driven by stacking interactions between nucleobases and by the
formation of complementary base pairs within a single RNA molecule when the RNA chain folds back on itself. In this case, the
resulting double-stranded structure contains a loop that links the
oppositely directed strands. If the loop is small, the structure is
called a hairpin; when the double-stranded region is closed by a
large loop, it is known as a stem-loop.
Significant negative charges along the RNA phosphodiester
backbone and base stacking stiffen RNA helices and restrict the
ability of RNA to form complex structures. Disruptions within the
helix and neutralization of negative charges by counter ions relieve
stiffness and facilitate formation of tertiary structure and adaptation
of unique functional conformations [33]. Fundamental RNA properties such as favorable thermodynamics of stacking and hydrogen
bonding, rapid kinetics of secondary, relative to tertiary, structure
formation, and directional in vivo folding [34, 35] dictate a hierarchical manner by which RNA adopts its complex structure. This
hierarchical folding, initiated by the formation of secondary structure elements from consecutively transcribed regions, proceeds by
joining independently formed elements to form tertiary structures.
The hairpin is the most common secondary structural elements
in RNA, which can function on its own as a ligand-binding region
or nucleate formation of a complex RNA structure through
RNA-RNA interactions [34, 36]. The stem of a hairpin is comprised mainly of Watson-Crick base pairs formed between two
antiparallel stretches of RNA, and ranges in length from 1 base
pair (bp) to more than 10, with an average length of 3–4 bp
[37]. Due to steric repulsion, a loop connecting the strands contains a minimum of three nucleotides. RNA hairpin folding can
often be described as a cooperative event, especially for short hairpins in which the thermodynamic worth of each base pair is more
significant and the formation of a loop brings more disorder than in
hairpins with longer helices [38].
To gain a better understanding of hairpin folding, RNA loops
and their closing base pairs have been thermodynamically dissected
for various systems, including for most prevalent four-nucleotide
loops called tetraloops [39, 40]. Atomic resolution structures of
phylogenetically common tetraloops UNCG, GNRA, and CUUG
(where N represents any nucleotide, and R represents A or G) [41–
43] have shown that these motifs undergo base stacking and extensive hydrogen bonding that make them extremely stable. Thermal
studies revealed that some tetraloops undergo a two-state all-ornone folding, indicative of high cooperativity in the system
[38]. Other studies have pointed out that in relationship to DNA,
RNA is less cooperative in its folding, reflecting a smaller thermodynamic effect upon mutating 1–3 nucleotides of a loop [44]. This
may be a beneficial feature of RNA allowing for a diverse primary
262
Alla Peselis and Alexander Serganov
formation of complementary base pairs within a single RNA molecule when the RNA chain folds back on itself. In this case, the
resulting double-stranded structure contains a loop that links the
oppositely directed strands. If the loop is small, the structure is
called a hairpin; when the double-stranded region is closed by a
large loop, it is known as a stem-loop.
Significant negative charges along the RNA phosphodiester
backbone and base stacking stiffen RNA helices and restrict the
ability of RNA to form complex structures. Disruptions within the
helix and neutralization of negative charges by counter ions relieve
stiffness and facilitate formation of tertiary structure and adaptation
of unique functional conformations [33]. Fundamental RNA properties such as favorable thermodynamics of stacking and hydrogen
bonding, rapid kinetics of secondary, relative to tertiary, structure
formation, and directional in vivo folding [34, 35] dictate a hierarchical manner by which RNA adopts its complex structure. This
hierarchical folding, initiated by the formation of secondary structure elements from consecutively transcribed regions, proceeds by
joining independently formed elements to form tertiary structures.
The hairpin is the most common secondary structural elements
in RNA, which can function on its own as a ligand-binding region
or nucleate formation of a complex RNA structure through
RNA-RNA interactions [34, 36]. The stem of a hairpin is comprised mainly of Watson-Crick base pairs formed between two
antiparallel stretches of RNA, and ranges in length from 1 base
pair (bp) to more than 10, with an average length of 3–4 bp
[37]. Due to steric repulsion, a loop connecting the strands contains a minimum of three nucleotides. RNA hairpin folding can
often be described as a cooperative event, especially for short hairpins in which the thermodynamic worth of each base pair is more
significant and the formation of a loop brings more disorder than in
hairpins with longer helices [38].
To gain a better understanding of hairpin folding, RNA loops
and their closing base pairs have been thermodynamically dissected
for various systems, including for most prevalent four-nucleotide
loops called tetraloops [39, 40]. Atomic resolution structures of
phylogenetically common tetraloops UNCG, GNRA, and CUUG
(where N represents any nucleotide, and R represents A or G) [41–
43] have shown that these motifs undergo base stacking and extensive hydrogen bonding that make them extremely stable. Thermal
studies revealed that some tetraloops undergo a two-state all-ornone folding, indicative of high cooperativity in the system
[38]. Other studies have pointed out that in relationship to DNA,
RNA is less cooperative in its folding, reflecting a smaller thermodynamic effect upon mutating 1–3 nucleotides of a loop [44]. This
may be a beneficial feature of RNA allowing for a diverse primary
262
Alla Peselis and Alexander Serganov