A Nanochannel Platform for Single DNA Studies: From Crowding, Protein DNA Interaction, to Sequencing of Genomic Information. Issue 11 (13th October 2014)

• Record Type: Journal Article
• Authors: van der Maarel, Johan R. C.; Zhang, Ce; van Kan, Jeroen A.
• Is Part Of: Israel journal of chemistry. Volume 54:Issue 11/12(2014)
• Page Start: 1573
• Page End: 1588
• Publication Date: 2014-10-13
• Subjects: Chemistry -- Periodicals; 540.5
• DOI: 10.1002/ijch.201400091
• Languages: English
• ISSNs: 0021-2148

Abstract

<abstract abstract-type="main" xml:lang="en"> <title>Abstract</title> <p>The study of nanochannel‐confined DNA is important from biotechnological and biophysical points of view. We produce nanochannels in elastomer with soft lithography and proton beam writing. Issues concerning DNA confined in such quasi one‐dimensional channels are discussed. We describe DNA stretching via the control of channel diameter and buffer conditions and how the extension can be interpreted with theory and computer simulation. We then discuss the conformation of nano‐confined DNA crowded by neutral polymers and like‐charged proteins. As an example of a protein that has an affinity to DNA, the effect of heat‐stable nucleoid‐structuring protein, H‐NS, on the folding and compaction of DNA is reviewed. Compaction of DNA by eukaryotic protamine and unpacking of pre‐compacted DNA through an increase in salt concentration are discussed. We review results obtained with a novel, cross‐channel device that allows the monitoring of the dynamic, conformational response of DNA after exposure to a ligand or protein and/or a change in buffer conditions <italic>in situ</italic>. As a biotechnological application, linearization of DNA by bottlebrush coating with a polypeptide copolymer is discussed. It is demonstrated that large‐scale genomic organization can be sequenced using single DNA molecules on an array of elastomeric nanochannels. Overall, our results show that the effects of ligands and proteins on the conformation, folding, and condensation of DNA are not only related to classical controlling factors, such as osmotic pressure, charge, and binding, but that the interplay with confinement in a nanospace is of paramount importance.</p> </abstract>