How can DNA replication result in hair pin structures?

Question

My professor said that one of the reasons SSB proteins are so important was to prevent the formation of hair pin structures, I can't see how or why DNA would form hairpin structures and there's not much about it on the internet so can anybody explain this hair pin thing and how SSB proteins prevent it from happening ?

Answer 1

DNA Hairpins are formed when two regions in same single stranded DNA are complementary in nucleotide sequence but in the opposite directions (as represented in image below). These two sets of nucleotide sequences base-pair with each other by forming hydrogen bonds between adenine-thymine and guanine-cytosine respectively to form hairpin loop. Same structures can be seen in case of RNA.

(Figure via: https://brilliant.org/problems/dna-zipper/)

Single stranded binding (SSB) proteins bind to single DNA nucleotide sequences and prevent the breakdown of newly synthesized DNA because of nucleases and it also removes the secondary structure of the DNA strands like hairpin loops so that other enzymes can bind to DNA strand and operate properly. As represented in figure below SSB bind to ssDNA through electrostatic interactions and prevent the bond formation within the nucleotides of single DNA strand, thus preventing formation of hairpin loops in DNA.

(Figure via: http://helicase.pbworks.com/w/page/17605582/Amanda-Kinney)

(via: https://proteopedia.org/wiki/index.php/Single_stranded_binding_protein)

Answer 2

If you have a stretch of single-stranded DNA that is palindromic, that palindromic region can form hydrogen bonds to itself, forming a hairpin. SSB proteins bound to and travelling along ssDNA physically get in the way of and undo hairpin folding.