3DNA contains 55 fiber models compiled from literature, plus a derived RNA model (as of v2.1). To the best of my knowledge, this is the most comprehensive collection of regular DNA/RNA models. Please see Table 4 of the 2003 3DNA NAR paper for detailed structural features of these models and references.
The 55 models are based on the following works:
- Chandrasekaran & Arnott (from #1 to #43) — the most well-known set of fiber models
- Alexeev et al. (#44-#45)
- van Dam & Levitt (#46-#47)
- Premilat & Albiser (#48-#55)
The utility program fiber makes the generation of all these fiber models in a simple, consistent interface, and produces coordinate files in either PDB or PDBML format. Of those models, some can be built with an arbitrary sequence of A, C, G and T (e.g., A-/B-/C-DNA from calf thymus), while others are of fixed sequences (e.g., Z-DNA with GC repeats). The sequence can be specified either from command-line or a plain text file, in either lower, UPPER, or MixED cases.
Once 3DNA in properly installed, the command-line interface is the most versatile and convenient way to generate, e.g., a regular double-stranded DNA (mostly, B-DNA) of arbitrary sequence. The command-help message (generated with fiber -h) is as below:
NAME
fiber - generate 55 fiber models based on Arnott and other's work
SYNOPSIS
fiber [OPTION] PDBFILE
DESCRIPTION
generate 55 fiber models based on the repeating unit from Arnott's
work, including the canonical A-, B-, C- and Z-DNA, triplex, etc
-xml output structure coordinates in PDBML format
-num a structure identification number in the range (1-55)
-m, -l brief description of the 55 fiber structures
-a, -1 A-DNA model (calf thymus)
-b, -4 B-DNA (calf thymus, default)
-c, -47 C-DNA (BII-type nucleotides)
-d, -48 D(A)-DNA ploy d(AT) : ploy d(AT) (right-handed)
-z, -15 Z-DNA poly d(GC) : poly d(GC)
-rna for RNA with arbitrary base sequence
-seq=string specifying an arbitrary base sequence
-single output a single-stranded structure
-h this help message (any non-recognized options will do)
INPUT
An structural identification number (symbol)
EXAMPLES
fiber fiber-BDNA.pdb
# fiber -4 fiber-BDNA.pdb
# fiber -b fiber-BDNA.pdb
fiber -a fiber-ADNA.pdb
fiber -seq=AAAGGUUU -rna fiber-RNA.pdb
fiber -seq=AAAGGUUU -rna -single fiber-ssRNA.pdb
OUTPUT
PDB file
SEE ALSO
analyze, anyhelix, find_pair
AUTHOR
3DNA v2.3-2016sept06, created and maintained by Xiang-Jun Lu (PhD)
Please post questions/comments on the 3DNA Forum: http://forum.x3dna.org/
Moreover, the w3DNA, 3D-DART web-interfaces, and the PyMOL wrapper make it easy to generate a regular DNA (or RNA) model, especially for occasional users or for educational purposes.
In principle, nothing is worth showing off with regard to 3DNA’s fiber model generation functionality. Nevertheless, this handy tool serves as a clear example of the differences between a “proof of concept” and a pragmatic software application. I initially decided to work on this tool simply for my own convenience. At that time, I had access to A-DNA and B-DNA fiber model generators, each as a separate program. Moreover, the constructed models did not comply to the PDB format in atom naming, among other subtitles.
I started with the Chandrasekaran & Arnott fiber models which I had a copy of data files. However, there were many details to work out, typos to correct, etc. to put them in a consistent framework. For other models, I had to read each original publication, and to type raw atomic cylindrical coordinates into computer. Again, quite a few inconsistencies popped up between the different publications with a time span over decades.
Overall, it was a quite tedious undertaking, requiring great attention to details. I am glad that I did that: I learned so much from the process, and more importantly, others can benefit from my effort. As I put in the 3DNA Nature Protocol paper (BOX 6 | FIBER-DIFFRACTION MODELS),
In preparing this set of fiber models, we have taken great care to ensure the accuracy and consistency of the models. For completeness and user verification, 3DNA includes, in addition to 3DNA-processed files, the original coordinates collected from the literature.
For those who want to understand what’s going on under the hood, there is no better way than to try to reproduce the process using, e.g., fiber B-DNA as an example.
From the very beginning, I had expected the 3DNA fiber functionality to serve as a handy tool for building a regular DNA duplex of chosen sequence. Over the years, the fiber program has gradually attracted attention from the community. The recent PyMOL wrapper by Thomas Holder is a clear sign of its increased popularity, and has prompted me to write this post, adapted largely from the one titled Fiber models in 3DNA make it easy to build regular DNA helices (dated Friday, October 9, 2009).
See also PyMOL wrapper to 3DNA fiber models
Given below is the content of the README file for fiber models in 3DNA:
1. The repeating units of each fiber structure are mostly based on the
work of Chandrasekaran & Arnott (from #1 to #43). More recent fiber
models are based on Alexeev et al. (#44-#45), van Dam & Levitt (#46
-#47) and Premilat & Albiser (#48-#55).
2. Clean up of each residue
a. currently ignore hydrogen atoms [can be easily added]
b. change ME/C7 group of thymine to C5M
c. re-assign O3' atom to be attached with C3'
d. change distance unit from nm to A [most of the entries]
e. re-ordering atoms according to the NDB convention
3. Fix up of problem structures.
a. str#8 has no N9 atom for guanine
b. str#10 is not available from the disk, manually input
c. str#14 C5M atom was named C5 for Thymine, resulting two C5 atoms
d. str#17 has wrong assignment of O3' atom on Guanine
e. str#33 has wrong C6 position in U3
f. str#37 to #str41 were typed in manually following Arnott's
new list as given in "Oxford Handbook of Nucleic Acid Structure"
edited by S. Neidle (Oxford Press, 1999)
g. str#38 coordinates for N6(A) and N3(T) are WRONG as given in the
original literature
h. str#39 and #40 have the same O3' coordinates for the 2nd strand
4. str#44 & 45 have fixed strand II residues (T)
5. str#46 & 47 have +z-axis upwards (based on BI.pdb & BII.pdb)
6. str#48 to 55 have +z-axis upwards
List of 55 fiber structures
id# Twist Rise Structure description
(dgrees) (A)
-------------------------------------------------------------------------------
1 32.7 2.548 A-DNA (calf thymus; generic sequence: A, C, G and T)
2 65.5 5.095 A-DNA poly d(ABr5U) : poly d(ABr5U)
3 0.0 28.030 A-DNA (calf thymus) poly d(A1T2C3G4G5A6A7T8G9G10T11) :
poly d(A1C2C3A4T5T6C7C8G9A10T11)
4 36.0 3.375 B-DNA (calf thymus; generic sequence: A, C, G and T)
5 72.0 6.720 B-DNA poly d(CG) : poly d(CG)
6 180.0 16.864 B-DNA (calf thymus) poly d(C1C2C3C4C5) : poly d(G6G7G8G9G10)
7 38.6 3.310 C-DNA (calf thymus; generic sequence: A, C, G and T)
8 40.0 3.312 C-DNA poly d(GGT) : poly d(ACC)
9 120.0 9.937 C-DNA poly d(G1G2T3) : poly d(A4C5C6)
10 80.0 6.467 C-DNA poly d(AG) : poly d(CT)
11 80.0 6.467 C-DNA poly d(A1G2) : poly d(C3T4)
12 45.0 3.013 D-DNA poly d(AAT) : poly d(ATT)
13 90.0 6.125 D-DNA poly d(CI) : poly d(CI)
14 -90.0 18.500 D-DNA poly d(A1T2A3T4A5T6) : poly d(A1T2A3T4A5T6)
15 -60.0 7.250 Z-DNA poly d(GC) : poly d(GC)
16 -51.4 7.571 Z-DNA poly d(As4T) : poly d(As4T)
17 0.0 10.200 L-DNA (calf thymus) poly d(GC) : poly d(GC)
18 36.0 3.230 B'-DNA alpha poly d(A) : poly d(T) (H-DNA)
19 36.0 3.233 B'-DNA beta2 poly d(A) : poly d(T) (H-DNA beta)
20 32.7 2.812 A-RNA poly (A) : poly (U)
21 30.0 3.000 A'-RNA poly (I) : poly (C)
22 32.7 2.560 Hybrid poly (A) : poly d(T)
23 32.0 2.780 Hybrid poly d(G) : poly (C)
24 36.0 3.130 Hybrid poly d(I) : poly (C)
25 32.7 3.060 Hybrid poly d(A) : poly (U)
26 36.0 3.010 10-fold poly (X) : poly (X)
27 32.7 2.518 11-fold poly (X) : poly (X)
28 32.7 2.596 Poly (s2U) : poly (s2U) (symmetric base-pair)
29 32.7 2.596 Poly (s2U) : poly (s2U) (asymmetric base-pair)
30 32.7 3.160 Poly d(C) : poly d(I) : poly d(C)
31 30.0 3.260 Poly d(T) : poly d(A) : poly d(T)
32 32.7 3.040 Poly (U) : poly (A) : poly(U) (11-fold)
33 30.0 3.040 Poly (U) : poly (A) : poly(U) (12-fold)
34 30.0 3.290 Poly (I) : poly (A) : poly(I)
35 31.3 3.410 Poly (I) : poly (I) : poly(I) : poly(I)
36 60.0 3.155 Poly (C) or poly (mC) or poly (eC)
37 36.0 3.200 B'-DNA beta2 Poly d(A) : poly d(U)
38 36.0 3.240 B'-DNA beta1 Poly d(A) : poly d(T)
39 72.0 6.480 B'-DNA beta2 Poly d(AI) : poly d(CT)
40 72.0 6.460 B'-DNA beta1 Poly d(AI) : poly d(CT)
41 144.0 13.540 B'-DNA Poly d(AATT) : poly d(AATT)
42 32.7 3.040 Poly(U) : poly d(A) : poly(U) [cf. #32]
43 36.0 3.200 Beta Poly d(A) : Poly d(U) [cf. #37]
44 36.0 3.233 Poly d(A) : poly d(T) (Ca salt)
45 36.0 3.233 Poly d(A) : poly d(T) (Na salt)
46 36.0 3.38 B-DNA (BI-type nucleotides; generic sequence: A, C, G and T)
47 40.0 3.32 C-DNA (BII-type nucleotides; generic sequence: A, C, G and T)
48 87.8 6.02 D(A)-DNA ploy d(AT) : ploy d(AT) (right-handed)
49 60.0 7.20 S-DNA ploy d(CG) : poly d(CG) (C_BG_A, right-handed)
50 60.0 7.20 S-DNA ploy d(GC) : poly d(GC) (C_AG_B, right-handed)
51 31.6 3.22 B*-DNA poly d(A) : poly d(T)
52 90.0 6.06 D(B)-DNA poly d(AT) : poly d(AT) [cf. #48]
53 -38.7 3.29 C-DNA (generic sequence: A, C, G and T) (depreciated)
54 32.73 2.56 A-DNA (generic sequence: A, C, G and T) [cf. #1]
55 36.0 3.39 B-DNA (generic sequence: A, C, G and T) [cf. #4]
-------------------------------------------------------------------------------
List 1-41 based on Struther Arnott: ``Polynucleotide secondary structures:
an historical perspective'', pp. 1-38 in ``Oxford Handbook of Nucleic
Acid Structure'' edited by Stephen Neidle (Oxford Press, 1999).
#42 and #43 are from Chandrasekaran & Arnott: "The Structures of DNA
and RNA Helices in Oriented Fibers", pp 31-170 in "Landolt-Bornstein
Numerical Data and Functional Relationships in Science and Technology"
edited by W. Saenger (Springer-Verlag, 1990).
#44-#45 based on Alexeev et al., ``The structure of poly(dA) . poly(dT)
as revealed by an X-ray fiber diffraction''. J. Biomol. Str. Dyn, 4,
pp. 989-1011, 1987.
#46-#47 based on van Dam & Levitt, ``BII nucleotides in the B and C forms
of natural-sequence polymeric DNA: a new model for the C form of DNA''.
J. Mol. Biol., 304, pp. 541-561, 2000.
#48-#55 based on Premilat & Albiser, ``A new D-DNA form of poly(dA-dT) .
poly(dA-dT): an A-DNA type structure with reversed Hoogsteen Pairing''.
Eur. Biophys. J., 30, pp. 404-410, 2001 (and several other publications).
