DSHIFT

DSHIFT predicts proton, carbon and phosphorus NMR chemical shifts for DNA sequences in random coil and double helical B-form to support NMR resonance assignment and analysis of nucleic acid structure.

Key Features:

• Reference-based prediction: Uses published reference chemical shift values with sequence-dependent correction factors to account for shielding and deshielding effects of neighboring nucleotides.
• Supported nuclei and forms: Provides predictions for proton, carbon and phosphorus chemical shifts in random coil DNA and proton chemical shifts in double helical B-DNA.
• Phosphorus trimer model: Predicts phosphorus random coil shifts using a trimer model dependent on 5'- and 3'-nearest neighbors with reported accuracy of 0.02 ppm.
• Carbon triplet database: Derives carbon shift predictions from a triplet database compiled from sixteen 17-nucleotide sequences with RMSDs of 0.09–0.10 ppm and correlation coefficients 0.978–0.999.
• Proton triplet parameters: Predicts aromatic H6/H8 proton shifts from central nucleotide measurements within 64 triplets with next-nearest-neighbor adjustments yielding an RMSD of ≈0.02 ppm and correlation 0.998.
• Sugar-proton accuracy: Predicts sugar protons (H1', H2', H2'', H3') with RMSDs ranging from 0.02 to 0.03 ppm.
• Sequence and temperature analysis: Incorporates analyses of sequence and temperature effects, noting phosphorus random coil shifts are temperature-independent but sequence-dependent.

Scientific Applications:

• NMR resonance assignment: Assists assignment of DNA NMR resonances by providing expected chemical shift values for multiple nuclei.
• Structural analysis of solution DNA: Supports exploration of structural features and nucleic acid chemistry in solution through sequence-dependent chemical shift predictions.

Methodology:

Computational predictions use published reference shifts plus correction factors for nearest- and next-nearest-neighbor effects; a trimer model for phosphorus, a triplet database for carbon derived from 17-nucleotide sequence analyses, and proton parameters based on central nucleotide measurements within 64 triplets, with sequence and temperature effects analyzed explicitly.