This command will analyze sequences between 8 and 100 nucleotides long for the formation of dimers and hairpins and send the result to the Output window.

1. Choose Analysis > Dimers & Hairpins in the main menu or Sequence Analysis > Dimers & Hairpins in the selection contextual menu:

or click on the Dimers & Hairpins button in the Sequence toolbar:

2. Open the Output multitab window to access the structures.

Methods

Instead of attempting to calculate all possible secondary structures, GenBeans uses its own algorithm to quickly identifies short stretches of sequences that could induce stable secondary structures and interfere with e.g. PCR. The algorithm is based on the nearest neighbor method for calculating interactions between adjacent nucleotides and include mismatches and presence of single nucleotide bulges. Larger bulges involving more than one nucleotide are considered as separate structures. The occurrence of stable short loops is also considered. Calculations are made for a temperature of 37ºC in the presence of 50 mM monovalent cations.

Results

Representation

Pairings are represented with the character '|' and mismatches are represented by the character '.'. Bulges are indicated by superscripting the nucleotide that is bulging out of the duplex. For example the sequence CCCACGTT can anneal with the sequence AATGGGG while forming a single nucleotide bulge and a mismatch; the resulting duplex will be represented as follow:

         A    
       CCCCGTT
       ||||.||
       GGGGTAA

Energies

Variations in free energy (DeltaG) are reported in kcal per mole at 37ºC and 50 mM NaCl.

Example of report

      DNA oligo   33 bp   tggataggaactatccaatggggtcgtaacccc
       1.......10........20........30...
       tggataggaactatccaatggggtcgtaacccc
      
      1. Self-Dimer Length = 12; Mismatches = 2; Bulges = 2
         DeltaG [37ºC, 50 mM NaCl] = -5.36 kcal/mole
      
                                  T                           
      5' TGGATAGGAACTATCCAATGGGGTCGAACCCC 3'                  
                            |||.||||.|||                      
                        3' CCCCAAGCTGGGGTAACCTATCAAGGATAGGT 5'
                                 T                            

      
      2. Self-Dimer Length = 5
               DeltaG [37ºC, 50 mM NaCl] = -5.22 kcal/mole
      
      5' TGGATAGGAACTATCCAATGGGGTCGTAACCCC 3'                   
                            |||||    |||||                      
                         3' CCCCAATGCTGGGGTAACCTATCAAGGATAGGT 5'
      

      3. Self-Dimer Length = 7
         DeltaG [37ºC, 50 mM NaCl] = -4.95 kcal/mole
      
                      5' TGGATAGGAACTATCCAATGGGGTCGTAACCCC 3'
                         |||||||   |||||||                   
      3' CCCCAATGCTGGGGTAACCTATCAAGGATAGGT 5'                
      

      This oligo can form a hairpin structure with a GNA motif in the loop
      that is particularly stable:
      
                      5' TGGATAGG┐
                         ||||||| A
      3' CCCCAATGCTGGGGTAACCTATCA┘
      

      4. Self-Dimer Length = 7; Mismatches = 1
         DeltaG [37ºC, 50 mM NaCl] = -4.17 kcal/mole
      
      5' TGGATAGGAACTATCCAATGGGGTCGTAACCCC 3'  
                       |||.|||                 
        3' CCCCAATGCTGGGGTAACCTATCAAGGATAGGT 5'


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