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    The inter- and intra- molecular G-quadruplex structures generated by 3D-NuS are categorized into 17 classes of G-quadruplex folds. In which, Q1 to Q5 (frequently found) and Q14 to Q17 (rarely found) are monomeric folds, while Q6 to Q9 are dimeric folds. In contrast, Q10 to Q13 are intermolecular (tetrameric) in nature. Different classes of G-quadruplex folds are given in Figure 3. The user can check documentation page before giving input sequences and choose the desired class & sub-class according to requirement [Note: If the category of the molecule is not defined by user, then default values in the categories will be considered for molecule generation]. Then, user should select the desired length for the G-quadruplex. Here, length denotes the number of nucleotides in one strand.

    Click 'Submit' button to generate the 3-dimensional model. User can view the generated 3D structure in the given molecule viewer or 'Download' the coordinates in protein data bank (PDB) file format to view in other molecule visualizers.

Figure 3. Strand orientation in different classes of G-quadruplex (Purnima, Unpublished data). © IIT Hyderabad.

Special Instructions

[For generating intra-molecular quadruplexes, quadruplexes with loops.]

Considering the lesser amount of data and complexity of loop modelling, following instructions to be followed while inserting sequences for loop regions of the quadruplexes.

  • 3D-NuS generates intramolecular quadruplex for any loop sequence and quartet length.
  • Loop sequences for monomers (quadruplex class Qn, where n=1-5, 14-17) must be given in all three input boxes and for dimers (quadruplex class Qn, where n=6-9), sequences must be given only in 1st and 3rd input boxes, else the molecule generation will be failed.
  • The ratio between loop length to number of quartets has to be considered very firmly to generate models with better conformation of quartets.
  • If any intramolecular quartet model has distorted conformation or disconnected loops then, increase/decrease the number of nucleotides in loop region to genearte a better model.
  • The conformation of loop may not significantly reflect in-vitro quadruplexes but the quartets significantly mimic existing PDB structures.

Let's build the molecule of your choice...

Select the appropriate class of quadruplex under given options.

Quadruplex class [strand orientation]:   

Quadruplex sub-class [strand type]:   

Number of G-quartets:   

Insert sequence for 1st loop 5'---3':
Insert sequence for 2nd loop 5'---3':
Insert sequence for 3rd loop 5'---3':