Oligo Analyzer

Analyze DNA/RNA oligonucleotides to calculate melting temperature (Tm), GC percentage, molecular weight, and extinction coefficient with accurate salt correction.

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About This Tool

The IDT Oligo Analyzer is a comprehensive tool for analyzing DNA and RNA oligonucleotides. Enter your oligo sequence to calculate key parameters including melting temperature (Tm) using the nearest neighbor method with salt correction, GC percentage, molecular weight (g/mol), and extinction coefficient (L/mol·cm). The tool supports both DNA and RNA sequences, allows customization of salt concentration, oligo concentration, and provides detailed analysis results for molecular biology applications.

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How to Use

Enter your DNA or RNA oligonucleotide sequence in the input field (ACGTU characters only)
Select sequence type (DNA or RNA) from the dropdown
Adjust optional parameters: salt concentration (mM), oligo concentration (μM)
Click 'Analyze Oligo' to calculate Tm, GC%, molecular weight, and extinction coefficient
View detailed results including sequence length, base composition, and calculated values

Frequently Asked Questions

Find Quick Answers

What sequence characters are accepted?

DNA sequences: A, C, G, T (uppercase or lowercase). RNA sequences: A, C, G, U (uppercase or lowercase). Non-standard characters will be rejected.

How is melting temperature (Tm) calculated?

Tm is calculated using the nearest neighbor method with salt correction. For DNA: Tm = ΔH/(ΔS + R·ln(C/4)) - 273.15 + 16.6·log10([Na+]). For RNA, different thermodynamic parameters are used.

What is the default salt concentration?

Default is 50 mM Na+ concentration, which is typical for PCR and hybridization experiments. You can adjust this value from 1-1000 mM.

Can I analyze RNA sequences?

Yes, select 'RNA' from the sequence type dropdown. The tool uses appropriate thermodynamic parameters for RNA oligo analysis.

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