SerraNA

SerraNA calculates elastic properties of double-stranded nucleic acids from numerical simulation ensembles to quantify sequence-dependent DNA elasticity from dinucleotide scales to whole molecules.

Key Features:

• Elastic parameter calculation: Computes elastic parameters such as stretch resistance, twistability, and bendability from simulation ensembles.
• Scale range: Analyzes elasticity at scales ranging from dinucleotide lengths up to entire molecules.
• Sequence-dependent analysis: Reveals sequence dependence, including that local periodic bending angles are in phase with the helicoidal shape of DNA and contribute to global bendability.
• Comprehensive tetra-bp dataset: Applied to a complete set of 136 tetra-base pair (tetra-bp) combinations and reports sequence-dependent variability exceeding 200% among sequences.
• Identification of flexible and rigid base-pair steps: Identifies specific base-pair steps contributing to flexibility (e.g., TA and CA) or rigidity (e.g., AA and AT).
• AT-rich motif characterization: Shows that AT-rich motifs can display extreme mechanical properties depending on sequence ordering and phasing, affecting global bendability.

Scientific Applications:

• Gene regulation: Quantifies how sequence-dependent elasticity can influence DNA-mediated regulation mechanisms.
• Chromatin organization and chromosome packing: Provides metrics relevant to how DNA mechanics contribute to chromatin structure and higher-order packing.
• Structural biology and molecular biophysics: Supplies elastic parameters and sequence-level insights for studies of nucleic acid mechanics and structure.
• Genomics: Enables analysis of sequence-dependent mechanical variability across genomic motifs and combinations.

Methodology:

Analyzes ensembles from numerical simulations to derive elastic parameters and quantify how local sequence-dependent fluctuations contribute to bulk elastic constants.