Molecular deformation and free‐solution electrophoresis of DNA‐uncharged polymer conjugates at high field strengths: Theoretical predictions. Part 1: Hydrodynamic segregation

Abstract

Recent advancements in DNA sequencing by end-labeled free-solution electrophoresis (ELFSE) show the promise of this novel technique which overcomes the need for a gel by using a label (or drag-tag) to render the free solution mobility of the DNA size-dependent. It is the attachment of an uncharged drag-tag molecule of a set size to various lengths of DNA in the sample that selectively slows down smaller DNA chains which have less force to pull the drag-tag than larger DNA. So far, only globally random coil conformations have been associated with ELFSE, i.e., the DNA and the label together form a single, undeformed hydrodynamic unit. This paper investigates the conditions under which the DNA and label will segregate into two hydrodynamically distinct units, based on a theoretical approach developed for the electrophoresis of polyampholytes. Optimal experimental conditions tailored to the available label sizes and voltages are predicted along with insight into ideal label architecture.

Theory of end‐labeled free‐solution electrophoresis: Is the end effect important?

“…All data points are calculated numerically, as described in Section 2, using average inverse distances given by Eqs. (20), (21) and (34). The dashed lines are the linear fits, with the actual ranges used for fitting shown as thicker solid lines.…”

“…For the latter, theories and computer simulations of electrophoresis of composite objects are necessary. Besides generic theories not making specific assumptions about the drag-tag [3] and the simplest case of a flexible diblock copolymer in a weak field [15][16][17][18], the problems considered theoretically so far include globular [15,19] and branched [18,20] drag-tags, separation and stretching of a drag-tag-DNA composite in a strong field [21][22][23][24], and dragtags attached to both ends of the DNA [25]. Besides ELFSE, such studies can also be useful for understanding other situations of practical interest involving objects consisting of two or more parts with different electrophoretic properties, for instance, different variants of affinity electrophoresis [26][27][28][29][30].…”

Polyelectrolytes in multivalent salt solutions

“…Molecular dynamics simulations are a simple and economic tool, able to study systems in a controllable way and capture detailed information at the molecular level. Many simulation works investigate the structure of PEs in different solution conditions [10,14,[27][28][29][30] and the response to electric fields [7,8,16,19,20,25,31,32]. However, detailed information about the electrokinetics of different species of ions around the chains is lacking.…”

Optimizing End-Labeled Free-Solution Electrophoresis by Increasing the Hydrodynamic Friction of the Drag Tag

“…The chemistry and temperature dependent R L is a measure for the difference in hydrodynamic properties between the polyelectrolyte and the label and represents the number of polyelectrolyte monomers that provide a hydrodynamic friction equal to that of the label. 8,12,18,19,27 In order to characterize the effectiveness of an arbitrary (not necessarily linear) label for size separation, eq 3 has been used to define this specific label property from the measured mobilities:…”

“…Of course, it is beyond the scope of this article to cover all previous predictions. 12,14,[18][19][20][21] However, we will demonstrate that it is possible to study these factors, and that the standard theory appears to be sufficient for the cases treated here. More cases will be studied in future papers.…”