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General terms:
Kint: Kint is the equilibrium constant between the two conformers of the aptazyme in the absence of ligand.
: Cleavage tendency is the fraction of cleavagecompetent conformer in the absence of ligand.
Terms in the context of aptazymes as in vitro biosensors:
kapp: kapp is the apparent cleavage rate constant when a selfcleaving aptazyme is tested in vitro under certain concentration of ligand.
EMBED Equation.3 : Relative ligand concentration EMBED Equation.3 is the ratio of total ligand concentration to the Kd of the aptamer domain to its ligand, or in equation, EMBED Equation.3 = [Ltot]/Kd.
EMBED Equation.3 : EMBED Equation.3 is the concentration of total ligand at which the aptazyme is halfactivated or halfinhibited.
EMBED Equation.3 : EMBED Equation.3 is the relative ligand concentration at which the aptazyme is halfactivated or halfinhibited, or in equation, EMBED Equation.3 = EMBED Equation.3 /Kd. The relationships between EMBED Equation.3 and for ligandactivated aptazymes and ligandinhibited aptazymes are shown in equations (8) and (14), respectively.
EMBED Equation.3 : EMBED Equation.3 is the highest possible relative ligand concentration, or in other words, the highest possible ligand concentration divided by Kd of the aptamer domain to its ligand.
EMBED Equation.3 : For ligandactivated aptazymes, EMBED Equation.3 is the foldincrease of kapp when ligand concentration increases from 0 to infinite. The relationship between EMBED Equation.3 and is shown in equation (9). EMBED Equation.3 is not defined for ligandinhibited aptazymes.
EMBED Equation.3 : EMBED Equation.3 is the foldincrease or folddecrease of kapp when ligand concentration increases from 0 to the highest possible ligand concentration for ligandactivated aptazymes and ligandinhibited aptazymes, respectively. The dependences of EMBED Equation.3 on EMBED Equation.3 and for ligandactivated aptazymes and ligandinhibited aptazymes are shown in equations (11) and (16), respectively.
Terms in the context of aptazymes as in vivo riboswitches:
EMBED Equation.3 : Relative mRNA level EMBED Equation.3 is the steadystate concentration of mRNA that harbors an aptazyme or ribozyme at its 32 UTR divided by the steadystate concentration of the same mRNA without an aptazyme or ribozyme. Thus when the cleavage activity of the aptazyme or ribozyme is zero, EMBED Equation.3 = 1; when the activity of the aptazyme or ribozyme is infinitely high, EMBED Equation.3 = 0.
D: D is the ratio of the cleavage rate constant of a constitutively active ribozyme to the spontaneous degradation rate constant of the mRNA.
: is the ratio of the concentration of conformer A to the concentration of conformer I (in Figure 3C and 3D) at steady state (see equations S.11 and S.14).
: is the ratio of the concentration of conformer B to the concentration of conformer I (in Figure 3C and 3D) at steady state (see equations S.12 and S.15).
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h6hsduCJPJUVaJUjh6hsduUh6hsdu5h6hsduh6hsdu61ion.3 : EMBED Equation.3 is the apparent in vivo dissociation rate constant of the aptamer domain to its ligand in the presence of mRNA degradation and aptazyme cleavage. The definitions of EMBED Equation.3 for ligandactivated and ligandinhibited aptazyme are shown in equations (S.10 and S.13). EMBED Equation.3 usually has similar value to the true Kd of the aptamer domain to its ligand.
EMBED Equation.3 : Relative ligand concentration EMBED Equation.3 is the ratio of total ligand concentration to the EMBED Equation.3 of the aptazyme, or in equation, EMBED Equation.3 =[Ltot]/ EMBED Equation.3 .
EMBED Equation.3 : EMBED Equation.3 is the concentration of total ligand at which the relative mRNA level EMBED Equation.3 is in the middle of the theoretical dynamic range of EMBED Equation.3 .
EMBED Equation.3 : EMBED Equation.3 is the relative concentration of total ligand at which the relative mRNA level EMBED Equation.3 is in the middle of the theoretical dynamic range of EMBED Equation.3 , or in equation, EMBED Equation.3 = EMBED Equation.3 / EMBED Equation.3 . The dependences of EMBED Equation.3 on and D for ligandactivated aptazymes and ligandinhibited aptazymes are shown in equations (27) and (37), respectively.
EMBED Equation.3 : EMBED Equation.3 is the highest possible relative ligand concentration, or in other words, the highest possible ligand concentration divided by EMBED Equation.3 .
EMBED Equation.3 : EMBED Equation.3 is the foldincrease or folddecrease of EMBED Equation.3 when ligand concentration increases from 0 to infinite for ligandinhibited aptazymes and ligandactivated aptazymes, respectively.
EMBED Equation.3 : EMBED Equation.3 is the foldincrease or folddecrease of EMBED Equation.3 when ligand concentration increases from 0 to the highest possible ligand concentration for ligandinhibited aptazymes and ligandactivated aptazymes, respectively. The dependences of EMBED Equation.3 on EMBED Equation.3 , and D for ligandactivated aptazymes and ligandinhibited aptazymes are shown in equations (29) and (39), respectively.
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