conformational transitions in folding and function of proteins and
nucleic acids, resulting in the formation of multicomponent
complexes [8].
In this review, we primarily focus on various manifestations of
cooperativity and accompanying allosteric modulations in RNA.
We provide a brief explanation of thermodynamics related to cooperativity, and outline some helpful methods for interrogating RNA
folding and cooperativity. We further provide examples of cooperativity and allostery in RNA, including formation of secondary and
tertiary interactions, multiple binding of small ligands, and assembly of RNA-protein complexes.
2 Methods of Studying Cooperativity and Allosteric Modulations
2.1 Thermodynamic
Basis of Cooperativity
Despite the variety of instances of cooperativity, they all have a
thermodynamic quality, which actually defines the term cooperativity. The simplest system to explain cooperativity is a binding
reaction with 3 components, the RNA (R), ligand (L), and either
an identical or different ligand molecule (M), to yield a ternary
complex R:L:M from individual components (Fig. 1a) [8]. The
reaction could proceed through two pathways involving initial
interactions between R and L followed by addition of M, or with
initial binding of R to M followed by interactions with
L. Cooperativity is observed when the binding of L and M to R
depends on each other. The thermodynamic construction that
illustrates this principle is known as a thermodynamic cycle. Each
binary binding reaction is described by its own equilibrium constants K 1 and K 2 , while formation of ternary complexes gives
additional constants K 3 and K 4 . All reactions have their own free
energy terms ΔG
1 , ΔG
2 , ΔG
3 , and ΔG
4 . The overall thermodynamics of forming the ternary complex does not depend on the
assembly
pathway,
therefore
K 1 K 3
¼
K 2 K 4
and
ΔG
1 + ΔG
3 ¼ ΔG
2 + ΔG
4 . If binding of L does not stimulate
binding of M to the R:L complex, each binding event is independent, the free energy of the formation of binary and ternary complexes is identical, ΔG
1 ¼ ΔG
4 , and the system does not display
cooperativity. However, if binding of L enhances binding of M to
the R:L complex, ΔG
1 > ΔG
4 , and the system has positive cooperative binding. If binding of M is hindered by binding of L, then
ΔG
1 < ΔG
4 and the binding of L and M has negative cooperativity. Similar statements can be made for vertical reactions in
Fig. 1a. Thermodynamically, the extent of cooperativity could be
expressed
by
the
coupling
free
energy,
ΔΔG ¼ ΔG
1 À ΔG
4 ¼ ΔG
2 À ΔG
3 . The system has positive
and negative cooperativity if ΔΔG > 0 and ΔΔG < 0, respectively.
Thus, in order to dissect cooperativity in the biological system that
involves interactions between RNA and small ligands such as
RNA Cooperativity and Allostery
257
nucleic acids, resulting in the formation of multicomponent
complexes [8].
In this review, we primarily focus on various manifestations of
cooperativity and accompanying allosteric modulations in RNA.
We provide a brief explanation of thermodynamics related to cooperativity, and outline some helpful methods for interrogating RNA
folding and cooperativity. We further provide examples of cooperativity and allostery in RNA, including formation of secondary and
tertiary interactions, multiple binding of small ligands, and assembly of RNA-protein complexes.
2 Methods of Studying Cooperativity and Allosteric Modulations
2.1 Thermodynamic
Basis of Cooperativity
Despite the variety of instances of cooperativity, they all have a
thermodynamic quality, which actually defines the term cooperativity. The simplest system to explain cooperativity is a binding
reaction with 3 components, the RNA (R), ligand (L), and either
an identical or different ligand molecule (M), to yield a ternary
complex R:L:M from individual components (Fig. 1a) [8]. The
reaction could proceed through two pathways involving initial
interactions between R and L followed by addition of M, or with
initial binding of R to M followed by interactions with
L. Cooperativity is observed when the binding of L and M to R
depends on each other. The thermodynamic construction that
illustrates this principle is known as a thermodynamic cycle. Each
binary binding reaction is described by its own equilibrium constants K 1 and K 2 , while formation of ternary complexes gives
additional constants K 3 and K 4 . All reactions have their own free
energy terms ΔG
1 , ΔG
2 , ΔG
3 , and ΔG
4 . The overall thermodynamics of forming the ternary complex does not depend on the
assembly
pathway,
therefore
K 1 K 3
¼
K 2 K 4
and
ΔG
1 + ΔG
3 ¼ ΔG
2 + ΔG
4 . If binding of L does not stimulate
binding of M to the R:L complex, each binding event is independent, the free energy of the formation of binary and ternary complexes is identical, ΔG
1 ¼ ΔG
4 , and the system does not display
cooperativity. However, if binding of L enhances binding of M to
the R:L complex, ΔG
1 > ΔG
4 , and the system has positive cooperative binding. If binding of M is hindered by binding of L, then
ΔG
1 < ΔG
4 and the binding of L and M has negative cooperativity. Similar statements can be made for vertical reactions in
Fig. 1a. Thermodynamically, the extent of cooperativity could be
expressed
by
the
coupling
free
energy,
ΔΔG ¼ ΔG
1 À ΔG
4 ¼ ΔG
2 À ΔG
3 . The system has positive
and negative cooperativity if ΔΔG > 0 and ΔΔG < 0, respectively.
Thus, in order to dissect cooperativity in the biological system that
involves interactions between RNA and small ligands such as
RNA Cooperativity and Allostery
257