Biomaterial Database

Driving denaturation: nanoscale thermal transport as a probe of DNA melting. 2011

Kirill A Velizhanin, and Chih-Chun Chien, and Yonatan Dubi, and Michael Zwolak

Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. kirill@lanl.gov

DNA denaturation has been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear structural transition. Many aspects of this phenomenon, however, remain poorly understood. Existing models fit quite well with experimental results on the fraction of unbound base pairs versus temperature, but yield incorrect results for other essential quantities such as the base pair fluctuation time scales. Here we demonstrate that nanoscale thermal transport can serve as a sensitive probe of the underlying microscopic physics responsible for the dynamics of DNA denaturation. Specifically, we show that the heat transport properties of DNA are altered significantly as it denatures, and this alteration encodes detailed information on the dynamics of thermal fluctuations and their interaction along the strand. This finding allows for the discrimination between models of DNA denaturation and will help shed new light on the nonlinear vibrational dynamics of this important molecule.

UI	MeSH Term	Description	Entries
D008958	Models, Molecular	Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.	Molecular Models,Model, Molecular,Molecular Model
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D009691	Nucleic Acid Denaturation	Disruption of the secondary structure of nucleic acids by heat, extreme pH or chemical treatment. Double strand DNA is "melted" by dissociation of the non-covalent hydrogen bonds and hydrophobic interactions. Denatured DNA appears to be a single-stranded flexible structure. The effects of denaturation on RNA are similar though less pronounced and largely reversible.	DNA Denaturation,DNA Melting,RNA Denaturation,Acid Denaturation, Nucleic,Denaturation, DNA,Denaturation, Nucleic Acid,Denaturation, RNA,Nucleic Acid Denaturations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D006046	Gold	A yellow metallic element with the atomic symbol Au, atomic number 79, and atomic weight 197. It is used in jewelry, goldplating of other metals, as currency, and in dental restoration. Many of its clinical applications, such as ANTIRHEUMATIC AGENTS, are in the form of its salts.
D017711	Nonlinear Dynamics	The study of systems which respond disproportionately (nonlinearly) to initial conditions or perturbing stimuli. Nonlinear systems may exhibit "chaos" which is classically characterized as sensitive dependence on initial conditions. Chaotic systems, while distinguished from more ordered periodic systems, are not random. When their behavior over time is appropriately displayed (in "phase space"), constraints are evident which are described by "strange attractors". Phase space representations of chaotic systems, or strange attractors, usually reveal fractal (FRACTALS) self-similarity across time scales. Natural, including biological, systems often display nonlinear dynamics and chaos.	Chaos Theory,Models, Nonlinear,Non-linear Dynamics,Non-linear Models,Chaos Theories,Dynamics, Non-linear,Dynamics, Nonlinear,Model, Non-linear,Model, Nonlinear,Models, Non-linear,Non linear Dynamics,Non linear Models,Non-linear Dynamic,Non-linear Model,Nonlinear Dynamic,Nonlinear Model,Nonlinear Models,Theories, Chaos,Theory, Chaos
D044366	Transition Temperature	The temperature at which a substance changes from one state or conformation of matter to another.	Temperature, Transition,Boiling Point Temperature,Freezing Point Temperature,Melting Point Temperature,Boiling Point Temperatures,Freezing Point Temperatures,Melting Point Temperatures,Temperature, Boiling Point,Temperature, Freezing Point,Temperature, Melting Point,Temperatures, Boiling Point,Temperatures, Freezing Point,Temperatures, Melting Point,Temperatures, Transition,Transition Temperatures
D049329	Nanostructures	Materials which have structured components with at least one dimension in the range of 1 to 100 nanometers. These include NANOCOMPOSITES; NANOPARTICLES; NANOTUBES; and NANOWIRES.	Nanomaterials,Nanostructured Materials,Material, Nanostructured,Materials, Nanostructured,Nanomaterial,Nanostructure,Nanostructured Material