Novel Method Reveals Sub-Microsecond Dynamics of DNA Molecules on Graphene
Researchers have developed a method to observe conformational fluctuations in individual DNA molecules at sub-microsecond timescales by anchoring nucleic acids vertically on graphene and measuring distance-dependent fluorescence energy transfer. The approach reveals how ionic strength and structural defects such as nucleotide gaps or mismatches alter DNA dynamics. The technique bridges single-molecule experimentation with atomistic simulations, offering a new window into how thermal fluctuations govern nucleic acid function.
A new experimental framework described in a bioRxiv preprint enables direct observation of rapid conformational dynamics in single DNA molecules at timescales shorter than one microsecond. The method works by immobilizing oligonucleotides vertically on a graphene surface and exploiting graphene's distance-dependent energy transfer properties to convert nanoscale molecular movements into measurable fluorescence intensity fluctuations. The researchers demonstrated that varying ionic strength modulates these fluctuations, while structural defects in the DNA strand — including nucleotide gaps and base mismatches — produce distinct dynamic signatures. Experimental results were validated and interpreted using both atomistic molecular dynamics simulations and kinetic Monte Carlo simulations, establishing a quantitative link between theoretical structural predictions and observed fluctuation timescales. The work addresses a longstanding challenge in biophysics: disentangling functionally relevant structural transitions from the background of rapid thermal motion at the single-molecule level. The authors suggest the platform could be broadly applicable to studying how external conditions and internal sequence features shape nucleic acid behavior.
What's missing
As a preprint, this work has not yet undergone peer review, so the validity of the methodology and the generalizability of findings to longer or more complex nucleic acid structures remain to be independently assessed.
What different sources said
- bioRxivCenter
Resolving Sub-Microsecond Conformational Dynamics of Vertical Nucleic Acids on Graphene
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