Sensing the structural and conformational properties of single-stranded nucleic acids using electrometry and molecular simulations.
Disordered molecules
Molecular dynamics
Molecular electrostatics
Single stranded nucleic acids
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
04 Sep 2024
04 Sep 2024
Historique:
received:
26
03
2024
accepted:
20
08
2024
medline:
5
9
2024
pubmed:
5
9
2024
entrez:
4
9
2024
Statut:
epublish
Résumé
Inferring the 3D structure and conformation of disordered biomolecules, e.g., single stranded nucleic acids (ssNAs), remains challenging due to their conformational heterogeneity in solution. Here, we use escape-time electrometry (ETe) to measure with sub elementary-charge precision the effective electrical charge in solution of short to medium chain length ssNAs in the range of 5-60 bases. We compare measurements of molecular effective charge with theoretically calculated values for simulated molecular conformations obtained from Molecular Dynamics simulations using a variety of forcefield descriptions. We demonstrate that the measured effective charge captures subtle differences in molecular structure in various nucleic acid homopolymers of identical length, and also that the experimental measurements can find agreement with computed values derived from coarse-grained molecular structure descriptions such as oxDNA, as well next generation ssNA force fields. We further show that comparing the measured effective charge with calculations for a rigid, charged rod-the simplest model of a nucleic acid-yields estimates of molecular structural dimensions such as linear charge spacings that capture molecular structural trends observed using high resolution structural analysis methods such as X-ray scattering. By sensitively probing the effective charge of a molecule, electrometry provides a powerful dimension supporting inferences of molecular structural and conformational properties, as well as the validation of biomolecular structural models. The overall approach holds promise for a high throughput, microscopy-based biomolecular analytical approach offering rapid screening and inference of molecular 3D conformation, and operating at the single molecule level in solution.
Identifiants
pubmed: 39232063
doi: 10.1038/s41598-024-70641-x
pii: 10.1038/s41598-024-70641-x
doi:
Substances chimiques
DNA, Single-Stranded
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
20582Subventions
Organisme : HORIZON EUROPE European Research Council
ID : 724180
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/W017415/1
Pays : United Kingdom
Informations de copyright
© 2024. The Author(s).
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