DNA Questions *PLEASE HELP*

[EdZehtab]

Hi, I'm a first year undergraduate at the University of Warwick in the UK. I have been given an assignment of DNA questions and I am really struggling with some of the latter questions on the sheet. Please could someone help me answer these questions? I honestly have spent a lot of time trying to work out what to do but can't work these last three out!

1. An elegant chemical and enzymatic technique devised by Arthur Kornberg enables one to identify the dinucleotide frequencies in a sample of DNA. There are 16 possible dinucleotides (AA, AT, AG, AC, TA, TG, TC, TT, CA, CT, CG, CC, GT, GC, GA, GG - written with the 5' end at the left and the 3' end at the right.

Frequency of dinucleotide AT in sample of DNA =
Concentration of the dinucleotide AT / Sum of the concentrations of all 16 dinucleotides

Assume you have determined the following dinucleotide frequencies in a sample of double-stranded DNA:

AG=0.15, GT=0.03, GA=0.08, TT=0.10

a) what are the dinucleotide frequencies of CT, AC, TC and AA?
b) If DNA had a parallel (rather than anti-parallel) structure what dinucleotide frequencies would you deduce from the observed values?

[I have looked at this for ages I don't understand how you can use this formula to find out the answer to this question because I don't know what to substitute in!]

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2. When a solution containing dsDNA is heated to 100degrees to separate the strands and then allowed to cool slowly the two strands can find each other and reform the double helix (renaturation.) Consider the following DNA molecule:

5' GCGCGCGCGCGCGC 3'
3' CGCGCGCGCGCGCG 5'

If this DNA is heated to 100degrees what would the structure be if the 2 strands never find one another?

[I read that strands containing C and G have a higher boiling point and are more stable but I don't know what structure they will reform into, maybe they will form a single stranded helix?]

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3. Here are 4 characteristics of one 5'-3' strand of a particular long double-stranded DNA molecule:

a) 35% of As have Gs as their 3' neighbours
b) 30% of As have Ts as their 3' neighbours
c) 25% of As have Cs as their 3' neighbours
d) 10% of As have As as their 3' neighbours

Use this information to answer the following questions, explaining your reasoning:

a) In the complementary strand what will the frequencies of the various bases on the 3' side of A be?
b) In the complementary strand what will the frequencies of the various bases on the 3' side of T be?
c) In the complementary strand what will the frequencies of the various bases on the 5' side of T be?
d) Why is the percentage of A not equal to the percentage of T among the 3' neighbours of A in the 5'-3' DNA strand described?

[I have looked at this question and can only work out at 10% of Ts have T as their neighbour on the complementary strand. 25% of G have T as a neighbour on the complementary strand. 35% of Cs have T as a neighbour on the complementary strand. 30% of As have T as a neighbour on the complementary strand, but this is obvious from the data I'm provided! Where can I take this!?]
Many thanks for any help that you can give me!

Ed

[JackBean]

2 I'm not sure, whether single stranded helix is the correct term, but it will probably self-bind making loop

[EdZehtab]

Any idea why it would loop? Does it have any relation to the bases present in the strand? Would it be different if there were A and T present?

[canalon]

1a- you do not need the formula. The key clues are:

written with the 5' end at the left and the 3' end at the right

and

Assume you have determined the following dinucleotide frequencies in a sample of double-stranded DNA:

look at the dinucleotides whose frequency you have, and the one that are given to you. The answer is obvious and do not need any calculations.
1b- basically the same question, just a different set of dinucleotide in the second list.

2- Hairpin is the traditional term. Think of it as self complementation. The real sequence doesn't matter, it is all about the self complementation.

[EdZehtab]

Hi, thanks for your help.
For the first one, AG is 0.15. Does this mean that CT is 0.15 because:

5'---A---G---3'
3'---T---C---5'

Many thanks,
Ed

[canalon]

yep