Separation of Long Double-Stranded DNA by Nanoparticle-Filled Capillary Electrophoresis

Abstract

We present the first example of the analysis of long double-stranded (ds) DNA molecules by nanoparticle-filled capillary electrophoresis (NFCE). To avoid aggregation of the gold nanoparticles (GNPs) and to allow strong interactions with the DNA molecules, the gold nanoparticles were modified with poly(ethylene oxide) (PEO) via noncovalent bonding to form gold nanoparticle/polymer composites (GNPPs). The neutral GNPPs are heavy (approximately 2.0 x 10(8) g/mol for the 32-nm GNP) and thus slow the DNA molecules that they encounter during the electrophoretic process. Compared to linear polymer solutions, such as hydroxyethyl cellulose and PEO, the GNPPs provide greater efficiency and require significantly shorter times to separate long dsDNA. The separation of lambda-DNA (0.12-23.1 kbp) by NFCE at -250 V/cm was accomplished in 3 min. The ability to separate high molecular weight DNA markers (8.27-48.5 kbp) with plate numbers greater than 10(6) suggests that this novel method may hold great promise for the analysis of long-stranded DNA molecules such as chromosomes. Moreover, this method is simple and affordable when compared to those that use micro- and nanofabricated devices for separating long DNA molecules.

Label-free Electrochemical Cocaine Aptasensor Based on a Target-inducing Aptamer Switching Conformation

“…The proposed aptasensor can be easily regenerated by the denaturalization of aptamer-target complexes in a heated water bath at 80 -90 C. Besides, this biosensor has a high reproducibility and selectivity, which can be a promising method to detect cocaine in real samples. After introducing cocaine, nucleic acid aptamers combine with cocaine to form three-way junction complexes, 20 which increase the charge density and the steric hindrance on the surface of the electrode, and block the diffusion of [Fe(CN)6] 3-/4-onto the electrode surface. 21,22 All changes lead to an obvious decrease of the peak current of [Fe(CN)6] 3-/4-, which is in direct proportion to a quantity of an added cocaine.…”

Electrophoretic Separation of Proteins in Capillaries Filled with Poly(ethylene oxide)-stabilized Silver Nanoparticles

“…14 Chang's group employed gold nanoparticles (GNPs) as additives in CE separation of DNA fragments. [23][24][25][26] Due to the interaction of DNA fragments with the GNPs, the apparent mobilities of DNA fragments changed, and the plate numbers doubled.…”

Analysis of Broad-Range DNA Fragments with Yttrium Oxide or Ytterbium Oxide Nanoparticle/Polymer Sieving Matrix Using High-Performance Capillary Electrophoresis

“…This concentration is far below PEO (M r = 8,000,000)'s entanglement (overlap) threshold (c*) of 0.07%. 23 It should be noted that for the concentration above c*, the polymer begins to form "pores" to provide DNA fragments with size-dependant separation. With our low PEO concentration, it is known that instead of forming pores, DNA molecules drag the polymer along as they are encountered during migration (transient entanglement mechanism), 24 which was supported by dynamic formation and deformation of U-shape in DNA conformation.…”

“…With our low PEO concentration, it is known that instead of forming pores, DNA molecules drag the polymer along as they are encountered during migration (transient entanglement mechanism), 24 which was supported by dynamic formation and deformation of U-shape in DNA conformation. 23 When the drag force by DNA is not enough due to smaller mass of DNA, it is expected that the resolution suffers as shown in Figure 1(c) for relatively smaller size of DNA fragments. An excellent separation efficiency was obtained with the separation medium of the mixture of PEO and YNP as shown in Figure 1(d).…”