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    Short Oligonucleotides Aligned in Stretched Humid Matrix: Secondary DNA Structure in Poly(vinyl alcohol) Environment

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    Type
    Article
    Authors
    Hanczyc, Piotr
    Åkerman, Björn
    Nordén, Bengt
    Date
    2012-04-09
    Online Publication Date
    2012-04-09
    Print Publication Date
    2012-04-24
    Permanent link to this record
    http://hdl.handle.net/10754/599360
    
    Metadata
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    Abstract
    We 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.
    Citation
    Hanczyc 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.
    Sponsors
    We 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.
    Publisher
    American Chemical Society (ACS)
    Journal
    Langmuir
    DOI
    10.1021/la300960q
    PubMed ID
    22452613
    ae974a485f413a2113503eed53cd6c53
    10.1021/la300960q
    Scopus Count
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