calculation: frequency of recognition site restricted by RE

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sarahrahim
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calculation: frequency of recognition site restricted by RE

Post by sarahrahim » Sun Oct 19, 2008 5:11 pm

can somebody tell me if i calculate these questions correctly? if not, may i know the correct way to calculate it?


1. how often would you expect to find ATCG restriction site in a genomic base composition of 50% G+C? show calculation.


if G + C is 50% = A + T is 50%

therefore the chance to find the base A, T, C or G is 25 % or 1/4 each.

so the probability to find site with ATCG is = 1/4 * 1/4 * 1/4 * 1/4 = 1/256 = once in 256 bases.


2. how often would you find GGCC restriction site in a genomic base composition of 45 % G +C. show your calculation.


if G + C = 45%, therefore A+ T is 55 %

G and C alone is 22.5 % or 1/ 0.225

therefore frequency to find GG is (1/0.225) ^ 2 = a

frequency to find CC is also (1/0.225)^2 = b

so, the frequency to find GGCC is a * b = 390.1844

round down the figure because the DNA must at least be a complete 1 figure

so the answer would be once in every 390 bases.


c. how often would you find GAGTC restriction site in a genomic base with the composition of 65% G+ C?

G + C = 65%

A + T = 35%

G and C each is 32.5 % or 1/ 0.325

A and T each is 17.5 % or 1/0.175

therefore frequency to find

GAGTC would be = (1/0.325) * (1/0.175) * (1/0.325) * (1/0.175) * (1/0.325)
= 951.20
= once in every 951 bases.


4. listed all the assumptions that you made when calculating this

1. all the bases is randomly and evenly distributed
2. dna used is long enough
3. (have no idea)
4. (have no idea)


any answer or websites suggestion to help me on this is very much appreciated. tq

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mith
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Post by mith » Mon Oct 20, 2008 5:50 am

It specifies that you need 2 more reasons?
Living one day at a time;
Enjoying one moment at a time;
Accepting hardships as the pathway to peace;
~Niebuhr

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MrMistery
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Post by MrMistery » Mon Oct 20, 2008 7:22 pm

you might want to include "DNA is not methylated", because that is the strategy bacteria use to hide their DNA from endonucleases.
Other than that, you're all set
"As a biologist, I firmly believe that when you're dead, you're dead. Except for what you live behind in history. That's the only afterlife" - J. Craig Venter

sarahrahim
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Post by sarahrahim » Tue Oct 21, 2008 7:32 am

it said three or more assumptions. just need to know if i calculate it right.. i guess mrmistery said i get it right

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