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An Introduction to Extinction Coefficients and Molecular Weights of Oligos

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Extinction Coefficient of Oligos
The extinction coefficient of a substance is a measure of the ability of that substance to absorb light of a particular wavelength. The extinction coefficient of an oligonucleotide can be determined by measuring the absorbance of an oligonucleotide at 260 nm and dividing by its concentration and path length. Alternatively, the extinction coefficient can be calculated theoretically using a non-empirical approximation based on the nearest neighbor model. Measured and calculated extinction coefficients may differ by up to 20%.

Factors Affecting the Extinction Coefficient of Oligonucleotides
The extinction coefficient of an oligonucleotide can be affected by several factors, including the sequence, length, and secondary structure of the oligonucleotide, and the presence of impurities or contaminants. Therefore, it is important to determine the extinction coefficient for each oligonucleotide individually.

Extinction Coefficient Unit
The extinction coefficient of oligonucleotides is usually expressed in units of M^-1 cm^-1. The unit reflects the concentration of oligonucleotide in moles per liter (M) and the path length of light traveling through the sample in centimeters (cm). The extinction coefficient can also be expressed in units of OD (optical density)/μg/ml, which is a measure of the absorbance of a sample normalized to concentration and optical path length.

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Molecular Weight of Oligos
The molecular weight of an oligonucleotide can be calculated by summing the molecular weights of its constituent nucleotides. The molecular weight of a nucleotide is equal to the sum of the molecular weights of its base, sugar, and phosphate groups. For example, deoxyadenosine monophosphate (dAMP) has a molecular weight of 331.2 g/mol.

The molecular weight of oligonucleotides can be determined experimentally by mass spectrometry or gel electrophoresis. Mass spectrometry can provide accurate molecular weight measurements for individual oligonucleotides, while gel electrophoresis can estimate molecular weight based on the mobility of oligonucleotides in a gel.

Importance of Extinction Coefficient of Oligos
Quantitative Determination – The extinction coefficient of an oligonucleotide can be used to quantitatively determine its concentration. By measuring the absorbance of a solution and using the extinction coefficient, the concentration of an oligonucleotide can be calculated.
Data Analysis – By measuring the change in absorbance of an oligonucleotide, the degree of interaction with other molecules can be inferred to understand the character and strength of the interaction.
Importance of Molecular Weight of Oligos
Reaction Design and Optimization – The molecular weight of an oligonucleotide is important for the design and optimization of an experimental reaction. By knowing the molecular weight of an oligonucleotide, the number of reactants can be determined based on the desired molar ratio.
Concentration Calculation – The molecular weight of an oligonucleotide can be used to calculate molar concentration and molar mass for quantitative determination.
Quality Control – By measuring the molecular weight of an oligonucleotide and comparing it to theoretical values, purity and consistency can be verified.
The extinction coefficients and molecular weights of oligonucleotides are very significant and are needed to calculate important data such as determining molar concentrations and preparing stock solutions. Based on our technology and experience, BOC Sciences will support you with accurate extinction coefficient and molecular weight data while providing you with DNA & RNA synthesis raw materials and services to ensure high purity and compliance.

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