Search results
15 maj 2024 · In RNA molecules, hairpin loops act as nucleation sites for RNA folding, impacting RNA-protein recognition and gene regulation. Stem-loop structures, like molecular beacons, enable specific detection of target sequences, providing opportunities for innovative diagnostic sensors and therapeutic methods.
Stem-loops are nucleic acid secondary structural elements which form via intramolecular base pairing in single-stranded DNA or RNA. They are also referred to as hairpins or hairpin loops.
Hairpin molecules have attracted a great deal of interest for many years. On one hand, this is because of their role in cellular processes, the recognition between the codon on mRNA and the anti-codon loop of tRNA being the most outstanding example.
The hairpin loop forms in an mRNA strand during transcription and causes the RNA polymerase to become dissociated from the DNA template strand. This process is known as rho-independent or intrinsic termination, and the sequences involved are called terminator sequences.
A 2D free energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy.
This review focuses on DNA hairpins, i.e., DNA with intrastrand base pairing, and their functions and properties in light of the specific behavior of DNA in horizontal gene transfer between bacterial cells. Hairpin structures can be formed by sequences with inverted repeats (IRs), also termed palindromes, following two main mechanisms.
In this chapter we will review the progress obtained through thermodynamic and structural studies of hairpin molecules. We will try to delineate factors that are important for hairpin loop stabilities, and attempt to uncover common folding patterns in hairpin loop structures.
