-specific structural features across different DNA sequences.

Scientific Applications:

• Protein Binding Sites: Characterizing indirect read-out mechanisms by assessing how sequence-dependent DNA shape influences protein–DNA interactions.
• Nucleosome Positioning: Evaluating sequence tendencies to favor or disfavor nucleosome formation based on predicted ground state configurations.
• Phased A-Tracts and Structural Motifs: Investigating the role of sequence-dependent stiffness and fluctuations in the formation of phased A-tracts and other DNA structural motifs.

Methodology:

Uses the cgDNA coarse-grain rigid-base model to simulate the equilibrium statistical mechanics of double-stranded DNA, computing ground state (minimum free-energy) configurations and associated fluctuations determined by sequence-dependent stiffness for sequences from a few bp to several hundred bp.