Oligo Analyzer 3.1

Analyze DNA/RNA oligonucleotide sequences to calculate molecular properties including molecular weight, GC content, melting temperature, and extinction coefficient.

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About This Tool

Oligo Analyzer 3.1 is a comprehensive online tool for analyzing DNA and RNA oligonucleotide sequences. Enter your nucleotide sequence to calculate essential molecular properties including molecular weight (g/mol), GC content percentage, melting temperature (Tm) using the nearest-neighbor method, extinction coefficient (L/mol·cm), and nmol/OD260. The tool validates sequence input, supports both DNA and RNA, and provides detailed results in an easy-to-read format. Perfect for molecular biology research, PCR primer design, and oligonucleotide synthesis quality control.

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How to Use

Enter your DNA or RNA sequence in the input field (ACGTU characters only)
Select sequence type (DNA or RNA) from the dropdown
Adjust optional parameters like sodium concentration and oligonucleotide concentration if needed
Click 'Analyze Sequence' to calculate all properties
View detailed results including molecular weight, GC content, melting temperature, and more
Use 'Reset' to clear all inputs and start over

Frequently Asked Questions

Find Quick Answers

What characters are allowed in the sequence input?

Only standard nucleotide characters are allowed: A, C, G, T for DNA sequences and A, C, G, U for RNA sequences. The tool automatically converts lowercase to uppercase and removes whitespace.

How is melting temperature (Tm) calculated?

Melting temperature is calculated using the nearest-neighbor method with salt correction. The formula accounts for nucleotide composition, sequence length, and sodium ion concentration for accurate Tm prediction.

What is the extinction coefficient used for?

The extinction coefficient (ε260) measures how strongly oligonucleotides absorb UV light at 260nm. It's used to determine oligonucleotide concentration from absorbance readings (A260) using Beer-Lambert law.

Can I analyze modified nucleotides or mixed DNA/RNA sequences?

This version analyzes standard DNA and RNA sequences only. Modified nucleotides or mixed DNA/RNA sequences may produce inaccurate results as the calculations assume standard nucleotide properties.

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