Abstract
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.
Highlights
The double-helix structure of DNA stores genetic information linearly as a sequence of bases at the molecular level, entropy randomizes the three-dimensional conformations of DNA polymers in free solution, making accessing genomic information from long polymers exceedingly challenging
Genetic information is stored in a linear sequence of base pairs; thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis
A coarse-grained dissipative particle dynamics (DPD) numerical model is used to simulate generic DNA molecules to extend our understanding of DNA dynamics in three-dimensional azimuthal flows at various rotation rates with hydrodynamic interactions
Summary
The double-helix structure of DNA stores genetic information linearly as a sequence of bases at the molecular level, entropy randomizes the three-dimensional conformations of DNA polymers in free solution, making accessing genomic information from long polymers exceedingly challenging. While single strands of untethered DNA are observed to elongate substantially in agreement with scaling theory and simulations, full DNA extension becomes obtainable by combining tethering with this DNA spooling approach. By slowly increasing the experimentally realizable rotation rate above an additional critical value, our simulations show that a substantial portion of the tethered DNA is spooled into a strongly stretched, single-file curvilinear conformation. Since the conformation consists of a shofartype tail and a base-ordered stem, we refer to this as a “French-horn” conformation. In this rotation-induced macromolecular spooling, the fraction of the polymer in the fully ordered stem of the French-horn conformation is found to increase with strand length
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