Hairpins and Hairpin Promoters

This article discusses the molecular basis of hairpin formation, the properties and functions of hairpin promoters, and the priming of replication on hairpins. It will also touch on the importance of hairpins in human hair. You should read it for further understanding. Here are some tips to understand hairpins:

Molecular basis of hairpin formation

DNA’s double helix structure is a perfect example of hairpin formation. Hairpin loop structures can be described by their end-to-end distance. This distance can be measured using FRET spectroscopy, a long-established photo-physical phenomenon in which energy transfer occurs over different distances. The relative distance between the donor and acceptor is a key factor determining the energy transfer efficiency. Molecular interaction can also be studied with FRET, and the noninvasive nature of the procedure makes it ideal for this purpose.

A similar process can be used to study the folding kinetics of small nucleic acid structural motifs. In this case, the nuleobases at the N-glycosidic bond misfold and form the syn conformation. Similar trapping mechanisms may be applicable to folding other nucleic acid structural motifs. Furthermore, MD simulations in explicit solvent allow the analysis of the sequence dependence of hairpin formation.

Properties of hairpins

The properties of hairpins are determined by their kinetics, which are the reactions of a hairpin to a force. The length of the loop determines the percentage of open hairpins, and the ratio of the length of the loop to its diameter, known as th, affects the reaction rates. A hairpin has a kinetics of three to six times as long as a bolt or screw.

The binding of a hairpin to its target molecule occurs in a negative band near 215 nm, which correlates with the strength of the interaction between the two molecules. This negative band is most visible in hairpins that have undergone modifications, and its intensity is inversely proportional to the number of modified bases. A lower mobility band means that the hairpin is more stable, as shown by melting experiments.

Functions of hairpin promoters

Hairpin promoters have multiple functions. They aid in phage replication by allowing only one strand of DNA to be copied and recognize the hairpin as a template. They are also useful for plasmid conjugation as they require both DNA strands for successful recombination. However, this strand selectivity can be a problem for inverted repeats, which generate hairpins on both the top and bottom strands.

These proteins may have been important early in the development of life because they recognize hairpin DNA. Moreover, they are recognized by several proteins, such as the RCR Rep proteins, the IS608 transposase, and the phage N4 vRNAP. These proteins then recognize and activate the genes containing these sequences, thereby ensuring that the mobile elements spread in the host cell.

Priming of replication on hairpins

In this article, we will examine the mechanism of priming of replication on hairpins. Generally, this process occurs in one of two ways: either the hairpin is directly attached to a strand of DNA (G4-type priming), or the strand contains a Y fork. In the latter case, the primosome is assembled from the hairpin and the RNA polymerase RNAP synthesizes an RNA primer to initiate the replication process.

The first hypothesis is based on the discovery of DNA hairpins at the ends of poxvirus genomes. They suggest that DNA replication on hairpins is self-priming, and that the process involves rolling hairpin strand displacement. In the former scenario, a nuclease generates the 3′ OH end of the hairpin, allowing deoxynucleotides to be added to the distal hairpin and around it. Upon the strands folding back due to self-complementarity, the replication complex continues to add deoxynucleotides to the distal hairpin. The reiteration of this process could produce higher-order concatemers.