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Sound packing DNA: packing open circular DNA with low-intensity ultrasound.

Park D, Jung BK, Park H, Lee H, Lee G, Park J, Shin U, Won JH, Jo YJ, Chang JW, Lee S, Yoon D, Seo J, Kim CW - Sci Rep (2015)

Bottom Line: Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research.Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form.We anticipate our results to be a starting point for improved non-viral gene delivery.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Tumor Immunity Medical Research Center, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.

ABSTRACT
Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm(2) intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery.

No MeSH data available.


Related in: MedlinePlus

Representative sample of image processed DNA images for the follow up experiment.TOP LEFT: control group (at one hour) with folding index value 135. TOP RIGHT: control group (at one week) with folding index value 175. BOTTOM LEFT: 30-second group (at one hour) with folding index value 206. TOP RIGHT: 30-second group (at one week) with folding index value 121. White contours were the extracted contours of a given ROI using the image processing approach.
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f3: Representative sample of image processed DNA images for the follow up experiment.TOP LEFT: control group (at one hour) with folding index value 135. TOP RIGHT: control group (at one week) with folding index value 175. BOTTOM LEFT: 30-second group (at one hour) with folding index value 206. TOP RIGHT: 30-second group (at one week) with folding index value 121. White contours were the extracted contours of a given ROI using the image processing approach.

Mentions: As indicated in the introduction, the supercoiled format of DNA is energetically unfavorable, so that the DNA packed by ultrasound can uncoil as time passes. Hence, we performed a follow-up experiment to explore whether sonication-induced folding could be reversed (i.e., unfolds or becomes less folded). The AFM images of the control and the 30-second group were taken at one hour and one week after the experiment, as can be seen in Fig. 3. The 30-second group was chosen since it was sufficiently effective for DNA packing. Only two images were taken for each group, at a given time point. We applied the same image processing procedures to quantify the degree of folding. We measured the folding index for 12 structures in a given group at each time point. The results were given in Table 2. P-values were not reported in the Table below since we did not accumulate enough samples for a fair comparison for the follow up experiment. For the control group, the folding index did not change significantly (130 (one hour) −> 150 (one week)) considering the SD value. For the 30-second group, the folding index reduced significantly (203 (one hour) −> 154(one week)) considering the SD value. We observed that the degree of folding decreased as time passed; thus, the process of sonication-induced folding was reversible to some extent, based on limited samples from the 30-second group. Further experiments are required to quantitatively measure the time constant for reversing the packing effect induced by ultrasound sonication.


Sound packing DNA: packing open circular DNA with low-intensity ultrasound.

Park D, Jung BK, Park H, Lee H, Lee G, Park J, Shin U, Won JH, Jo YJ, Chang JW, Lee S, Yoon D, Seo J, Kim CW - Sci Rep (2015)

Representative sample of image processed DNA images for the follow up experiment.TOP LEFT: control group (at one hour) with folding index value 135. TOP RIGHT: control group (at one week) with folding index value 175. BOTTOM LEFT: 30-second group (at one hour) with folding index value 206. TOP RIGHT: 30-second group (at one week) with folding index value 121. White contours were the extracted contours of a given ROI using the image processing approach.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402968&req=5

f3: Representative sample of image processed DNA images for the follow up experiment.TOP LEFT: control group (at one hour) with folding index value 135. TOP RIGHT: control group (at one week) with folding index value 175. BOTTOM LEFT: 30-second group (at one hour) with folding index value 206. TOP RIGHT: 30-second group (at one week) with folding index value 121. White contours were the extracted contours of a given ROI using the image processing approach.
Mentions: As indicated in the introduction, the supercoiled format of DNA is energetically unfavorable, so that the DNA packed by ultrasound can uncoil as time passes. Hence, we performed a follow-up experiment to explore whether sonication-induced folding could be reversed (i.e., unfolds or becomes less folded). The AFM images of the control and the 30-second group were taken at one hour and one week after the experiment, as can be seen in Fig. 3. The 30-second group was chosen since it was sufficiently effective for DNA packing. Only two images were taken for each group, at a given time point. We applied the same image processing procedures to quantify the degree of folding. We measured the folding index for 12 structures in a given group at each time point. The results were given in Table 2. P-values were not reported in the Table below since we did not accumulate enough samples for a fair comparison for the follow up experiment. For the control group, the folding index did not change significantly (130 (one hour) −> 150 (one week)) considering the SD value. For the 30-second group, the folding index reduced significantly (203 (one hour) −> 154(one week)) considering the SD value. We observed that the degree of folding decreased as time passed; thus, the process of sonication-induced folding was reversible to some extent, based on limited samples from the 30-second group. Further experiments are required to quantitatively measure the time constant for reversing the packing effect induced by ultrasound sonication.

Bottom Line: Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research.Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form.We anticipate our results to be a starting point for improved non-viral gene delivery.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Tumor Immunity Medical Research Center, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.

ABSTRACT
Supercoiling DNA (folding DNA into a more compact molecule) from open circular forms requires significant bending energy. The double helix is coiled into a higher order helix form; thus it occupies a smaller footprint. Compact packing of DNA is essential to improve the efficiency of gene delivery, which has broad implications in biology and pharmaceutical research. Here we show that low-intensity pulsed ultrasound can pack open circular DNA into supercoil form. Plasmid DNA subjected to 5.4 mW/cm(2) intensity ultrasound showed significant (p-values <0.001) supercoiling compared to DNA without exposure to ultrasound. Radiation force induced from ultrasound and dragging force from the fluid are believed to be the main factors that cause supercoiling. This study provides the first evidence to show that low-intensity ultrasound can directly alter DNA topology. We anticipate our results to be a starting point for improved non-viral gene delivery.

No MeSH data available.


Related in: MedlinePlus