Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment
Online Publication Date2012-04-09
Print Publication Date2012-04-24
Permanent link to this recordhttp://hdl.handle.net/10754/599360
MetadataShow full item record
AbstractWe report that short, synthetic, double- as well as single-stranded DNA can be aligned in stretched humid poly(vinyl alcohol) (PVA) matrix, and the secondary structure (nucleobase orientation) can be characterized with linear dichroism (LD) spectroscopy. Oligonucleotides of lengths varying between 10 (3.4 nm) and 60 bases (20.4 nm) were investigated with respect to structural properties in the gel-like polymer environment. The DNA conformation as a function of relative humidity reveals a strong dependence of helical structure of DNA on PVA hydration level, results of relevance for nanotechnical studies of DNA-based supramolecular systems. Also, the PVA gel could provide possibilities to test models for nucleic acid interactions and distribution in cell contexts, including structural stability of genetic material in the cell and PVA-packaging for gene delivery. A method by which duplex oligonucleotides, with sequences designed to provide specific binding sites, become amenable to polarized-light spectroscopy opens up new possibilities for studying structure in DNA complexes with small adduct molecules as well as proteins. © 2012 American Chemical Society.
CitationHanczyc P, Åkerman B, Nordén B (2012) Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment. Langmuir 28: 6662–6669. Available: http://dx.doi.org/10.1021/la300960q.
SponsorsWe thank Bobo Feng for discussions and useful comments on the manuscript. The research was supported by grants from the King Abdullah University of Science and Technology (KAUST) and the European Research Council (ERC) to B.N.
PublisherAmerican Chemical Society (ACS)
CollectionsPublications Acknowledging KAUST Support
- Interactions of binuclear ruthenium(II) complexes with oligonucleotides in hydrogel matrix: enantioselective threading intercalation into GC context.
- Authors: Hanczyc P, Lincoln P, Norden B
- Issue date: 2013 Mar 14
- DNA in a polyvinyl alcohol matrix and interactions with three intercalating cyanine dyes.
- Authors: Hanczyc P, Norden B, Åkerman B
- Issue date: 2011 Oct 27
- Birefringence and dichroism of poly(vinyl-alcohol) foils containing phthalazinium ylids.
- Authors: Rogojanu A, Dascalu CF, Zelinschi BC, Caprosu M, Dorohoi DO
- Issue date: 2011 Oct 15
- Implications of cytosine methylation on (+)-anti-Benzo[a]pyrene 7, 8-dihydrodiol 9,10-epoxide N(2)-dG adduct formation in 5'-d(CGT), 5'-d(CGA), and 5'-d(CGC) sequence contexts of single- and double-stranded oligonucleotides.
- Authors: Pradhan P, Gräslund A, Seidel A, Jernström B
- Issue date: 1999 Sep
- Structural and functional characterisation of poly(vinyl alcohol) and heparin hydrogels.
- Authors: Nilasaroya A, Poole-Warren LA, Whitelock JM, Jo Martens P
- Issue date: 2008 Dec