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Relation between DNA ionization potentials, single base substitutions and pathogenic variants.

Fabrizio Pucci1,2, Marianne Rooman3

  • 1Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave. 50, Bruxelles, 1050, Belgium.

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|July 17, 2019
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Summary
This summary is machine-generated.

Single base substitutions in the human genome are influenced by flanking sequences. Lower vertical ionization potential (vIP) correlates with higher substitution probability and pathogenicity, suggesting electron-hole transport

Keywords:
Charge transportDNA base stackingPathogenic mutationsSingle base substitutionsVertical ionization potential

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Area of Science:

  • Genomics
  • Biophysics
  • Computational Chemistry

Background:

  • Single base substitutions in the human genome are non-random and influenced by flanking nucleobase sequences.
  • Understanding these "non-local" effects remains a challenge in genomics.

Purpose of the Study:

  • To investigate the relationship between base mutability and electron-hole transport along DNA.
  • To explore the connection between single base substitution frequency, ionization potential, and pathogenicity.

Main Methods:

  • Analysis of normalized single base substitution frequency.
  • Estimation of vertical ionization potential (vIP) using MP2/6-31G* ab initio quantum chemistry calculations.
  • Correlation analysis between vIP, substitution frequency, and pathogenicity.

Main Results:

  • A statistically significant anticorrelation was found between vIP and substitution probability (lower vIP, higher probability).
  • The correlation strength varied across genomic regions (introns vs. exons) and substitution types (synonymous vs. missense).
  • A significant correlation was observed between vIP and base substitution pathogenicity, particularly with larger changes in vIP.

Conclusions:

  • New insights into the biophysical mechanisms of mutagenesis and pathogenicity were gained.
  • The role of electron-hole transport in influencing base substitution and pathogenicity was supported.