TY - JOUR
T1 - A thermodynamic approach for the targeting of nucleic acid structures using their complementary single strands
AU - Lee, Hui Ting
AU - Carr, Caroline
AU - Siebler, Hollie
AU - Waters, Lela
AU - Khutsishvili, Irine
AU - Iseka, Fany
AU - Domack, Brian
AU - Olsen, Chris M.
AU - Marky, Luis A.
PY - 2011
Y1 - 2011
N2 - The main focus of our investigations is to further our understanding of the physicochemical properties of nucleic acid structures. We report on a thermodynamic approach to study the reaction of a variety of intramolecular nucleic acid structures with their respective complementary strands. Specifically, we have used a combination of isothermal titration (ITC) and differential scanning calorimetry (DSC) and spectroscopy techniques to determine standard thermodynamic profiles for the reaction of a triplex, G-quadruplex, hairpin loops, pseudoknot, and three-arm junctions with their complementary strands. Reaction enthalpies are measured directly in ITC titrations, and compared with those obtained indirectly from Hess cycles using DSC unfolding data. All reactions investigated yielded favorable free energy contributions, indicating that each single strand is able to invade and disrupt the corresponding intramolecular DNA structure. These favorable free energy terms are enthalpy-driven, resulting from a favorable compensation of exothermic contributions due to the formation of additional base-pair stacks in the duplex product, and endothermic contributions, from the disruption of base stacking contributions of the reactant single strands. The overall results provide a thermodynamic approach that can be used in the targeting of nucleic acids, especially the secondary structures formed by mRNA, with oligonucleotides for the control of gene expression.
AB - The main focus of our investigations is to further our understanding of the physicochemical properties of nucleic acid structures. We report on a thermodynamic approach to study the reaction of a variety of intramolecular nucleic acid structures with their respective complementary strands. Specifically, we have used a combination of isothermal titration (ITC) and differential scanning calorimetry (DSC) and spectroscopy techniques to determine standard thermodynamic profiles for the reaction of a triplex, G-quadruplex, hairpin loops, pseudoknot, and three-arm junctions with their complementary strands. Reaction enthalpies are measured directly in ITC titrations, and compared with those obtained indirectly from Hess cycles using DSC unfolding data. All reactions investigated yielded favorable free energy contributions, indicating that each single strand is able to invade and disrupt the corresponding intramolecular DNA structure. These favorable free energy terms are enthalpy-driven, resulting from a favorable compensation of exothermic contributions due to the formation of additional base-pair stacks in the duplex product, and endothermic contributions, from the disruption of base stacking contributions of the reactant single strands. The overall results provide a thermodynamic approach that can be used in the targeting of nucleic acids, especially the secondary structures formed by mRNA, with oligonucleotides for the control of gene expression.
KW - Antisense
KW - DNA secondary structures
KW - Heat
KW - Targeting nucleic acid strands
KW - Thermodynamics
UR - http://www.scopus.com/inward/record.url?scp=79951974140&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79951974140&partnerID=8YFLogxK
U2 - 10.1016/B978-0-12-381268-1.00013-6
DO - 10.1016/B978-0-12-381268-1.00013-6
M3 - Article
C2 - 21333787
AN - SCOPUS:79951974140
SN - 0076-6879
VL - 492
SP - 1
EP - 26
JO - Methods in Enzymology
JF - Methods in Enzymology
ER -