Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel.
نویسندگان
چکیده
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.
منابع مشابه
Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel.
The effect of dextran nanoparticles on the conformation and compaction of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. It was observed that the DNA molecules elongate and eventually condense into a compact form with increasing volume fraction of the crowding agent. Under crowded conditions, the channel diameter is effectively reduced, which is in...
متن کاملA Nanochannel Platform for Single DNA Studies: From Crowding, Protein DNA Interaction, to Sequencing of Genomic Information
Advances in nanolithography have made it possible to fabricate nanofluidic devices with at least one dimension of around a few tens of nanometers. Nano-devices featuring entropic trap arrays, pillar arrays, pores, or channels have been designed and used for the analysis of the properties of long biopolymers, including DNA. Here, we discuss long and straight quasi one-dimensional channel devices...
متن کاملEffect of H-NS on the elongation and compaction of single DNA molecules in a nanospace.
The effect of the bacterial heat-stable nucleoid-structuring protein (H-NS) on the conformation of single DNA molecules confined in a nanochannel was investigated with fluorescence microscopy. With increasing concentration of H-NS, the DNA molecules either elongate or contract. The conformational response is related to filamentation of H-NS on DNA through oligomerization and H-NS mediated bridg...
متن کاملپتانسیل الکتروستاتیک یک مولکول زیستی مارپیچی در رژیم دیبای- هوکل با در نظر گرفتن ناهمگنی دیالکتریک
Inside living cells, many essential processes involve deformations of charged helical molecules and the interactions between them. Actin filaments and DNA molecules are important examples of charged helical molecules. In this paper, we consider an impermeable double stranded charged molecule in the solvent. According to the nature, the dielectric constant of the molecule is considerably differe...
متن کاملThe dynamics of genomic-length DNA molecules in 100-nm channels
We show that genomic-length DNA molecules imaged in nanochannels have an extension along the channel that scales linearly with the contour length of the polymer, in agreement with the scaling arguments developed by de Gennes for self-avoiding confined polymers. This fundamental relationship allows us to measure directly the contour length of single DNA molecules confined in the channels, and th...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- The Journal of chemical physics
دوره 128 22 شماره
صفحات -
تاریخ انتشار 2008