10 research outputs found

    Nanoscale Structure and Interaction of Condensed Phases of DNA–Carbon Nanotube Hybrids

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    Condensation of DNA–carbon nanotube (CNT) hybrids dispersed in aqueous solutions can be induced by elevated hybrid concentrations, salts, or crowding agents. DNA–CNT condensates exhibit either nematic ordering or amorphous aggregates, dependent on the nature of interhybrid interactions. This study employed X-ray diffraction (XRD) to determine nanoscale structures of the condensates, including the presence of positional ordering, interaxial distances, and the range of ordered domains. To probe the effects of DNA sequence, two types of CNT hybrids, dispersed by genomic DNA of random sequence and synthetic oligonucleotides respectively, were studied under identical conditions. The osmotic stress method was further used to quantify force–distance dependencies of the DNA–CNT hybrids to elucidate the relation between interhybrid interactions and condensate structures. We observed that, independent of DNA sequence, lyotropic DNA–CNT phases showed weak positional ordering with long interhybrid distances, salt-induced condensates were amorphous, crowding-condensed DNA–CNTs were the most ordered with pronounced XRD peaks, and interhybrid interactions were defined by short-range hydration repulsion and long-range electrostatic repulsion. Conversely, the effects of DNA sequence became evident as to their quantitative force–distance relationships. Genomic DNA of random sequence consistently gave longer interhybrid distances than synthetic oligonucleotides, which we attribute to the likely differences in their hybrid diameters

    Thermal denature curves of calf thymus and plasmid DNA.

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    <p>Plasmid DNA: hollow symbols; calf thymus DNA: solid symbols. C = 16 µg/mL.</p

    LLS results of plasmid DNA and calf thymus DNA in TE buffer and in 95%DMF.

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    <p>LLS results of plasmid DNA and calf thymus DNA in TE buffer and in 95%DMF.</p

    TEM measurements of (A) calf thymus and (B) plasmid DNA air dried from 95% DMF.

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    <p>TEM measurements of (A) calf thymus and (B) plasmid DNA air dried from 95% DMF.</p

    Temperature effect on hydrodynamic radius of plasmid DNA in 95% DMF at 30°.

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    <p>The inset shows the temperature dependence of R<sub>h,app</sub> at zero angle.</p

    Agarose gel electrophoresis of DNA samples.

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    <p>(A) Plasmid DNA: M<sub>W</sub> marker (lane 1), control DNA (lane 2), control DNA cut with <i>Eco</i>RI, which linearized the plasmid but would not alter the size (lane 3), control DNA cut with <i>Pst</i>I showing 2 fragments with different lengths (lane 4), DNA treated with DMF and cut with <i>Eco</i>RI (lane 5) or <i>Pst</i>I (lane 6); (B) Calf thymus DNA: M<sub>W</sub> marker (lane 1), control DNA (lane 2), DNA treated with water (lane 3), DNA treated with DMF (lane 4).</p

    DMF-content dependence of zeta potential measurements of calf thymus DNA and plasmid DNA.

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    <p>DMF-content dependence of zeta potential measurements of calf thymus DNA and plasmid DNA.</p

    Attractive Interactions between DNA–Carbon Nanotube Hybrids in Monovalent Salts

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    DNA–carbon nanotube (DNA-CNT) hybrids are nanometer-sized, highly charged, rodlike molecules with complex surface chemistry, and their behaviors in aqueous solutions are governed by multifactorial interactions with both solvent and cosolutes. We have previously measured the force between DNA-CNTs as a function of their interaxial distance in low monovalent salts where interhybrid electrostatic repulsion dominates. The characteristics of DNA-CNT forces were further shown to closely resemble that of double-stranded DNA (dsDNA) in low salts. However, contrasting behaviors emerge at elevated monovalent salts: DNA-CNT condenses spontaneously, whereas dsDNA remains soluble. Here we report force–distance dependencies of DNA-CNTs across wide-ranging monovalent salt concentrations. DNA-CNT force curves are observed to deviate from dsDNA curves above 300 mmol/L NaCl, and the deviation grows with increasing salts. Most notably, DNA-CNT forces become net attractive above 1 mol/L NaCl, whereas dsDNA forces are repulsive at all salt concentrations. We further discuss possible physical origins for the observed DNA-CNT attraction in monovalent salts, in consideration of the complex surface chemistry and unique polyelectrolyte properties of DNA-CNT hybrids
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