iGEM 2013 — Team IIT_Madras

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# Team:IIT Madras/Notebook

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| Contents   * [1 Phase I : Ideation](#Phase_I_:_Ideation) * [2 Phase II : Experimentation](#Phase_II_:_Experimentation)   + [2.1 e-Notebook](#e-Notebook)   + [2.2 Experimental results](#Experimental_results)   + [2.3 Protocol](#Protocol) * [3 Phase III](#Phase_III)   + [3.1 Troubleshooting](#Troubleshooting)   + [3.2 Discussions](#Discussions) |

## Phase I : Ideation

## Phase II : Experimentation

### e-Notebook

| May 13 | | | | | | |  | | | | | | | June 13 | | | | | | |  | | | | | | | July 13 | | | | | | |
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|  |  |  | [1](/May_1 "May 1") | [2](/wiki/index.php?title=May_2&action=edit&redlink=1 "May 2 (page does not exist)") | [3](/wiki/index.php?title=May_3&action=edit&redlink=1 "May 3 (page does not exist)") | [4](/wiki/index.php?title=May_4&action=edit&redlink=1 "May 4 (page does not exist)") |  |  |  |  |  |  |  |  |  |  |  |  |  | [1](/wiki/index.php?title=June_1&action=edit&redlink=1 "June 1 (page does not exist)") |  |  |  |  |  |  |  |  | [1](/wiki/index.php?title=July_1&action=edit&redlink=1 "July 1 (page does not exist)") | [2](/wiki/index.php?title=July_2&action=edit&redlink=1 "July 2 (page does not exist)") | [3](/wiki/index.php?title=July_3&action=edit&redlink=1 "July 3 (page does not exist)") | [4](/wiki/index.php?title=July_4&action=edit&redlink=1 "July 4 (page does not exist)") | [5](/wiki/index.php?title=July_5&action=edit&redlink=1 "July 5 (page does not exist)") | [6](/wiki/index.php?title=July_6&action=edit&redlink=1 "July 6 (page does not exist)") |
| [5](/wiki/index.php?title=May_5&action=edit&redlink=1 "May 5 (page does not exist)") | [6](/wiki/index.php?title=May_6&action=edit&redlink=1 "May 6 (page does not exist)") | [7](/wiki/index.php?title=May_7&action=edit&redlink=1 "May 7 (page does not exist)") | [8](/wiki/index.php?title=May_8&action=edit&redlink=1 "May 8 (page does not exist)") | [9](/wiki/index.php?title=May_9&action=edit&redlink=1 "May 9 (page does not exist)") | [10](/wiki/index.php?title=May_10&action=edit&redlink=1 "May 10 (page does not exist)") | [11](/wiki/index.php?title=May_11&action=edit&redlink=1 "May 11 (page does not exist)") |  |  |  |  |  |  |  | [2](/wiki/index.php?title=June_2&action=edit&redlink=1 "June 2 (page does not exist)") | [3](/wiki/index.php?title=June_3&action=edit&redlink=1 "June 3 (page does not exist)") | [4](/June_4 "June 4") | [5](/wiki/index.php?title=June_5&action=edit&redlink=1 "June 5 (page does not exist)") | [6](/wiki/index.php?title=June_6&action=edit&redlink=1 "June 6 (page does not exist)") | [7](/wiki/index.php?title=June_7&action=edit&redlink=1 "June 7 (page does not exist)") | [8](/wiki/index.php?title=June_8&action=edit&redlink=1 "June 8 (page does not exist)") |  |  |  |  |  |  |  | [7](/wiki/index.php?title=July_7&action=edit&redlink=1 "July 7 (page does not exist)") | [8](/wiki/index.php?title=July_8&action=edit&redlink=1 "July 8 (page does not exist)") | [9](/wiki/index.php?title=July_9&action=edit&redlink=1 "July 9 (page does not exist)") | [10](/wiki/index.php?title=July_10&action=edit&redlink=1 "July 10 (page does not exist)") | [11](/wiki/index.php?title=July_11&action=edit&redlink=1 "July 11 (page does not exist)") | [12](/wiki/index.php?title=July_12&action=edit&redlink=1 "July 12 (page does not exist)") | [13](/wiki/index.php?title=July_13&action=edit&redlink=1 "July 13 (page does not exist)") |
| [6](/wiki/index.php?title=May_6&action=edit&redlink=1 "May 6 (page does not exist)") | [7](/wiki/index.php?title=May_7&action=edit&redlink=1 "May 7 (page does not exist)") | [8](/wiki/index.php?title=May_8&action=edit&redlink=1 "May 8 (page does not exist)") | [9](/wiki/index.php?title=May_9&action=edit&redlink=1 "May 9 (page does not exist)") | [10](/wiki/index.php?title=May_10&action=edit&redlink=1 "May 10 (page does not exist)") | [11](/wiki/index.php?title=May_11&action=edit&redlink=1 "May 11 (page does not exist)") | [12](/wiki/index.php?title=May_12&action=edit&redlink=1 "May 12 (page does not exist)") |  |  |  |  |  |  |  | [9](/wiki/index.php?title=June_9&action=edit&redlink=1 "June 9 (page does not exist)") | [10](/wiki/index.php?title=June_10&action=edit&redlink=1 "June 10 (page does not exist)") | [11](/June_11 "June 11") | [12](/June_12 "June 12") | [13](/June_13 "June 13") | [14](/June_14 "June 14") | [15](/June_15 "June 15") |  |  |  |  |  |  |  | [14](/wiki/index.php?title=July_14&action=edit&redlink=1 "July 14 (page does not exist)") | [15](/wiki/index.php?title=July_15&action=edit&redlink=1 "July 15 (page does not exist)") | [16](/wiki/index.php?title=July_16&action=edit&redlink=1 "July 16 (page does not exist)") | [17](/wiki/index.php?title=July_17&action=edit&redlink=1 "July 17 (page does not exist)") | [18](/wiki/index.php?title=July_18&action=edit&redlink=1 "July 18 (page does not exist)") | [19](/wiki/index.php?title=July_19&action=edit&redlink=1 "July 19 (page does not exist)") | [20](/wiki/index.php?title=July_20&action=edit&redlink=1 "July 20 (page does not exist)") |
| [13](/wiki/index.php?title=May_13&action=edit&redlink=1 "May 13 (page does not exist)") | [14](/wiki/index.php?title=May_14&action=edit&redlink=1 "May 14 (page does not exist)") | [15](/wiki/index.php?title=May_15&action=edit&redlink=1 "May 15 (page does not exist)") | [16](/wiki/index.php?title=May_16&action=edit&redlink=1 "May 16 (page does not exist)") | [17](/wiki/index.php?title=May_17&action=edit&redlink=1 "May 17 (page does not exist)") | [18](/wiki/index.php?title=May_18&action=edit&redlink=1 "May 18 (page does not exist)") | [19](/wiki/index.php?title=May_19&action=edit&redlink=1 "May 19 (page does not exist)") |  |  |  |  |  |  |  | 16 | [17](/wiki/index.php?title=June_17&action=edit&redlink=1 "June 17 (page does not exist)") | [18](/wiki/index.php?title=June_18&action=edit&redlink=1 "June 18 (page does not exist)") | [19](/wiki/index.php?title=June_19&action=edit&redlink=1 "June 19 (page does not exist)") | [20](/wiki/index.php?title=June_20&action=edit&redlink=1 "June 20 (page does not exist)") | [21](/wiki/index.php?title=June_21&action=edit&redlink=1 "June 21 (page does not exist)") | [22](/wiki/index.php?title=June_22&action=edit&redlink=1 "June 22 (page does not exist)") |  |  |  |  |  |  |  | [21](/wiki/index.php?title=July_21&action=edit&redlink=1 "July 21 (page does not exist)") | [22](/wiki/index.php?title=July_22&action=edit&redlink=1 "July 22 (page does not exist)") | [23](/wiki/index.php?title=July_23&action=edit&redlink=1 "July 23 (page does not exist)") | [24](/wiki/index.php?title=July_24&action=edit&redlink=1 "July 24 (page does not exist)") | [25](/wiki/index.php?title=July_25&action=edit&redlink=1 "July 25 (page does not exist)") | [26](/wiki/index.php?title=July_26&action=edit&redlink=1 "July 26 (page does not exist)") | [27](/wiki/index.php?title=July_27&action=edit&redlink=1 "July 27 (page does not exist)") |
| [20](/wiki/index.php?title=May_20&action=edit&redlink=1 "May 20 (page does not exist)") | [21](/wiki/index.php?title=May_21&action=edit&redlink=1 "May 21 (page does not exist)") | [22](/wiki/index.php?title=May_22&action=edit&redlink=1 "May 22 (page does not exist)") | [23](/wiki/index.php?title=May_23&action=edit&redlink=1 "May 23 (page does not exist)") | [24](/wiki/index.php?title=May_24&action=edit&redlink=1 "May 24 (page does not exist)") | [25](/wiki/index.php?title=May_25&action=edit&redlink=1 "May 25 (page does not exist)") | [26](/wiki/index.php?title=May_26&action=edit&redlink=1 "May 26 (page does not exist)") |  |  |  |  |  |  |  | [23](/wiki/index.php?title=June_23&action=edit&redlink=1 "June 23 (page does not exist)") | [24](/wiki/index.php?title=June_24&action=edit&redlink=1 "June 24 (page does not exist)") | [25](/wiki/index.php?title=June_25&action=edit&redlink=1 "June 25 (page does not exist)") | [26](/wiki/index.php?title=June_26&action=edit&redlink=1 "June 26 (page does not exist)") | [27](/wiki/index.php?title=June_27&action=edit&redlink=1 "June 27 (page does not exist)") | [28](/wiki/index.php?title=June_28&action=edit&redlink=1 "June 28 (page does not exist)") | [29](/wiki/index.php?title=June_29&action=edit&redlink=1 "June 29 (page does not exist)") |  |  |  |  |  |  |  | [28](/wiki/index.php?title=July_28&action=edit&redlink=1 "July 28 (page does not exist)") | [29](/wiki/index.php?title=July_29&action=edit&redlink=1 "July 29 (page does not exist)") | [30](/wiki/index.php?title=July_30&action=edit&redlink=1 "July 30 (page does not exist)") | [31](/wiki/index.php?title=July_31&action=edit&redlink=1 "July 31 (page does not exist)") |  |  |  |
| [27](/wiki/index.php?title=May_27&action=edit&redlink=1 "May 27 (page does not exist)") | [28](/wiki/index.php?title=May_28&action=edit&redlink=1 "May 28 (page does not exist)") | [29](/wiki/index.php?title=May_29&action=edit&redlink=1 "May 29 (page does not exist)") | [30](/wiki/index.php?title=May_30&action=edit&redlink=1 "May 30 (page does not exist)") | [31](/wiki/index.php?title=May_31&action=edit&redlink=1 "May 31 (page does not exist)") |  |  |  |  |  |  |  |  |  | [30](/wiki/index.php?title=June_30&action=edit&redlink=1 "June 30 (page does not exist)") |  |  |  |  |  |  |  |  |  |  |  |  |  |  |

### Experimental results

### Protocol

---

**1. Transformation:**

(a) Added 1-2µl of DNA to competent cell.

(b) Kept on ice for 30 minutes.

(c) Heat Shock was given at 42°C for 90 sec.

(d) Kept on ice for 5 min.

(e) Added 400µl of LB media.

(f) Incubated at 37°C for 1h in shaker.

(g) Plating was done with 250µl of culture.

(h) Plates were incubated overnight at 37°C.

---

**2. Mini Prep : DNA Isolation using HiPura Silica Kit**

(a) Single Isolated colonies were picked and inoculated in 8ml media.

(b) Overnight incubation was done at 37°C.

(c) 1.5ml of culture was taken and centrifuged at 12,000 rpm for 2 min.

(d) Supernatant was discarded and pellet was kept on Ice.

(e) The pellet was resuspended with 100µl of chilled TGE buffer(25mM Tris pH 8.0, 50mM Glucose, 10mM EDTA) treated with RNAse was added to it.

(f) 200µl of Sol II containing 0.2N NaOH and 1% SDS was added and the solution was mixed gently and then kept on ice for 3-5 min.

(g) 150µl of cold potassium acetate solution (3M Potassium and 5M acetate) was added and the solution was mixed gently and finally kept on ice for 3-5 min.

(h) Centrifugation was done at 14,000 rpm for 5 min.

(i) The supernatant was transferred to a clean centrifuge tube.

(j) 3 volume of Chaotropic Salt Solution was added.

(i) 10µl of Glass Powder Suspension was added and then kept for mixing in rotospin for 30 min.

(j) Centrifugation was done at 14,000 rpm for 2 min and the supernatant was discarded.

(k) The glass powder pellet was re-suspended in 500µl of diluted wash solution (1 volume of wash Solution as provided with the HiPura Silica kit added to 9 volume of milliQ and 10 volume of absolute Ethanol.)

(l) Centrifugation was done at 12,000 rpm for 2 min and the supernatant was discarded.

(m) Step (k) & (l) were repeated twice. After the last wash, the supernatant was removed completely and the pellet was air dried for 5 min.

(n) Glass Powder Pellet was re-suspended into 20µl of autoclaved double distilled water (or TE buffer, pH 8.0 for long term storage).

(o) Incubation at 55°C for 20 min was done.

(p) Centrifugation at 14,000 rpm was done for 2 min and the supernatant was carefully taken out and was stored in -20°C

(q) Confirmation was done by running 2µl of isolated plasmid DNA on agarose gel against a standard marker.

---

**3. Restriction Digestion**

(a) 20µl of restriction digestion was set up on ice.

(b) 2µl of NEB buffer 4 was used for the High Fidelity enzymes *Pst*I and *Spe*I.

(c) 5µl of DNA was added to it.

(d) 0.2µl each of restriction enzymes were added to the mixture.

(e) Autoclaved double distilled water was used to make up the volume to 20µl.

(f) The reaction mixture was kept at 37°C for 8-12h.

(g) The restriction digestion was confirmed by loading on agarose gel against a standard marker.

---

**4. Elution of Plasmid DNA using HiPura Silica Kit.**

(a) Digested Sample was run on agarose gel.

(b) The required size band was excised under UV light and the gel pieces were kept in vial.

(c) 3 volume of Chaotropic Salt Solution was added to it.

(d) Incubated at 55°C till agarose melt completely.

(e) 10µl of Glass Powder was Suspension was added to it.

(f) The mixture was mixed and incubated at room temperature for 15-20 min in the rotospin.

(g) Centrifugation was done at 12,000 rpm for 2min and the supernatant was discarded.

(h) 500µl of diluted Wash Solution(1 volume of wash Solution as provided with the HiPura Silica kit added to 9 volume of milliQ and 10 volume of absolute Ethanol.) was added to the pellet.

(i) Centrifugation was done at 12,000 rpm for 2 min and the supernatant was discarded.

(j) Step (h) & (i) were repeated twice. After the last wash, the supernatant was removed completely and the pellet was air dried for 5 min.

(k) Glass Powder Pellet was re-suspended into 20µl of autoclaved double distilled water (or TE buffer, pH 8.0 for long term storage).

(l) Incubation at 55°C for 20 min was done.

(m) Centrifugation at 14,000 rpm was done for 2 min and the supernatant was carefully taken out and was stored in -20°C

(n) Confirmation was done by running 2µl of isolated plasmid DNA on agarose gel against a standard marker.

---

**5. Ligation**

(a) 10µl of reaction was set up.

(b) Purified Vector and Insert were taken in the ratio of 1:3.

(c) 1µl of 10X Ligase buffer was added to it.

(d) 1µl of T4 Ligase was added to the mixture.

(e) Finally, the volume was made upto 10µl by adding autoclaved double distilled water.

(f) Ligation reaction mixture was kept overnight at gradient temperature over the range of 8-22°C.

---

## Phase III

### Troubleshooting

### Discussions

This page is under construction. For more information contact Rohan or Aman.

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