References
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of
RNA
architecture.
Cell
136:604–609.
https://doi.org/10.1016/j.
cell.2009.02.003
2. Dethoff EA, Chugh J, Mustoe AM,
Al-Hashimi HM (2012) Functional complexity
and regulation through RNA dynamics.
Nature 482:322–330. https://doi.org/10.
1038/nature10885
3. Breaker RR (2002) Engineered allosteric ribozymes as biosensor components. Curr Opin
Biotechnol 13:31–39. https://doi.org/10.
1016/S0958-1669(02)00281-1
4. Alema ´n EA, Lamichhane R, Rueda D (2008)
Exploring RNA folding one molecule at a time.
Curr Opin Chem Biol 12:647–654. https://
doi.org/10.1016/j.cbpa.2008.09.010
5. Peselis A, Gao A, Serganov A (2015) Cooperativity, allostery and synergism in ligand binding
to riboswitches. Biochimie 117:100–109.
https://doi.org/10.1016/j.biochi.2015.06.
028
6. Royer WE, Knapp JE, Strand K, Heaslet HA
(2001) Cooperative hemoglobins: conserved
fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem Sci
26:297–304.
https://doi.org/10.1016/
S0968-0004(01)01811-4
7. Bohr C, Hasselbalch K, Krogh A (1904)
Concerning
a
biologically
important
relationship-the influence of the carbon dioxide content of blood on its oxygen binding.
Skand Arch Physiol 16:401–412
8. Williamson JR (2008) Cooperativity in macromolecular assembly. Nat Chem Biol
4:458–465.
https://doi.org/10.1038/
nchembio.102
9. Moody EM, Bevilacqua PC (2003) Folding of
a stable DNA motif involves a highly cooperative network of interactions. J Am Chem Soc
125:16285–16293.
https://doi.org/10.
1021/ja038897y
10. Siegfried NA, Bevilacqua PC (2009)
Chapter 13 Thinking inside the box. Designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in
RNA and DNA folding. Methods Enzymol
455:365–393.
https://doi.org/10.1016/
S0076-6879(08)04213-4
11. Laing LG, Draper DE (1994) Thermodynamics of RNA folding in a conserved ribosomal
RNA domain. J Mol Biol 237:560–576.
https://doi.org/10.1006/jmbi.1994.1255
12. Tuschl T, Gohlke C, Jovin TM et al (1994) A
three-dimensional model for the hammerhead
ribozyme based on fluorescence measurements. Science 266:785–789
13. Walter NG, Burke JM, Millar DP (1999) Stability of hairpin ribozyme tertiary structure is
governed by the interdomain junction. Nat
Struct Biol 6:544–549. https://doi.org/10.
1038/9316
14. Haller A, Soulie `re MF, Micura R (2011) The
dynamic nature of RNA as key to understanding riboswitch mechanisms. Acc Chem Res
44:1339–1348.
https://doi.org/10.1021/
ar200035g
15. Bothe JR, Nikolova EN, Eichhorn CD et al
(2011) Characterizing RNA dynamics at
atomic resolution using solution-state NMR
spectroscopy. Nat Methods 8:919–931.
https://doi.org/10.1038/nmeth.1735
16. Tochtrop GP, Richter K, Tang C et al (2002)
Energetics by NMR: site-specific binding in a
positively cooperative system. Proc Natl Acad
Sci 99:1847–1852. https://doi.org/10.1073/
pnas.012379199
17. Velazquez-Campoy A, Freire E (2005) ITC in
the post-genomic era...? Priceless. Biophys
Chem 115:115–124
18. Brown A (2009) Analysis of cooperativity by
isothermal titration calorimetry. Int J Mol Sci
10:3457–3477.
https://doi.org/10.3390/
ijms10083457
19. Houtman JCD, Brown PH, Bowden B et al
(2007) Studying multisite binary and ternary
protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein
complexes in cell signaling. Protein Sci
16:30–42.
https://doi.org/10.1110/ps.
062558507
20. Huang L, Serganov A, Patel DJ (2010) Structural insights into ligand recognition by a sensing domain of the cooperative glycine
riboswitch. Mol Cell 40:774–786. https://
doi.org/10.1016/j.molcel.2010.11.026
21. Salim NN, Feig AL (2009) Isothermal titration
calorimetry of RNA. Methods 47:198–205.
https://doi.org/10.1016/j.ymeth.2008.09.
003
22. Recht MI, Williamson JR (2004) RNA tertiary
structure and cooperative assembly of a large
ribonucleoprotein complex. J Mol Biol
344:395–407.
https://doi.org/10.1016/j.
jmb.2004.09.009
23. Feig AL (2009) Studying RNA-RNA and
RNA-protein interactions by isothermal titration
calorimetry.
Methods
Enzymol
RNA Cooperativity and Allostery
269
1. Cruz JA, Westhof E (2009) The dynamic landscapes
of
RNA
architecture.
Cell
136:604–609.
https://doi.org/10.1016/j.
cell.2009.02.003
2. Dethoff EA, Chugh J, Mustoe AM,
Al-Hashimi HM (2012) Functional complexity
and regulation through RNA dynamics.
Nature 482:322–330. https://doi.org/10.
1038/nature10885
3. Breaker RR (2002) Engineered allosteric ribozymes as biosensor components. Curr Opin
Biotechnol 13:31–39. https://doi.org/10.
1016/S0958-1669(02)00281-1
4. Alema ´n EA, Lamichhane R, Rueda D (2008)
Exploring RNA folding one molecule at a time.
Curr Opin Chem Biol 12:647–654. https://
doi.org/10.1016/j.cbpa.2008.09.010
5. Peselis A, Gao A, Serganov A (2015) Cooperativity, allostery and synergism in ligand binding
to riboswitches. Biochimie 117:100–109.
https://doi.org/10.1016/j.biochi.2015.06.
028
6. Royer WE, Knapp JE, Strand K, Heaslet HA
(2001) Cooperative hemoglobins: conserved
fold, diverse quaternary assemblies and allosteric mechanisms. Trends Biochem Sci
26:297–304.
https://doi.org/10.1016/
S0968-0004(01)01811-4
7. Bohr C, Hasselbalch K, Krogh A (1904)
Concerning
a
biologically
important
relationship-the influence of the carbon dioxide content of blood on its oxygen binding.
Skand Arch Physiol 16:401–412
8. Williamson JR (2008) Cooperativity in macromolecular assembly. Nat Chem Biol
4:458–465.
https://doi.org/10.1038/
nchembio.102
9. Moody EM, Bevilacqua PC (2003) Folding of
a stable DNA motif involves a highly cooperative network of interactions. J Am Chem Soc
125:16285–16293.
https://doi.org/10.
1021/ja038897y
10. Siegfried NA, Bevilacqua PC (2009)
Chapter 13 Thinking inside the box. Designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in
RNA and DNA folding. Methods Enzymol
455:365–393.
https://doi.org/10.1016/
S0076-6879(08)04213-4
11. Laing LG, Draper DE (1994) Thermodynamics of RNA folding in a conserved ribosomal
RNA domain. J Mol Biol 237:560–576.
https://doi.org/10.1006/jmbi.1994.1255
12. Tuschl T, Gohlke C, Jovin TM et al (1994) A
three-dimensional model for the hammerhead
ribozyme based on fluorescence measurements. Science 266:785–789
13. Walter NG, Burke JM, Millar DP (1999) Stability of hairpin ribozyme tertiary structure is
governed by the interdomain junction. Nat
Struct Biol 6:544–549. https://doi.org/10.
1038/9316
14. Haller A, Soulie `re MF, Micura R (2011) The
dynamic nature of RNA as key to understanding riboswitch mechanisms. Acc Chem Res
44:1339–1348.
https://doi.org/10.1021/
ar200035g
15. Bothe JR, Nikolova EN, Eichhorn CD et al
(2011) Characterizing RNA dynamics at
atomic resolution using solution-state NMR
spectroscopy. Nat Methods 8:919–931.
https://doi.org/10.1038/nmeth.1735
16. Tochtrop GP, Richter K, Tang C et al (2002)
Energetics by NMR: site-specific binding in a
positively cooperative system. Proc Natl Acad
Sci 99:1847–1852. https://doi.org/10.1073/
pnas.012379199
17. Velazquez-Campoy A, Freire E (2005) ITC in
the post-genomic era...? Priceless. Biophys
Chem 115:115–124
18. Brown A (2009) Analysis of cooperativity by
isothermal titration calorimetry. Int J Mol Sci
10:3457–3477.
https://doi.org/10.3390/
ijms10083457
19. Houtman JCD, Brown PH, Bowden B et al
(2007) Studying multisite binary and ternary
protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: application to adaptor protein
complexes in cell signaling. Protein Sci
16:30–42.
https://doi.org/10.1110/ps.
062558507
20. Huang L, Serganov A, Patel DJ (2010) Structural insights into ligand recognition by a sensing domain of the cooperative glycine
riboswitch. Mol Cell 40:774–786. https://
doi.org/10.1016/j.molcel.2010.11.026
21. Salim NN, Feig AL (2009) Isothermal titration
calorimetry of RNA. Methods 47:198–205.
https://doi.org/10.1016/j.ymeth.2008.09.
003
22. Recht MI, Williamson JR (2004) RNA tertiary
structure and cooperative assembly of a large
ribonucleoprotein complex. J Mol Biol
344:395–407.
https://doi.org/10.1016/j.
jmb.2004.09.009
23. Feig AL (2009) Studying RNA-RNA and
RNA-protein interactions by isothermal titration
calorimetry.
Methods
Enzymol
RNA Cooperativity and Allostery
269