Label Type Influence on DNA Translocation Velocity in Solid-State Nanopores

Area of Science:

• Nanotechnology
• Molecular Biology
• Biophysics

Background:

• Solid-state nanopores facilitate single-molecule detection of nucleic acids, enabling precise localization of molecular labels on DNA carriers.
• Applications include molecular barcoding, protein mapping, and DNA data storage, often assuming minimal perturbation by these labels.
• The impact of dense molecular labeling on DNA translocation dynamics and positional readout accuracy is not well-quantified.

Purpose of the Study:

• To systematically quantify the effect of dense molecular labeling on DNA carrier translocation times in solid-state nanopores.
• To assess the influence of different label types (DNA nanostructures, streptavidin, PEG) on translocation dynamics.
• To determine if label-specific velocity corrections are necessary for applications like molecular barcoding.

Main Methods:

• Utilized glass nanopipettes (8-12 nm diameter) as solid-state nanopores.
• Employed 7.2 kbp DNA carriers with up to 60 labels of various types (DNA nanostructures, streptavidin, PEG).
• Systematically measured and analyzed translocation times and label-associated event timings.

Main Results:

• Despite significant increases in mass (up to 83%) and charge (up to 23%), all tested labels caused modest changes (<±15%) in global translocation time, below measurement variability (∼20%).
• The velocity profile during translocation remained consistent across label types.
• A substantial portion (40-70%) of the translocation time shift occurred in labeled regions, though these comprised only 20% of the carrier.

Conclusions:

• Dense molecular labeling has a minimal impact on overall DNA carrier translocation times in nanopores.
• Relative label positions are largely unaffected, preserving positional readout accuracy.
• Molecular barcoding and protein-positioning assays can generally proceed without label-specific velocity corrections under studied conditions.