Fig. 1 shows a brief outline of our experiments.
We designed four types of origami by using caDNAno. Their schematics are summarized in Fig. 2. In addition, source codes of the designs in json format are available in the lists below.
By using different sets of Shaft-staples, it is possible to change the angles of the shaft. This time, we prepared four sets of staple strands for the shaft. here.
Our DNA origami samples were prepared by mixing a stoichiometric quantity as shown in Table 1.
SEA buffer contains a mixture of irons, Na+, Mg2+, Ca2+
To find out the most suitable condition, we changed the proportion of concentration.(Table 2)
We annealed DNA origami samples by the following conditions (Fig. 3). Furthermore, we tried different annealing conditions as shown in Fig.4-5 to figure out the best annealing condition
Gel electrophoresis was conducted by a standard procedure as follows.
AFM imaging was conducted as follows. We used an observation buffer in Table 3.
The histogram in Experiment page was based on AFM images below. (Fig. 6)
All cryo-TEM images were taken by Terabase Inc. at Okazaki, Aichi, Japan (http://www.terabase.co.jp/English.html). Fig. 10 in Experiment page was trimmed from Fig. 7 which is shown below.
Reconstructed cryo-TEM images in cross and longitudinal section were created from 16 images (cross) and 35 images (longitudinal) respectively. They are shown below. (Fig. 8)
We appreciate Yoko Kayama in Terabase for the kind assists related to TEM observation. Table 4 shows the condition of the observation.
|The length of one side||1333.68nm|
Each material was purchased from companies below. (Table 5)
|SYBR gold||TAKARA, JAPAN|
|50xTAE||Wako Pure Chemical Industries, JAPAN|
|6xloading buffer||TAKARA, JAPAN|
|Staples||Eurofins Genomics, JAPAN|
Each equipment was purchased from companies below. (Table 6)
|Mupid-2plus(Electrophoresis chamber)||Mupid, JAPAN|
|ChemiDoc MP (gel imager)||BIO-RAD, USA|
|Mastercycler pernonal (thermal cycler)||Eppendorf, USA|
|Nano Live Vision (AFM)||RIBM, JAPAN|
|Mica||Furuuchi Chemical Corporation, JAPAN|
|Micro Cantilever||OLYMPUS, JAPAN|