What is an RNA Tetraloop?
An RNA tetraloop structure is composed of a Watson–Crick base-paired stem and four loop nucleotides. The structure is compact and stable. A sharp turn in the backbone is stabilized by ribose–base, base–phosphate hydrogen bonds and base stacking interactions.
What is GNRA?
GNRA tetraloops (N is A, C, G, or U; R is A or G) are basic building blocks of RNA structure that often interact with proteins or other RNA structural elements. Comparison of tetraloop structures shows a common backbone geometry for each of the eight possible tetraloop sequences and suggests a common hydration.
Which RNA Tetraloop is most stable?
UUCG tetraloop
The UUCG tetraloop is the most stable tetraloop. UUCG and GNRA tetraloops make up 70% of all tetraloops in 16S-rRNA .
What is the secondary structure of RNA?
The secondary structure of RNA consists of a single polynucleotide. Base pairing in RNA occurs when RNA folds between complementarity regions. Both single- and double-stranded regions are often found in RNA molecules.
What is Pseudoknot in RNA?
What is an RNA pseudoknot? As defined originally3, a pseudoknot is a structure formed upon base-pairing of a single-stranded region of RNA in the loop of a hairpin to a stretch of complementary nucleotides elsewhere in the RNA chain (Fig. 2).
What is an example of secondary structure of RNA?
There are many secondary structure elements of functional importance to biological RNA’s; some famous examples are the Rho-independent terminator stem-loops and the tRNA cloverleaf.
What causes RNA secondary structure?
In the first step—for example, as the RNA is cooled from a high temperature—base pairs form to produce a secondary structure of stems, mismatches, loops, and bulges. In the second step, the tertiary structure forms with specific loop–loop or loop–bulge interactions or with other long-range RNA–RNA interactions.
What is RNA kissing?
RNA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop, base pair with the unpaired nucleotides in another hairpin loop. When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex.
Can RNA form Pseudoknots?
RNA pseudoknots are structural motifs in RNA that are increasingly recognized in viral and cellular RNAs. Pseudoknots are formed upon base pairing of a single-stranded region of RNA in the loop of a hairpin to a stretch of complementary nucleotides elsewhere in the RNA chain.
Does RNA have a secondary structure?
The RNA secondary structure is mainly composed of a stem structure formed by complementary pairing of contiguous bases and a cyclic structure formed by non-pairing of bases.
Does RNA have a helix?
Although usually single-stranded, some RNA sequences have the ability to form a double helix, much like DNA.
What is kissing complex?
A kissing stem-loop, or kissing stem loop interaction, is formed in RNA when two bases between two hairpin loops pair. When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex. These interactions generally form between stem-loops.
What are the different types of tetraloops in RNA?
Tetraloops are a type of four-base hairpin loop motifs in RNA secondary structure that cap many double helices. There are many variants of the tetraloop. The published ones include ANYA, CUYG, GNRA, UNAC and UNCG.
Which is better a GNRA or a tetraloop?
Tetraloops with the sequence UMAC have essentially the same backbone fold as the GNRA tetraloop, but may be less likely to form tetraloop-receptor interactions. They may therefore be a better choice for closing stems when designing artificial RNAs.
How are the base pairs of tetraloops stabilized?
The first and the fourth nucleotides form a base pair in most of the tetraloops, leaving two unpaired nucleotides in the loop. A sharp turn in the backbone is stabilized by ribose–base, base–phosphate hydrogen bonds and base stacking interactions. Tetraloops help in the folding of RNA by initiating the process.
Why does GNRA occur more than other tetranucleotides?
GNRA occurs 50% more than other tetranucleotides due to their ability to withstand temperatures 4° C higher than other RNA hairpins. This allows them to act as nucleation sites for proper folding of RNA.