Why do more complex DNA strands take longer to anneal?

Question

My textbook and several websites told me that more complex DNA strands take longer to anneal because it is harder to find the correct sequence. A simpler, repeating sequence like ATATATATA would be faster to anneal since it would be really easy to find a spot to reanneal.

I kind of get the logic here. Yet, this wouldn't always produce the exact complement strand. Consider the following:

The point is to illustrate that there could be matching of strands without correctly pairing the whole thing (i.e. there is a shift of the strands).

This means that if you want to fully anneal the strands, you need to find the correct spot in the second strand to begin annealing - which is no better than if these were completely random strands.

So then, why is annealing more complex strands slower? I've tried searching it up on the internet but all I get are people telling me it is true, and without much of an explanation.

Answer 1

What is meant by complexity?

This is the crux of the matter. As is often the case, confusion arises from not defining one’s terms. In this case the three possibilities we have to deal with are:

1. The extent to which a sequence is not homogenous. e.g. ATATATAT is more complex than AAAAAAAA; ATGCATGC is more complex than ATATATAT; ATGCTCAG is more complex than ATGCATGC. This would seem to be the definition assumed by the questioner (and also in another answer).
2. The length of the sequence. This is the definition given in the article quoted in the question: “Complexity - the total length of different sequences”. However it is not one that would have occurred to me on encountering the expression.
3. The extent to which a length of DNA (especially a chromosome) has regions present in multiple copies. This seems not to have been considered in the question, but is historically what was meant be genome complexity deduced from annealing experiments. This is shown in these extracts from a venerable text on nucleic acids, long out of print:

In human cells unique DNA has a C_ot_1/2 value of 1000 (moles nucleotide seconds litre^–1)…Repetitive DNA includes all of the rest of the DNA. Among the repetitive DNA is a fraction which reanneals with a C_ot_1/2 value of between 100 and 1000…thought to be those [genes] coding for proteins which form major structural components of the cell… [some examples given of multi-copy genes like tRNA]…At the other extreme DNA with a C_ot_1/2 value as low as 10^–3 consists largely of satellite DNA.

Explanation for Case 3 (complex because of multiple copies)

As the article quoted in the question correctly states, “Renaturation, or duplex formation requires random collisions between two single-stranded molecules”. However such experiments are performed with fragmented DNA in solution, not whole chromosomes, so the two molecules that must collide are gene-size or smaller in length. The more copies of geneX or sequenceX there are in the DNA, the greater the number of targets there will be containing geneX or sequenceX, hence the faster fragments containing such genes will anneal.

Explanation for Case 1 (complex because less homogeneous)

Assuming that one is comparing single-copy genes of different degrees of homogeneity, one can imagine that for something like ATATATAT there will be more ‘hits’ that give partial overlaps that may be detected as double-stranded:

A T A T A T A T A T A T A T A T
        T A T A T A T A T A T A T A T A

Alternatively, once bound imperfectly, there may be a greater chance of perfect binding after dissociation because of proximity.

However, it is also possible that writers are confusing or amalgamating this with Case 3, as simpler DNA may actually be present in more copies in a genome.

Explanation for Case 2 (complex because longer)

The explanation here is trivial. If you perform reannealing experiments with two geneomes — E.coli (4.6 Mbp, c. 4000 protein-coding genes) and Carsonella ruddii (0.16 Mbp, 182 protein-coding genes) — employing the same amounts of DNA as 300bp fragments, the fragments from the smaller genome will be approximately 20x more likely to make a random collision with a complementary fragment.

Answer 2

You are correct that this won't produce the correctly complemented strands 100% of the time, indeed that's what the experiments outlined in the link you provided are aiming to measure... how much DNA is duplexed over time after a single denaturation. Simple sequences will be so alike that an approximation of 100% can anneal fairly quickly, as measured by the sensitivity of the experiment (A260/A280 is not sensitive; these things are done much differently these days).

The information that you are missing is that if those bits in the middle don't match then the DNA there won't anneal - it will still exist as single-stranded or partially duplexed strands and so will show up as not 100% annealed in the assay. To fully anneal you need full complementarity of the strands, and given that you have a single denaturation, the chance that 100% will anneal in any given aliquot is low, so in a rate equation it will take a "long" time.

I'm no chemist or physicist, so if someone has a better answer, please feel free to chime in.

Answer 3

From physics point of view, annealing is about finding the lowest energy configuration of the two DNA strands. The configuration space of two strands has many minima, and after every annealing cycle the strands settle in one of them, which is not necessarily the lowest. One then reheats the DNA to allow it to explore teh surrounding minima and hopefully settling in the one of even lower energy. In a sequence containg many identical elements, such lower energy minima a readily available - in the OP language it would be really easy to find a spot to reanneal. On the other hand, if the sequence elements are very different, a large deviation from the current configuration is required to find a more favorable configuration.