c. Consider the following oligomers (short chains) of DNA. The 5\' end has a pho
ID: 189730 • Letter: C
Question
c. Consider the following oligomers (short chains) of DNA. The 5' end has a phosphate group attached, whereas the 3' end is an -OH group. a. 5' -GCGCTTATTATGCGCTGACTGAT-3 b. 5-TATGGGGCCT-3 C. 5' -AGGTTGTGAGCCACAT-3' a piece of DNA that is 123 deoxynucleotides in length with an unknown sequence d. For “a", "b" and "c", assume that each exists as a double strand. Calculate the exact molecular weight for each double-strand piece of DNA, and estimate the total charge for each at pH 7.4. For "a" "b" and "c", calculate an estimated molecular weight for each double-strand piece of DNA by using the average molecular weight of a deoxynucleotide that you calculated, and estimate the total charge for each at pH 7.4 How do the exact and estimated values compare? How might you establish the mass and charge for a double-strand form of oligomer "d"? What is the mass/charge ratio for each oligomer?Explanation / Answer
Exact MW are (a) 14247.19 Da,(b) 6216 Da, and (c) 9922.4 Da
Approximate MW of ds DNA is calculated by the formula: (no. of nucleotide X 607.4)+157.9 Daltons
Therefore the approximated MWs are (a) 14128.1, (b) 6231.9 (c) 9876.3.
If you compare the two, you will see that depending on the %GC-content of the DNA, the error will be either positive or negative. This means that for DNA with high %GC content, the estimated value appears higher than the exact value.
In case of the sequence (d) the exact MW cannot be calculated as the sequence is unknown but the estimated MW if it is ds will be (123 X 607.4)+157.9= 74868.1 Da. The charge on this oligomer cannot be calculated without the sequence information.
Now, coming to the charge on each of the given DNA as a, b, and c, they will have a charge of (a) -8, (b) -3, and (c) -4 if considered as oligomers.
the maas/charge ratio for each oligomer is (a) -1766, (b) -2077.3, and (c) -2469, if calculated using the estimated MW.
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