What are stem-loop structures?
Definition. Stem-loop is an essential unit of the structure of single stranded RNA or DNA. A stem-loop consists of a stem, double helix, and a loop which links the stem. The length of the loop is typically 3–8. Tetraloops, stem-loops with four nucleotides in the loop, are frequently found in RNA.
What is the purpose of the stem-loop?
The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions.
What is required for transcription termination via a hairpin loop?
This RNA hairpin is followed by multiple uracil nucleotides. The bonds between uracil and adenine are very weak. A protein bound to RNA polymerase (nusA) binds to the stem-loop structure tightly enough to cause the polymerase to temporarily stall. Overall, the modified RNA structure is what terminates transcription.
How are RNA hairpins related to termination?
RNA hairpins are related to termination because the hairpins are formed from complementary base pairing and cause the separation of the RNA transcript and RNA polymerase. Hairpin is considered as one of the crucial structures that helps in transcript release.
Which sequence will form the most stable stem-loop structure?
Loops of four or five nucleotides are found to be the most stable loop size. This is consistent with the observation that four-membered loops are the most prevalent loop size in 16S-like RNAs. The contribution of each loop to hairpin stability was calculated by subtracting the known contribution of the helical stem.
What is stem in RNA?
Stem: When more than one base pair appears in the form of a group of contiguous base pairs, the resulting structure motif is described as a stem (Fig. S1a). For RNA, this stem motif appears as a flat object.
When hairpin loop is formed?
A hairpin loop is an unpaired loop of messenger RNA (mRNA) that is created when an mRNA strand folds and forms base pairs with another section of the same strand. The resulting structure looks like a loop or a U-shape. Hairpins are a common type of secondary structure in RNA molecules.
How are RNA hairpin loops related to termination in prokaryotic organisms?
Hairpin loops can also form in DNA molecules, but are most commonly observed in mRNA. One example of a hairpin loop is the termination sequence for transcription in some prokaryotes. Once a polymerase meets this loop, it falls of and transcription ends.
How do RNA hairpins differ from DNA hairpins?
The stem of the RNA hairpin exhibiting a A-form helical structure is shorter and therefore more compact than the stem of the DNA hairpin, which is a B-form double helix. In the RNA helix, the constraint caused by the opening fork may thus more easily extend over several base pairs than in the DNA helix.
What is a stem-loop structure?
Two nested stem-loop structures occur in RNA pseudoknots, where the loop of one structure forms part of the second stem. Many ribozymes also feature stem-loop structures.
How many stem loops are in a stem loop?
Stem-loops occur in pre- microRNA structures and most famously in transfer RNA, which contain three true stem-loops and one stem that meet in a cloverleaf pattern. The anticodon that recognizes a codon during the translation process is located on one of the unpaired loops in the tRNA.
Why is the stem-loop sequence followed by a 5-10 as sequence?
In some cases the stem-loop sequence is followed by a run of 5-10 As in the DNA which form weak A-U base pairs with the newly synthesized RNA. It is thought that the RNA polymerase pauses just after the stem-loop and that the weak A-U base pairs break causing the transcript to detach from the template.
What is stem loop intramolecular base pairing?
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. 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.