Oligonucleotide Properties Calculator

The Oligonucleotide Properties Calculator is a comprehensive tool designed to help researchers and scientists determine several important properties of oligonucleotides.

Oligonucleotide Properties Calculator

Oligonucleotide Properties Calculator

Sequence Length:
Molecular Weight:
GC Content:
Tm:
Reverse Complement:
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This calculator can calculate the molecular weight, GC content, melting temperature (Tm), reverse complement, and the optical density to nanomolar conversion. It is designed to handle single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), and single-stranded RNA (ssRNA) sequences.

How It Works

The calculator takes an input sequence and provides the following properties:

  1. Sequence Length: The number of nucleotides in the provided sequence.
  2. Molecular Weight: The total molecular weight of the sequence in Daltons (g/mol).
  3. GC Content: The percentage of guanine (G) and cytosine (C) bases in the sequence.
  4. Melting Temperature (Tm): The temperature at which half of the DNA strands are in the double-helix state and half are in the “melted” single-strand state.
  5. Reverse Complement: The sequence of the complementary strand in reverse order.
  6. Optical Density to Nanomolar (OD): The conversion of optical density to nanomolar concentration for ssDNA.

User Instructions

  1. Enter or Paste Sequence: Input the oligonucleotide sequence in the text area provided.
  2. Select Type: Choose the type of oligonucleotide (ssDNA, dsDNA, ssRNA).
  3. Select Source: Choose the source (PCR or Restriction Cut).
  4. Calculate MW: Click the “Calculate” button to perform the calculations.
  5. Clear Input: Click the “Clear Input” button to reset the form.

Formulas and Calculations

Sequence Length:

  • The length of the sequence is determined by counting the number of nucleotides.

Molecular Weight:

  • For ssDNA and dsDNA, the molecular weights of individual nucleotides are summed up.
  • Base weights used:
    • Adenine (A): 313.2 g/mol (DNA), 329.2 g/mol (RNA)
    • Thymine (T): 304.2 g/mol (DNA)
    • Uracil (U): 306.2 g/mol (RNA)
    • Cytosine (C): 289.2 g/mol (DNA), 305.2 g/mol (RNA)
    • Guanine (G): 329.2 g/mol (DNA), 345.2 g/mol (RNA)
  • For ambiguous bases, average weights are used.
  • Adjustments for ends:
    • dsDNA: Add 79 g/mol for each end if sourced from Restriction Cut.
    • ssDNA: Add 79 g/mol if sourced from Restriction Cut.
    • ssRNA: Add 159 g/mol for ssRNA.

GC Content:

  • GC Content = (Number of G and C bases / Total number of bases) Γ— 100

Melting Temperature (Tm):

  • For sequences shorter than 14 nucleotides:
    Tm = (A + T) Γ— 2 + (G + C) Γ— 4
  • For sequences longer than 14 nucleotides:
    Tm = 64.9 + 41 Γ— ((G + C – 16.4) / (A + T + G + C))

Reverse Complement:

  • The reverse complement is generated by reversing the sequence and substituting each base with its complement:
    • A ↔ T
    • T ↔ A
    • C ↔ G
    • G ↔ C
    • U ↔ A
    • For ambiguous bases, standard IUPAC complements are used.

Optical Density to Nanomolar (OD):

  • Conversion is based on the absorptivity of bases:
    OD of 1 = (1 / Absorptivity) Γ— 1 Γ— 10^9 nanoMolar (ssDNA)
  • Absorptivity values:
    • Adenine (A): 15200 (DNA), 15400 (RNA)
    • Thymine (T): 8400 (DNA)
    • Uracil (U): 10000 (RNA)
    • Cytosine (C): 7050 (DNA), 9000 (RNA)
    • Guanine (G): 12010 (DNA), 13700 (RNA)