Find binding sites in given DNA sequence and retrieve top-scoring recognition helix preferences by choosing either consensus or synergistic mode of binding

1) Enter a 9bp DNA sequence in the text box as shown below.

Press “Submit” for the binding mode you choose.

In the output screen that appears, a list of 9-bp binding sites appears, in a descending order of a relative score. This score for each site is a sum of the maximum IHBE values for each nucleotide triplet. A higher-scoring binding site will interact with its respective top-scoring recognition helix set with a higher relative affinity.

This generates a table at the bottom with the respective top-scoring recognition helices of the former. There is a different number of top-scorers for each triplet (at each finger-position) which is usually in the order of 10³. All these recognition helices for a particular finger are strong binders relatively according to this prediction approach as is any three-finger combination of recognition helices from the three lists.

Use the lower part of the form for this purpose.

Simply choose the finger using the radio buttons.Then click “Submit”.

 

Finding the score of a recognition helix of choice against a nucleotide triplet for a particular finger-position

THe energy displayed is the additive energy of the three helices chosen by the user against the DNA inut sequence of their choice.

What you see in the output:

1. The IHBE calculated by this approach in kcal/mol (the energies evaluated are negative in sign, hence higher the energy stronger the bond).

2. The tool by default gives the additive score for the top predicted helices but if the user makes a choice of combining different fingers from the list of top predictions ,then the appropriate score is displayed.