Extension distribution for DNA confined in a nanochannel near the Odijk regime

Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale

The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.

Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement

Coarse-grained modeling tools are employed to simulate the mechanics of DNA loading within a nanoscale confinement and predict semiflexible polymer conformations within the confinement, providing design recommendations for DNA-sequencing devices. A workflow is developed to quantify competing requirements of efficiency and accuracy and extract metrics that guide design optimization. The mean first-passage time for DNA loading is calculated as a function of the nanochannel geometry and the applied electric field. We analyze the interplay between the free energy of confinement and the electric potential energy in achieving high-throughput, base-pair detection. The single-read probability is investigated as informative metrics for sequencing accuracy and for sensing-strategy design. High cost, low throughput, and low accuracy have so far limited the adoption of nanochannel analysis and other long-read technologies. Our work directly addresses these limitations with a systematic approach that is scalable to long molecules and complex geometries.

Limitations of the equivalent neutral polymer assumption for theories describing nanochannel-confined DNA

The prevailing theories describing DNA confinement in a nanochannel are predicated on the assumption that wall-DNA electrostatic interactions are sufficiently short-ranged such that the problem can be mapped to an equivalent neutral polymer confined by hard walls with an appropriately reduced effective channel size. To determine when this hypothesis is valid, we leveraged a recently reported experimental data set for the fractional extension of DNA molecules in a 250-nm-wide poly(dimethyl siloxane) (PDMS) nanochannel with buffer ionic strengths between 0.075 and 48 mM. Evaluating these data in the context of the weakly correlated telegraph model of DNA confinement reveals that, at ionic strengths greater than 0.3 mM, the average fractional extension of the DNA molecules agree with theoretical predictions with a mean absolute error of 0.04. In contrast, experiments at ionic strengths below 0.3 mM produce average fractional extensions that are systematically smaller than the theoretical predictions with a larger mean absolute error of 0.15. The deviations between experiment and theory display a correlation coefficient of 0.82 with the decay length for the DNA-wall electrostatics, linking the deviations with a breakdown in approximating the DNA with an equivalent neutral polymer.