SimulateMeltingTemperature

SimulateMeltingTemperature[reaction, concentration]⟹meltingTemperatureObject

computes the melting temperature of the given reaction between two nucleic acid oligomers at the specified concentration with traditional Nearest Neighbor thermodynamic analysis.

SimulateMeltingTemperature[reactantAplusB, concentration]⟹meltingTemperatureObject

finds the product of reaction from 'reactantA' + 'reactantB', then computes the melting temperature.

SimulateMeltingTemperature[reactantEquilibriumProduct, concentration]⟹meltingTemperatureObject

infers the type of reaction from the given 'reactant' ⇌ 'product' state and computes the melting temperature for that reaction.

SimulateMeltingTemperature[reactionMechanism, concentration]⟹meltingTemperatureObject

computes the melting temperature from the reaction in the given mechanism.

SimulateMeltingTemperature[oligomer, concentration]⟹meltingTemperatureObject

considers the hybridization reaction between the given oligomer and its reverse complement.

SimulateMeltingTemperature[structure, concentration]⟹meltingTemperatureObject

considers the melting reaction whereby all of the bonds in the given structure are melted.

SimulateMeltingTemperature[enthalpy, entropy, concentration]⟹meltingTemperatureObject

computes the melting temperature from the given enthalpy and entropy of a reaction.

Details

Melting temperature is defined as the temperature at which half of the strands are in the double-helical state and half are in the random-coil state.
In first order folding or melting case, melting temperature is calculated from Tm = ΔH/ΔS.
In second order paring or melting case, melting temperature is calculated from Tm = ΔH/(ΔS-R ln[Ct]). For bimolecular self-complementary cases (A + A ⇌ A2), Ct = C[A] (C[A] represents the concentration of A). For bimolecular nonself-complimentary cases (A + B ⇌ AB), if C[A] = C[B], Ct = (C[A] + C[B]) / 4, if C[A] > C[B], Ct = C[A] - C[B]/2, and if C[A] < C[B], Ct = C[B] - C[A]/2. See reference: Object[Report,Literature,"id:o1k9jAKpjE8a"]: John SantaLucia. "A Unified View of Polymer,Dumbbell,and Oligonucleotide DNA Nearest-Neighbor Thermodynamics." Proceedings of the National Academy of Sciences of the United States of America 95.4 (1998):1460–1465.
DNA Nearest Neighbor parameters from Object[Report, Literature, "id:kEJ9mqa1Jr7P"]: Allawi, Hatim T., and John SantaLucia. "Thermodynamics and NMR of internal GT mismatches in DNA." Biochemistry 36.34 (1997): 10581-10594.
RNA Nearest Neighbor parameters from Object[Report, Literature, "id:M8n3rxYAnNkm"]: Xia, Tianbing, et al. "Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs." Biochemistry 37.42 (1998): 14719-14735.
If given a nucleic acid sequence, strand, or sequence length, this function assumes a two-state binding between the provided sequence and a perfect reverse complement.
Given a structure, considers only the bonded regions of the structure.
Supported polymer types are DNA and RNA.
Untyped sequences or lengths default to DNA if there is ambiguity.
Enthalpy is independent of salt concentration, while entropy values for a given salt concentration. MonovalentSaltConcentration and DivalentSaltConcentration can be used to specify the concentration of monovalent salt (Na+, K+) and divalent salt (Mg2+) respectively. The entropy correction term is calculated as: 0.368*(Sequence Length - 1)*ln[(Na+) + 140*(Mg2+)] from Object[Report,Literature, "id:eGakld09nLXo"]: von Ahsen, et al. "Application of a Thermodynamic Nearest-Neighbor Model to Estimate Nucleic Acid Stability and Optimize Probe Design:Prediction of Melting Points of Multiple Mutations of Apolipoprotein B-3500 and Factor V with a Hybridization Probe Genotyping Assay on the LightCycler" Clinical Chemistry 45.12 (1999) 2094-2101.
Assumes a second order reaction if enthalpy and entropy are provided.

Input

Output

General Options

Examples

Basic Examples (5)

Compute the melting temperature of a hybridization reaction between given sequence and its reverse complement:

Find the product of DNA['GGACTGACGCGTTGA']+DNA['TCAACGCGTCAGTCC'], then compute the melting temperature:

Specify reaction from one structure to another:

Compute the melting temperature of a bimolecular reaction from its enthalpy and entropy:

Additional Examples (17)

Input concentration as a distribution:

Two reactants have different concentrations:

Two reactants have different concentrations and one of them is specified as a distribution:

Two reactants have different concentrations as distributions:

Input enthalpy, entropy and concentration as distributions:

Compute the melting temperature from a simple ReactionMechanism contains only one reaction:

Pull strand from given sample:

Pull strand from given model:

Given reaction model:

Given structure, computes melting temperature of all bonded regions:

Compute the distribution of melting temperature of all 15-mer hybridization reactions with their reverse complements:

Given a strand:

Given a typed sequence:

Given untyped length:

Structure with no bonds returns 0K:

Can handle degenerate sequence:

Return melting temperature distribution instead of mean:

Options (9)

AlternativeParameterization (1)

Using AlternativeParameterization that is used if there is missing information in the thermo properties of the original polymer:

BufferModel (1)

Specify a specific buffer, from which salt concentration will be computed:

DivalentSaltConcentration (1)

Specify divalent salt concentration in buffer:

MonovalentSaltConcentration (1)

Specify monovalent salt concentration in buffer:

Polymer (1)

Specify polymer for untyped sequences:

ReactionType (1)

Given an object, specify if the strands should be hybridized or the structure melted:

Template (2)

The Options from a previous melting temperature simulation (object reference) can be used to preform an identical simulation on new oligomer:

The Options from a previous melting temperature simulation (object) can be used to preform an identical simulation on new oligomer:

ThermodynamicsModel (1)

Using ThermodynamicsModel to explicitly provide the thermodynamic parameters or to override the values taken from Thermodynamics field in the model oligomer: