3DNA Forum

Questions and answers => w3DNA -- web interface to 3DNA => web 3DNA 2.0 (http://web.x3dna.org) => Topic started by: xiangjun on May 30, 2019, 12:42:48 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G4 Structures · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: Figure 3. Commonly-used fiber models and base mutations
Post by: xiangjun on May 30, 2019, 12:42:48 pm
(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.
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 (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).

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.