Figure 3. Commonly-used fiber models and base mutations

[xiangjun]

Figure 3. Commonly-used fiber models and in silico base mutations. (A) Six commonly used models highlighted in the ‘Fiber’ module: single-stranded RNA, double-helical A-, B-, and C-form DNA, the Pauling triplex model (32), and the parallel polyI:polyI:polyI:polyI quadruplex. (B) Single-stranded RNA fiber model of base sequence AUCGAUCGAUCG. (C) Double-helical B-DNA fiber model with sequence ATCGATCGATCG on the leading strand. (D) Pauling triplex model with each strand of sequence AAAACCCCGGGG. (E) parallel polyI:polyI:polyI:polyI quadruplex model with 12 layers of hydrogen-bonded hypoxanthine tetrads. Models in (B-E) were generated using the default settings on the w3DNA 2.0 server, each taking just two mouse clicks. (F) All hypoxanthine bases along the poly I chains mutated to guanine via the ‘Mutation’ module, leading to a parallel G-quadruplex. Color code for base blocks: A, red; C, yellow; G, green; T, blue; U, cyan; I, dark green.
Reproducing the results reported in the figure is straightforward via the w3DNA 2.0 interface, by simply clicking a few buttons in each case. Please read tutorials on the 'Fiber' module and the 'Mutation' module online or in the corresponding sections of the supplemental PDF. See also the blogpost "Pauling's triplex model of nucleic acids is available in 3DNA" for details and background information about this model of historical significance. Note the schematic representation allows direct readout of base identity.
Fig. 3A is a screenshot of the header of the 'Fiber' module. The list includes the six commonly used fiber models: single-stranded RNA, double-helical A-, B-, and C-form DNA, the Pauling triplex model, and the parallel polyI:polyI:polyI:polyI quadruplex.
Fig. 3B-D are easily created by clicking two buttons each via the w3DNA 2.0 interface. Please read tutorial on the 'Fiber' module online or the section "S4.5 Modeling module: 56 fiber models" in the supplemental PDF.

Listed below are the 3DNA command-line scripts.

Code: Bash

1.     # Fig. 3B, single-stranded RNA
2. fiber -seq=AUCGAUCGAUCG -rna -single fiber-ssRNA.pdb
3. blocview -x 180 -i fiber-ssRNA.png fiber-ssRNA.pdb
4.     # Fig. 3C, double-stranded DNA
5. fiber -seq=ATCGATCGATCG fiber-B-dsDNA.pdb
6. blocview -i fiber-B-dsDNA.png fiber-B-dsDNA.pdb
7.     # Fig. 3D, Pauling triplex
8. fiber --pauling -seq=AAAACCCCGGGG Pauling-triplex.pdb
9. blocview -x 180 -i Pauling-triplex.png Pauling-triplex.pdb

Fig. 3E is generated by selecting "poly(I) : poly(I) : poly(I) : poly(I)" ("use this model" button) and then clicking "Build" with default repeat number of 12. In the w3DNA 2.0 output, the image is rotated 90 degrees to be in a horizontal orientation.
Fig. 3F is produced by clicking the link "[Use this structure for mutation]", directly after Fig. 3E, to the "Mutation" module. At the top, select the "Mutate to All: G" radio button, and then "Continue".
For Fig. 3E and 3F, please read tutorial on the 'Mutation' module online or the section "S4.6 Modeling module: base mutations" (especially "Example 6-3: Construction of a G-quadruplex DNA model") in the supplemental PDF.