WEB-THERMODYN

WEB-THERMODYN computes DNA helical stability by calculating the free energy required to unwind double-stranded DNA, enabling identification of regions prone to strand separation.

Key Features:

• Helical Stability Computation: Calculates the free energy required to disrupt hydrogen bonds between base pairs to quantify DNA helical stability from nucleotide sequences.
• Sliding-Window Analysis: Employs a sliding-window approach to generate helical stability profiles across selected regions or entire sequences to reveal local variation.
• Prediction of Low Stability Sites: Identifies regions of low helical stability predictive of transcription and replication initiation sites and notes accessibility to proteins such as RNA polymerase and DNA helicases.
• Mutation Analysis: Assesses the impact of sequence variants on helical stability to evaluate how mutations alter DNA structural properties.

Scientific Applications:

• ARS and replication origin analysis: Analysis of autonomously replicating sequence (ARS) elements and plasmid replication origins, relating stability minima to origin function.
• Nuclease hypersensitivity correlation: Demonstrated correlation between nuclease hypersensitivity and minima in helical stability in yeast replication origins.
• Regulatory site identification: Prediction and analysis of stability profiles to highlight potential regulatory regions involved in transcription and replication initiation for experimental investigation.

Methodology:

Analyzes nucleotide sequences, computes the free energy required for strand separation, and applies a sliding-window technique to produce helical stability profiles.