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Chromatin experiment

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Chromatin experiment

Postby 2468 » Thu Nov 01, 2012 12:57 pm

Hey,
I need help with this question...does anyone have any idea?
I've uploaded the results as a attachment.

Question: Consider the six lanes from the left (where the most left lane is lane 1 and lane 4 and 5 are empty). Match the correct explanation for the bands visible in the different lanes.

Explanations:
1. In this lane the DNA has been almost completely digested because the nucleosome had been extracted before nuclease treatment

2. The high molecular weight bands in this lane represent DNA protected from the nuclease

3. The strong low molecular band in this lane represents the DNA that stretches between nucleosomes

4. High molecular weight bands in this lane represent the undigested DNA

5. The bands in this lane represent the molecular weight standards

6. The band at approximately 200 bp in this lane represents the DNA that is wrapped around the nucleosomes

7. The lack of bands in this lane (except for a very faint band at at 200bp) demonstrates that EDTA has effectively inhibited the nuclease enzyme


Answers to match the explanations: Lane 1, Lane 2, Lane 3, Lane 6, Wrong Interpretation.


Thank you :)
Attachments
chromatin results pic.jpg
Results pic
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Postby JackBean » Thu Nov 01, 2012 4:19 pm

So what's your idea?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re:

Postby 2468 » Fri Nov 02, 2012 6:19 pm

JackBean wrote:So what's your idea?


Well so far i got : explanation 2 = lane 1
explanation 3 = lane 3
explanation 4 = lane 2
explanation 7 = lane 1

Not to sure about the rest...so need help with them! :)
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Postby JackBean » Fri Nov 02, 2012 10:15 pm

how can you have two explanations for one lane?

Do you really think that the lane 3 has such strong band?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re:

Postby 2468 » Fri Nov 02, 2012 10:27 pm

JackBean wrote:how can you have two explanations for one lane?

Do you really think that the lane 3 has such strong band?



Just to help you count...Theres 7 explanations and 5 options. Some answers MIGHT be a repeat... :)

Well, I wouldnt be asking for help if I knew the answers myself if that isnt obvious... :/
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Re: Chromatin experiment

Postby JackBean » Sat Nov 03, 2012 2:40 pm

OR some of them may not be used ;) :roll:

Don't you think that explanations 2 and 7 are contradictory (high-molecular bands vs. lack of bands)?
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Postby Cat » Sat Nov 03, 2012 3:46 pm

I am not completely sure about lanes 1 and 2, but 100% sure about 3 and 6.

Lane 2 (smear starting in the middle of the gel ending with strong band of low molecular weight)= 1. In this lane the DNA has been almost completely digested because the nucleosome had been extracted before nuclease treatment

Lane 1 (smear starting at the well and ending in the middle of the gel means undigested DNA)= 4. High molecular weight bands in this lane represent the undigested DNA

Lane 6 = 5. The bands in this lane represent the molecular weight standards
Lane 3 = 7. The lack of bands in this lane (except for a very faint band at at 200bp) demonstrates that EDTA has effectively inhibited the nuclease enzyme
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Re:

Postby 2468 » Sat Nov 03, 2012 4:32 pm

Cat wrote:I am not completely sure about lanes 1 and 2, but 100% sure about 3 and 6.

Lane 2 (smear starting in the middle of the gel ending with strong band of low molecular weight)= 1. In this lane the DNA has been almost completely digested because the nucleosome had been extracted before nuclease treatment

Lane 1 (smear starting at the well and ending in the middle of the gel means undigested DNA)= 4. High molecular weight bands in this lane represent the undigested DNA

Lane 6 = 5. The bands in this lane represent the molecular weight standards
Lane 3 = 7. The lack of bands in this lane (except for a very faint band at at 200bp) demonstrates that EDTA has effectively inhibited the nuclease enzyme



Thank you! :)
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Re:

Postby JackBean » Sat Nov 03, 2012 6:02 pm

Cat wrote:Lane 6 = 5. The bands in this lane represent the molecular weight standards

Really? You see there distinct bands? Something in regular distances?
http://www.biolib.cz/en/main/

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Re: Re:

Postby Cat » Sun Nov 04, 2012 6:54 pm

JackBean wrote:
Cat wrote:Lane 6 = 5. The bands in this lane represent the molecular weight standards

Really? You see there distinct bands? Something in regular distances?


This is a bad picture of a bad gel as far as I can tell. And yes, I do see familiar pattern. Here is another example of poor gel:

http://aem.asm.org/content/66/4/1423/F1.expansion.html
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Postby 2468 » Thu Nov 08, 2012 7:48 pm

Hey,
Can someone please confirm my answers before I submit it....correct me if i am wrong instead of beating around the bush! :D

explantion 1= lane 2
2= wrong interpretation
3= lane 3
4= lane 1
5= lane 6
6= wrong interpretation
7= lane 3


Which of the following protocols modifications could remove the high molecular weight bands?
1. Increase the EDTA concentration

2. Expose the cells to the detergent for longer time

3. Increase the concentration of the nuclease

4. Decrease the concentration of the nuclease

5. Increase the incubation time with the nuclease.

6. Increase the number of cells used

I've put down 1,2,3,5

Thank u!
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