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The radiolabeled sisiRNA annealed well wth a yield above 90 %, and could consequently be used for attachement to the origami plate without further purification.
The radiolabeled sisiRNA annealed well wth a yield above 90 %, and could consequently be used for attachement to the origami plate without further purification.
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===Attachment of sisiRNA to the origami plate===
===Attachment of sisiRNA to the origami plate===

Revision as of 12:38, 24 October 2013

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System in action

Test of photosensitizers and cholesterols

Hybridization of the chemically modified DNA strands

In order to test the ability of the photosensitizers to induce apoptosis in cells, a test system was designed. This system consisted of two complementary DNA strands, of which one was modified with the photosensitizer, In(PPa)Cl, and the other with cholesterol. In order to achive the highest yield of annealing of the modified DNA strands, the annealing of three different designs was tested. The chosen design was design DII (see structure below). Gel analysis of this test system showed that the two modified DNA strands had annealed well (see fig. 42 below).

Fig. 42. Details of the design, DII.

The gel was scanned at 670 nm, where the photosensitizer absorb light, and subsequently stained for the nucleic acids with etidium bromide and scanned again.

Fig. 43. Native PAGE gel showing the annealing of modified DNA strands. A: Gel scanned for the photosensitizer. B: The gel after staining with ethidium bromide. 1) DNA ladder, 2) 5’ unmodified DNA, 3) 5’ cholesterol DNA design II, 4), 3’ cholesterol DNA design II, 5) 3’ In(PPa)Cl DNA, 6) 3’ In(PPa)Cl DNA + 5’ cholesterol DNA design II, 7) 3’ In(PPa)Cl DNA + 3’ cholesterol DNA design II, 8) 3’ amine unmodified DNA + 5’ amine unmodified DNA.

On the gel in fig. 43, the single stranded DNA modified with In(PPa)Cl (lane 5) gives rise to a band below the band for the two modified DNA strands together (lanes 6 and 7). This band shift is due to the annealing of the two strands. The gel, both stained and unstained, confirms that the modified DNA strands of DII anneal. On this gel it is also possible to see the two unmodified DNA strands (lane 8), which also anneal, although the annealing is not complete.

Cell experiments with DII

As the gel in fig. 43 showed a sufficient annealing of the two strands in DII, the system could consequently be tested on cells, to see if the cholesterols were able to bring the photosensitizers close enough to the cells to mediate photoinduced cellular death. First, the localization of the cholesterols to the membrane was assayed. HeLa cells were incubated with DII in a concentration of 5µM for 30 min.

Fig 44. Cells, treated with 5 µM DII for 30 minutes. A: Brightfield (BF)- image, 40x. B: Flourescence microscopy image, 40x.

As seen from fig. 44A, no bubble formation or flattening of the cells was observed, indicating that the cells were still viable after the treatment. This indicates that no dark toxicity was induced with the DII system. In fig 44B, a very weak fluorescence is observed. The cellular debris is seen as a bright spot at the center of the image. In order to obtain a higher degree of cellular interactions, the experiment was repeated with DII in a 5 µM concentration for a period of 2 hours. An increase in cellular interactions would also yield a higher fluorescence signal, that might help locating the position of the DII testsystem on the cell. The cells were again visualized with brightfield microscopy and fluorescence microscopy (fig. 45).

Fig. 45. Cells imaged after incubation with 5 µM DII for 2 hours. A: Brightfield microscopy image, 40x. B: Flourescence microscopy image, 40x.

The cells were examined after incubation with DII (fig. 45A), and appeared healthy, as neither bubbles, nor flattened cells were observed. This indicates that the DII system exhibits no dark toxicity. In order to locate the DII system, the flourescence was imaged (fig. 45B). All parts of the cells seems stained, and therefore it was not possible to conclude anything about the localization of DII. The flourescens is nonetheless better than after 30 minutes incubation, thus higher incubationtime has lead to higher cell interaction.

The DII system was then tested for the ability the photoinduce death in cells. Cells were incubated with 5 µM DII, and subsequently irradiated at 670 nm for 15 minutes.

Fig 46. Brightfield image, 40x 15 minutes after irradiation.

After irradiation, the formation of vacuoles (seen as bubbles, and marked as red arrows) was observed, as well as flattened cell bodies and pronounced nuclei (black arrows). As the image in fig 46, show clear signs of cell death, it can be concluded that the photosensitizer was able to emit singlet oxygen upon light exposure, and induce necrosis or apoptosis in these cells. The drug delivery system designed in this project and also the designed testsystem DII was aiming for the tight controlled selfinduced apoptosis pathway for cell death. In many cases photodynamic therapy (PDT) is highly efficient in inducing apoptosis, though high doses have been shown to result in the target cells becoming necrotic, while the surrounding tissue become apoptotic. [1] Thus DII might still induce apoptosis, but the applied dose is too high, and the cells have become necrotic. The brightfield image in fig. 47 shows that only cells in the irradiated area are affected, and thereby demonstrate the selective cytotoxicity of the system.

Fig. 47. Brightfield image, 10x. Only irradiated cells are necrotic, while surrounding cells are still healthy.

Since DII showed a very weak fluorescence signals, a new design, DII*, was made. In this system, In(PPa)Cl was replaced with PPa, which is known to be a very good flourophor. This system was then tested in cells, as described above.

Conjugation of 3’amine modified DNA strand with PPa-NHS ester (design DII*)

Fig. 48. Details of the design DII*.

Design DII* was made using, the automated oligonucleotide synthesizer. The product was obtained as a black solid (12 nmol, 52 %, 239.6 μM). ε=287300 for the DNA strand (found on [1]) MALDI-TOF linear possitive mode (appendix): m/z calcd. for 5’- GGATGCTTCACCTAGAATGTCGGTCGATCG-3-Amino Mod C7-C33H33N4O2 [M+H]+: 9967.4682 found 9962.361.

Cell experiments with DII*

In the experiments with DII, it was not possible to localize DII on the cells. To further test, if it is the cholesterol part of the construct that is inserted into the cell membrane, HELA cells were exposed to only PPa-DNA. This was done to verify, that the photosensitizer itself was note able to attach itself to the membrane, thereby indirectly establishing the role of the cholesterols in the attachment. The cells were incubated with a 1µM PPa-DNA for 30 min.

Fig. 49. B: Brightfield image of cells treated with 1µM PPa-DNA for 30 min. B: Fluorescence-image of irradiated cells incubated with 1µM PPa-DNA for 30 min.

The cells in fig. 49A appear healthy, thereby indicating that the PPa-DNA strands alone have no dark toxicity. Subsequently, the cells were irradiated to examine the flourescence and the cellular interactions. From fig. 49B it can be seen that the cells are only weakly fluorescent. This indicates that the cellular interactions of the PPa-DNA strand alone is very low. This could be explained by the lack of ability of PPa to bind to the cells without the cholesterols. Fig. 50 shows the somparison between untreated cells and irradiated cells, incubated with 1µM PPa-DNA for 30 min.

Fig 50. brightfield-image (40x) for comparison of untreated and treated cells. A: Untreated cells. B: cells that were incubated with 1µM PPa-DNA for 30 min and irradiated (the contrast has been increased)


From fig. 50, it is further demonstrated that no cells had died upon irradiation with PPa-DNA alone.. Thus PPa-DNA has no effect on the cells alone. Test of PPa-DNA along with cholesterol Cells were then incubated with a 1µM sample of PPa-DNA annealed with DNA-cholesterol strand (30 min eller to timer?) (fig 51).

Fig 51. Cells treated 1µM sample of PPa-DNA annealed with DNA-cholesterol strand. A: Brightfield image of cells before irradiation. B: Flourescence microscopy image of cells after irradiation.

As seen from fig 51A, the cells were healthy before the irradiation, demonstrating that DII* has no dark toxicity. After irradiation, an enhanced fluorescence signal is observed, compared to cells with PPa-DNA alone, (fig 49B), showing a higher degree of cellular interactions. This establishes the role of the cholesterols in the construct, to mediate a contact with the cell membrane and enable the cytotoxic function of the photosensitizer. To test the combined ability of the PPa-cholesterol duplex to induce (apoptosis/necrosis?) cells were again treated with a 1µM sample of PPa-DNA annealed with DNA-cholesterol strand (hvor lang tid?)

Fig 52. Brightfield images (40x) of cells treated with PPa-cholesterol duplex. A: Treated cells before irridation. B: Cells after irradiation.

In fig. 52B a prominent vacuole formation is prominent, which indicated that the cells were necrotic. Due to the high dose, that leads to necrosis, it is not possible from these experiments to determine if this construct primarily causes apoptosis or necrosis.

Conclusion From the cell experiments with the different test systems, it can be concluded that the In(PPa)Cl-DNA-DNA-Cholesterol has no dark toxicity, i.e. no cytotoxic effect is observed without irridiation. Furthermore, it is the cholesterol that binds to the cells, and only upon binding to the cells, the photosensitizer can exert its cytotoxic effect. To conclude whether the cells die following the necrotic or the apoptotic pathway, more cell experiments will be needed.

Attachment of the chemical modifications to the plate

In order to test the different components of the system together, we attached the cholesterols, photosensitizer and sisiRNAs to each their plate and tested their activities on cells.

Fig. 53. 16 % denaturing PAGE with modified strands. Lane 1: 100 bp ladder (purple). Lane 2: the unmodified ss (purple). Lane 3: the Cy3 modifies ss (red). Lane 4: the Cy5 modified ss (green).

Upon showing that the origamis were able to assemble correctly with non-modified staples, the functional components were added to make sure that the origamis could fold, even when the 3’ ends of several staple strands were modified with varying modifications.

First, fluorophores were added to the staple modules that were intended to carry the peptide lock and the photosensitizers. This was done to test the ability of the cholesterols to attach the plate to the cell membrane, using confocal microscopy. The peptide lock module was labeled with Cy5 and the photosensitizer module with Cy3. A co-localization of the two flourophores on the concfocal images would indicate the presence of an intact origami. In order to lable the modules with the desired Cydyes, a terminal transferase reaction was employed to elongate the staple strand with a Cy-ddUTP which is a ddUTP that has a fluorophore, attached to it. Using ddUTP instead of dUTP or dNTP will ensure that the terminal transferase will stop the elongation process. To test if the fluorophores had been attached to the staples, a PAGE gel with the modified strands was run. It showed a Cy3 and Cy5 signal colored red and green respectively at a slightly higher position than for the control in lane 2 (figure 53), showing that the two modules had been successfully labelled with the CyDyes. The higher bands that can be seen for both terminal transferase reactions are most likely Cy-ddUTPs bound to the terminal transferase enzyme or Cy-ddUMPs/UMPs.

Fig. 54. 1% agarose with the fluorescent labelled cholesterol-modified DNA origami plate. The upper overlayered band represents the structure of the baseplate with the two CyDyes and cholesterol. The lower yellow band is excess staples strands.

Having shown that Cy3/5-ddUTP had been attached to the staples using terminal transferase, a new batch of terminal transferase reaction was made. Three different plates were made for confocal microscopy: One labeled with Cy3 and Cy5 for a Lipofectamine transfected positive control, showing cellular uptake, one with Cy3, Cy5 and cholesterols and lastly one with only Cy3 and Cy5, which is another control to show that the cell-origami interaction is less efficient in this sample compared to the one with cholesterol. The three diffent plates were run on an agaroe gel, both to see if they had assembled correctly and to purify them using freeze n’ squeeze. As seen in fig. 54, the bands is clearly shifted up and shows limited aggregates. Overlay emissions from Cy3 and Cy5 makes the band appear orange. The band containing the plate was cut and purified with Freeze N’ Squeeze Spin Columns. Half of the sample with only Cy3 and Cy5 was used for Lipofectamine transfections.

KB-EGFPluc-Wagner cells were seeded out in an eight well plate, with 80,000 cells per well, and was 24 hours later treated with the differently modified plates. A negative control was included, containing untreated cells. After transfection the cells were incubated at 37°C for two hours, after which they were stained and fixated on the slide using Wheat Germ Agglutinin, Alexa Fluor® 488 Conjugate (WGA-A488), paraformaldehyde (PFM) and Prolong Gold with DAPI. No fluorescence signal was seen during confocal microscopy, (fig. 55) probably due to a too small molar amount of origami in the transfections and too short incubation time. Hence, it was not confirmed that cholesterol plays an important factor in the origami-cell interaction. Due to time constraints, the experiment could not be performed with a higher amount of origamis and a longer incubation time.

Fig. 55. Confocal pictures of origami baseplate +/- cholesterol - A: Cells untreated. B: Cells treated with Origami + cy3 + cy5 +lipofectamine (positive control). C: Cells treated with Origami + cy3 + cy5, Well 4: Cells treated with Origami + cy3 + cy5 + cholesterol. The nucleus is shown in blue while the membrane is shown in green.

Attachment of photosensitizers to the origami plate

A plate was folded with photosensitizers linked to a staple module through an amide modification. In order to confirm its attachment, a denaturing gel was run. Three different origami samples were made. The first reaction had photosensitizer-modified staples mixed in, but was not processed with a thermal ramp (negative control). The second reaction had the photosensitizer module and was processed with a non-linear thermal ramp. The third reaction had ModLeft (staple strands without photosensitizers) and was also processed with a non-linear thermal ramp (positive control) In the gel in figure 56, an orange band is seen in lane 4. This indicates that the photosensitizer had been successfully attached to the plate. In lane 3 and 5 green bands are visible which indicates that these plates do not have photosensitizers on them. The lower red bands which are staples with the photosensitizer module, indicate the same thing.

Fig. 56. Attachment of photosensitizer on origami plate: Lane 1: Ladder, Lane 2: Control M13ap18, Lane 3: Baseplate: + photosensitizer and – the annealing process on PCR, 5 µL + 3 Loading buffer of 30% glycerol, Lane 4: Baseplate: + photosensitizer and + the annealing process on PCR, 5 µL + 3 Loading buffer of 30% glycerol, Lane 5: Baseplate: – photosensitizer and + the annealing process on PCR, 5 µL + 3 Loading buffer of 30% glycerol, Lane 6: Staples strands.
Fig. 57. 1) 25 bp DNA ladder, 2) annealed duplex, 3) control W376

Melittin modified sisiRNA attached to the origami plate

To investigate if the melittin modified sisiRNA duplexes could be attached to the origami plate, the guide strand, W376, was radioactively labeled and annealed to the two segments of the passenger strand, W004 and W179. A sample of W376 was labeled using a T4 polynucleotide kinase kit and purified on a spin column. To determine the concentration of the purified, labeled W376 a sample of the labeled product was run on a 16 % denaturing PAGE gel alongside a series of samples of W376 in different, known concentrations (see supplementary data).

Annealing reaction

The labeled W376 was annealed with a 1.3 times excess of the two segments of the passenger strand, W004 and W179 and run on a 4 % agarose gel (fig. 57).

The radiolabeled sisiRNA annealed well wth a yield above 90 %, and could consequently be used for attachement to the origami plate without further purification. <html><br style="clear:both;"/></html>

Attachment of sisiRNA to the origami plate

An origami plate was folded [insert link to plate foldings] and purified and subsequently checked on a 1 % agarose gel to determine if it had folded properly (fig. 58).

Fig. 58. 1) 100 KB DNA ladder, 2) non-purified plate, 3) purified plate, 4) control M13

From the gel it is seen that a plate had been folded, and that this plate could be used for attachment of the sisiRNA. The labeled sisiRNA duplex was annealed to the plate by mixing the plate with a 3 times excess of sisiRNA per binding site, i.e. a 30 times excess per plate, as each plate contains 10 binding sites. A sample of this reaction was run on a 1 % agarose gel and visualized using a phosphor storage screen.

Fig. 59. A: 1) labeled sisiRNA annealed to plate, 2) control labeled W376 B: SYBR Gold stained gel. 1) labeled sisiRNA annealed to plate, 2) control labeled W376 (not visible).

To verify that the uppermost bond did correspond to a folded plate, the gel was stained with SYBR Gold and scanned (fig. 59B). When comparing the two gels, it is seen that the band containing plate and annealed sisiRNA on the storage phosphor screen corresponds to the folded plate, showing that the labeled sisiRNA did anneal to the plate.

Transfection with melittin conjugated sisiRNA attached to the origami plate

A sisiRNA duplex was annealed with W004-melittin and W179-melittin and run on a 4 % agarose gel to estimate the yield of the annealing (fig. 60).

Fig. 60. 1) 25 bp DNA ladder, 2) annealed duplex, 3) control W376

The yield of the annealing was estimated to 95 %, which would be sufficiently high to allow annealing to the origami plate without further purification. A larger batch of the plate was prepared and purified on a spin filter and subsequently checked on a 1 % agarose gel (fig. 61).

Fig. 61. 1) 100 KB DNA ladder, 2) non-purified plate, 3) purified plate, 4) M13 control

The purified plate was mixed a 30 times excess (three times excess per binding site) of the annealed sisiRNA and incubated for 20 minutes at 37°C to allow the overhang of the sisiRNA to anneal to the staple strands of the plate.

Luciferase assay

The cells were transfected with the doubly melittin-modified sisiRNA attached to the origami plate in two different concentrations of sisiRNA, 50 nM and 10 nM. As each plate contains 10 binding sites for the sisiRNA, the concentration of the origami plate was 5 nM and 1 nM in these samples. For each concentration two transfections were performed, one with Lipofectamine and one without it. The Lipofectamine control was included to be able to compare and see if the plate caused the construct to be endocytosed by the cell. The luciferase activity was measured and corrected to the cell viability.

Figure 62. Luciferase knockdown with sisiRNA annealed to the origami plate .As the value for 10 nM sisiRNA is calculated from the IC50 curve in the previous experiment, standard deviations are not shown.

From the results in fig. 62, it appears that treating the cells with the plate with sisiRNAs attached did not induce a knockdown of luciferase. An apparent increase in luciferase activity was seen, for both concentrations, with or without the plate, corresponding to the results seen for the previous transfections without Lipofectamine. The two controls that were transfected with Lipofectamine, a knockdown was observed, indicating that the the construct did have knockdown abilities, although the two attached melittin peptides were not sufficient to mediate cellular uptake of the sisiRNAs.


  1. Oleinick, N. L. et al. The role of apoptosis in response to photodynamic therapy: what, where, why, and how. Photochem. Photobiol. Sci. 1', 1-21 (2002).[1]


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</style> </head> <body> <div id="indexing"> <div id="sitemap"> <p id="sitemapTitle">SITEMAP | BIOMOD 2013 NANO CREATORS | Aarhus University</p> <div id="footer-contents"> <div class="footer-section"> <p class="footer-section-title">INTRODUCTION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus">Home, abstract, animation and video</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Introduction">Introduction</a></li </ul> </div> <div class="footer-section"> <p class="footer-section-title">RESULTS AND DISCUSSION</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Results_And_Discussion/System_In_Action">System in action</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">MATERIALS AND METHODS</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Origami">Origami</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Peptide_lock">Peptide lock</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Chemical_Modification">Chemical modification</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/sisiRNA">sisiRNA</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/System_In_Action">System in action</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Materials_And_Methods/Methods">Methods</a></li> </ul> </div> <div class="footer-section"> <p class="footer-section-title">SUPPLEMENTARY</p> <ul> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Team_And_Acknowledgments">Team and acknowledgments</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Optimizations">Optimizations</a></li> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Data">Supplementary data</a></li>


href="/wiki/Biomod/2013/Aarhus/Supplementary/Supplementary_Informations">Supplementary informations</a> <li><a href="/wiki/Biomod/2013/Aarhus/Supplementary/References">References</a></li> </ul> </div> </div> <div> <p id="copyright">Copyright (C) 2013 | BIOMOD Team Nano Creators @ Aarhus University | Programming by: <a href="mailto:pvskaarup@gmail.com?Subject=BIOMOD 2013:">Peter Vium Skaarup</a>.</p> </div> </div>

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