Published multiple files

Author: Quartz Syncer

content/6x DNA loading buffer.md

@@ -24,13 +24,13 @@ as the yellow color. Orange G is preferred since it migrates faster.
 | Water                         | -       | to 50 mL          |                           | -             |
 | Total                         | 50 mL   |                   |                           |               |
 
-
+	
 Recipe for 50 mL 6x DNA loading buffer:
 
 - add 6.25g [FICOLL 400](https://www.sigmaaldrich.com/catalog/product/sigma/f2637) powder to a new 50 mL FALCON tube.
 - add [[ddH2O]] to about 30 mL, shake to dissolve. This may take time, heating the tube in a water bath helps.
 - add 7.5 mg Xylene Cyanol FF powder
-- add 7.2 mL Orange G (1% w/v) *OR* 900 µL of VAHINE yellow contains [Tartrazine](http://en.wikipedia.org/wiki/Tartrazine)
+- add 7.2 mL Orange G (1% w/v) ***OR*** 900 µL of VAHINE yellow contains [Tartrazine](http://en.wikipedia.org/wiki/Tartrazine)
 - add water to 50 mL
 
 The resulting solution is about the same colour as the GoTaq green flexi buffer commercialized
@@ -49,7 +49,7 @@ is not known, but could be measured using a spectrophotometer at the absorption
 maximum of 472 nm. The molar absorptivity of Tartrazine at 472 nm is 20,330 L mol-1 cm-1.
 
 
-### Development
+### Developmen
 
 #### FICOLL 400 (Density)
 
@@ -72,7 +72,7 @@ Kramer, M. F., & Coen, D. M. (2001). Enzymatic amplification of DNA by PCR: stan
 #### Xylene Cyanol FF (Blue)
 
 PCR mastermix can tolerate 0.0025% Xylene Cyanol FF in the final solution.
-For example, commercial https://international.neb.com/products/m0271-quick-load-taq-2x-master-mix#Product Information
+For example, commercial <https://international.neb.com/products/m0271-quick-load-taq-2x-master-mix#Product> Information
 yields 0.0025% XyleneCyanol FF in the final 1x PCR mixture:
 
 [![[1X_Quick-Load_Taq_Master_Mix.png]]](M0271Datasheet-Lot0211206.pdf)
@@ -115,7 +115,7 @@ VAHINE food coloring comes in a package with blue, red and yellow. It has the fo
 ### Links
 
 
-- http://www.wendychao.com/science/protocols/loading_buffer/
-- http://www.protocol-online.org/biology-forums-2/posts/12397.html
-- http://www.geneticorigins.org/pv92/recipes2.htm
-- https://www.researchgate.net/post/Which_dye_doesnt_inhibit_PCR_reaction
+- <http://www.wendychao.com/science/protocols/loading_buffer/>
+- <http://www.protocol-online.org/biology-forums-2/posts/12397.html>
+- <http://www.geneticorigins.org/pv92/recipes2.htm>
+- <https://www.researchgate.net/post/Which_dye_doesnt_inhibit_PCR_reaction>

content/Agarose electrophoresis.md

@@ -0,0 +1,102 @@
+---
+publish: true
+aliases: gel
+created: 2026-03-13T08:01:11.777+00:00
+modified: 2026-03-13T08:02:06.968+00:00
+cssclasses: ""
+---
+
+
+## Purpose
+
+Agarose gel electrophoresis separates DNA fragments based on size. It is commonly used to verify:
+
+- PCR amplification products
+- Restriction enzyme digestions
+- Plasmid preparations
+- DNA fragment sizes
+
+DNA migrates through agarose toward the positive electrode because DNA is negatively charged. Smaller fragments move faster than larger ones.
+# Preparing DNA Samples for Loading
+
+DNA samples should be mixed with a **loading buffer** before loading into the gel in most cases.
+
+Loading buffer serves two purposes:
+
+1. **Adds density** so the sample sinks into the well
+2. **Contains tracking dyes** so migration during electrophoresis can be monitored
+
+Common dyes:
+
+- Xylene cyanol FF (light blue color)
+- Bromophenol blue (dark blue color)
+- Orange G
+
+![[GEL.png]]
+
+The dye migration roughly corresponds to DNA fragment sizes depending on agarose concentration.
+
+We use this buffer that we make ourselves [[6x DNA loading buffer]] it has Xylene cyanol FF and Orange G
+but no Bromophenol blue as this dye has a tendency to hide some DNA bands. Our loading buffer
+is also PCR compatible, which means that it can be added to the PCR mix prior to PCR.
+
+You can add loading buffer to PCR by substituting some of the water added. For each 100 µL of
+PCR reaction mix, substitute 17 µL of water with [[6x DNA loading buffer]].
+
+You can also prepare [[2x PCR mastermix]] with loading buffer. For each 100 µL of 2x mastermix, substitute
+17 * 2 = 34 µL of water with [[6x DNA loading buffer]].
+
+> [!WARNING]
+>Not all loading buffers are PCR compatible. Do not use other loading buffers in the lab without verifying tha
+>the buffer is compatible with PCR
+
+# Using 6× Loading Buffer
+
+A **6× loading buffer** must be diluted to **1× final concentration** in the DNA sample.
+
+1 part 6× loading buffer + 5 parts DNA sample
+
+The sample preparation depends on how much DNA we expect in the sample.
+It is not advisable to load more than 10 µL
+
+| 6× loading buffer (µL) | H2O | DNA sample | Total volume |                          |
+| ---------------------- | --- | ---------- | ------------ | ------------------------ |
+| 1                      | -   | 5          | 6            | Standard for PCR product |
+| 1.5                    | -   | 8.5        | 10           | For a weak PCR product   |
+| 1                      | 3   | 2          | 6            | Typical plasmid miniprep |
+
+If you analyse a [[restriction digestion]], it is important to load an equal amount of undigested DNA as a reference.
+
+For example, if you digested 2 µL plasmid DNA in a total of 10 µL and you want to analyze 5 µL on a gel, this sample effectively contains 1 µL of the original DNA.
+
+If you have several, samples, spot the loading buffer on a piece of parafilm as shown below. Add water if needed
+and then the DNA just before loading the gel. This saves a lot of time and plastic tubes.
+
+
+![[GEL-1.png]]
+
+# Typical Agarose Gel Percentages
+
+| Agarose % | DNA size resolution |                          |
+| --------- | ------------------- | ------------------------ |
+| 0.7 %     | 0.8–10 kb           |                          |
+| 1.0 %     | 0.5–7 kb            | We routinely use 1% gels |
+| 1.5 %     | 0.2–3 kb            |                          |
+| 2.0 %     | 0.1–2 kb            |                          |
+
+Higher agarose concentrations resolve smaller fragments better.
+
+
+<http://www.gelanalyzer.com/index.html>
+<http://sourceforge.net/projects/pyelph/files/releases/>
+
+
+
+
+- [[How many times can I reuse electrophoresis buffer?]]
+- [[TAE]]
+- [[FatVal]]
+- [[Turner]]
+- [[Bachman]]
+- [[Midori Green DNA loading buffer (LBx2wMidori)]]
+- [[LiAc Borate]]

content/FASII.md

@@ -1,7 +1,3 @@
-### Markdown
-
-
-
 
 
 | #      | fabH     | fabD     | fabG     | acpP         | ----     | fabB     | ----     | fabZ     | fabI     | tesA      | ----     | acpS     | ----     |

content/GEL-1.png

@@ -1,6 +1,4 @@
-This is a wide table. Use the scroll bars to see the rightmost columns.
-
-[Codon usage](https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4932) for S. cerevisiae
+This is a wide table. Use the scroll bars to see the rightmost columns. [Codon usage](https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=4932) for *S. cerevisiae*. Google doc with editable [table](https://docs.google.com/spreadsheets/d/12uem2ylfLvgNbsBN3HYOcjgVODG--HNb2HJ_8bKjce4/edit?usp=sharing)
 
 
 | Name           | Name            | NAME          | Three | THREE | One | KEGG                                       | Pubchem                                                  | Mw     | Mw-H2O | Solubility (g/100 mL H2O at 25°C) | UV Abs Log e (lmax)pH ~ 7.0 | Codons (S. cerevisiae) |     |     |     |     |     | S.cerevisiae | E.coli |
@@ -35,7 +33,7 @@ Varshavsky 1996 PMID: 8901547
 ![](Varshavsky1996.png)
 Tobias et al. 1991 PMID: 1962196
 ![](Tobias1991.png)
-Bachmair & Varshavsky 1989 PMID: 2538246
+Bachmair & Varshavsky 1989 PMID: 2538246scr
 ![](Bachmair1989.png)
 
 

content/GEL.png

@@ -40,7 +40,7 @@ Don't forget that creating the file from here may create the file in the wrong d
 - [[cuvete]] in [[catalase lab pt]]
 - [[água destilada]] in [[catalase lab pt]]
 - [[atividade enzimática]] in [[catalase lab pt]]
-- [[How many times can I reuse electrophoresis buffer?]] in [[electrophoresis]]
+- [[How many times can I reuse electrophoresis buffer?]] in [[Agarose electrophoresis]]
 - [[MB010_NZYMiniprep.pdf]] in [[pTAx/LAB10]]
 - [[NZYMiniprep]] in [[pTAx/LAB10]], [[pTAx/LAB9]]
 - [[black]] in [[misc/recept/Caesar salad - quick]]

content/M0271Datasheet-Lot0211206.pdf

@@ -2,7 +2,7 @@
 publish: true
 title: Metabolic Engineering CBMA - mec@CBMA
 created: 2026-02-01T09:08:30.665+00:00
-modified: 2026-02-01T09:08:30.666+00:00
+modified: 2026-03-12T18:56:01.609+00:00
 cssclasses: ""
 ---