Melt
Assistant
Predict Basic and Salt-Adjusted Melting Temperatures.
Melt Assistant finds the melting temperature of a unique DNA sequence using basic and salt-adjusted equations. Both approaches consider the type of nucleotide in the specific DNA sequence. The salt-adjusted method takes into account the concentration of Sodium (Na+) ions.
The formulas used for calculating the melting temperature of a DNA sequence depends on the sequence's length.
Basic
For sequences less than 14 nucleotides the formula is:
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Tm = (wA + xT) * 2 + (yG + zC) * 4
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where w,x,y,z are the number of the bases A,T,G,C in the sequence, respectively.
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For sequences longer than 14 nucleotides, the equation used is:
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Tm = 64.9 + 41 * (yG + zC - 16.4) / (wA + xT + yG + zC)
Salt-Adjusted
For sequences less than 14 nucleotides the formula is:
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Tm = (wA+xT) * 2 + (yG+zC) * 4 - log10(0.050) + 16.6*log10([Na+])
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where w,x,y,z are the number of the bases A,T,G,C in the sequence, respectively.
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For sequences longer than 14 nucleotides, the equation used is:
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Tm = 100.5 + (41 * (yG+zC) / (wA+xT+yG+zC)) - (820 / (wA+xT+yG+zC)) + 16.6*log10([Na+])
The basic melting temperature (Tm) is a measure of the temperature at which the double-stranded DNA structure of a molecule begins to denature and separate into single strands, taking into account the specific base composition of the DNA molecule.
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The first formula for calculating the basic Tm is: Tm = (wA + xT) * 2 + (yG + zC) * 4, where wA, xT, yG, and zC represent the number of A, T, G, and C nucleotides in the DNA molecule, respectively.
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In this formula, the term "(wA + xT) * 2" represents the contribution of A and T nucleotides to the stability of the DNA molecule, while the term "(yG + zC) * 4" represents the contribution of G and C nucleotides to the stability of the DNA molecule.
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The second formula for calculating the basic Tm is: Tm = 64.9 + 41 * (yG + zC - 16.4) / (wA + xT + yG + zC), where wA, xT, yG, and zC represent the number of A, T, G, and C nucleotides in the DNA molecule, respectively.
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In this formula, the term "64.9" is a constant value that is used in the formula to calculate the Tm. The term "41" is a constant value that is used in the formula to calculate the Tm. The term "(yG + zC - 16.4)" represents the contribution of G and C nucleotides to the stability of the DNA molecule, with a correction for the effect of A and T nucleotides on the stability of the DNA molecule. The term "(wA + xT + yG + zC)" represents the total number of nucleotides in the DNA molecule.
The salt-adjusted melting temperature (Tm) is a measure of the temperature at which the double-stranded DNA structure of a molecule begins to denature and separate into single strands, taking into account the effect of salt concentration on the stability of the DNA molecule.
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The Tm is calculated using the following formula: Tm = 100.5 + (41 * (yG+zC) / (wA+xT+yG+zC)) - (820 / (wA+xT+yG+zC)) + 16.6*log10([Na+]), where wA, xT, yG, and zC represent the number of A, T, G, and C nucleotides in the DNA molecule, respectively, and [Na+] represents the concentration of sodium ions in the solution.
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The term "100.5" is a constant value that is used in the formula to calculate the Tm. The term "(41 * (yG+zC) / (wA+xT+yG+zC))" represents the effect of G and C nucleotides on the stability of the DNA molecule. The term "(820 / (wA+xT+yG+zC))" represents the effect of A and T nucleotides on the stability of the DNA molecule.
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The term "16.6" is a constant value that is used in the formula to calculate the Tm. The term "log10" is the base-10 logarithm function, which is used to calculate the logarithm of the [Na+] concentration value.