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(http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-fig3.png)
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 (http://web.x3dna.org/index.php/fibermodel) and the 'Mutation' module (http://web.x3dna.org/index.php/doc/tutorial6) online or in the corresponding sections of the supplemental PDF (http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-supp.pdf). See also the blogpost "Pauling's triplex model of nucleic acids is available in 3DNA (http://home.x3dna.org/highlights/pauling-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 (http://home.x3dna.org/highlights/pauling-triplex-model-of-nucleic-acids-is-available-in-3dna), 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 (http://web.x3dna.org/index.php/fibermodel) online or the section "S4.5 Modeling module: 56 fiber models" in the supplemental PDF (http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-supp.pdf).
Listed below are the 3DNA command-line scripts.
# Fig. 3B, single-stranded RNA
fiber -seq=AUCGAUCGAUCG -rna -single fiber-ssRNA.pdb
blocview -x 180 -i fiber-ssRNA.png fiber-ssRNA.pdb
# Fig. 3C, double-stranded DNA
fiber -seq=ATCGATCGATCG fiber-B-dsDNA.pdb
blocview -i fiber-B-dsDNA.png fiber-B-dsDNA.pdb
# Fig. 3D, Pauling triplex
fiber --pauling -seq=AAAACCCCGGGG Pauling-triplex.pdb
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 (http://web.x3dna.org/index.php/doc/tutorial6) 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 (http://docs.x3dna.org/w3DNA2.0/w3DNA2.0-supp.pdf).
Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids
Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University