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.

A DNA hairpin, 6.8 kbp long, is synthesized by extending a 5′-biotinylated tailed primer annealed to circular single-stranded M13 DNA with a DNA polymerase. The resulting rolling circle product is linearized by digestion with a restriction enzyme and gel purified.

We describe here the cellular processes leading to DNA hairpin formation, biological functions involving hairpins, and the mechanisms of protein-hairpin recognition. Finally, we try to shed light on the evolution of folded DNA with biological functions and their cognate proteins.

A DNA hairpin is a type of DNA molecule that can be tethered to a glass surface and a magnetic bead in a Magnetic Tweezers setup. It can be unwound under tension, leading to changes in its extension that can be studied to investigate DNA/protein interactions in real time.

Hairpin structure is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a stem-loop structure. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop.

Four hairpin molecules are studied in comparison: two DNA and two RNA ones. We observe that the conformational dynamics is slower for the RNA hairpins than for their DNA counterparts. Our results indicate that structures made of RNA are dynamically more stable.

The hairpin itself is also a critical DNA secondary structure that is shown to exist in DNA as cruciform DNA (16,75). Hairpins are shown to play critical roles in transcription regulation by modifying the chromatin and also by interacting with specific proteins that …

In order to select suitable beads, we use the previously characterized mechanical properties of the DNA construct. For the hairpin substrate, the extension remains almost constant below ~ 15 pN and abruptly increases when the hairpin is unzipped above ~ 15 pN (see below).

2010年5月5日 · We have purified the RecN protein from Deinococcus radiodurans and characterized its DNA-dependent and DNA-independent ATPase activity. The RecN protein hydrolyzes ATP with a kcat of 24 min −1, and this rate is stimulated 4-fold by duplex DNA but not by single-stranded DNA.

2010年12月1日 · Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements.