DSSR-curated G4 structure: PDB entry 4l0a

Summary information

PDB id: 4l0a
Class: DNA, RNA
Method: X-ray (1.7 Å)
Summary: X-ray structure of an all lna quadruplex
Reference: Russo Krauss I, Parkinson GN, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F (2014): "A regular thymine tetrad and a peculiar supramolecular assembly in the first crystal structure of an all-LNA G-quadruplex." Acta Crystallogr.,Sect.D, 70, 362-370. doi: 10.1107/S1399004713028095.
Abstract: Locked nucleic acids (LNAs) are formed by bicyclic ribonucleotides where the O2' and C4' atoms are linked through a methylene bridge and the sugar is blocked in a 3'-endo conformation. They represent a promising tool for therapeutic and diagnostic applications and are characterized by higher thermal stability and nuclease resistance with respect to their natural counterparts. However, structural descriptions of LNA-containing quadruplexes are rather limited, since few NMR models have been reported in the literature. Here, the first crystallographically derived model of an all-LNA-substituted quadruplex-forming sequence 5'-TGGGT-3' is presented refined at 1.7 Å resolution. This high-resolution crystallographic analysis reveals a regular parallel G-quadruplex arrangement terminating in a well defined thymine tetrad at the 3'-end. The detailed picture of the hydration pattern reveals LNA-specific features in the solvent distribution. Interestingly, two closely packed quadruplexes are present in the asymmetric unit. They face one another with their 3'-ends giving rise to a compact higher-order structure. This new assembly suggests a possible way in which sequential quadruplexes can be disposed in the crowded cell environment. Furthermore, as the formation of ordered structures by molecular self-assembly is an effective strategy to obtain nanostructures, this study could open the way to the design of a new class of LNA-based building blocks for nanotechnology.
G4 notes: 6 G-tetrads, 2 G4 helices, 2 G4 stems, parallel(4+0), UUUU

Base-block schematics in six views

PyMOL session file	PDB file	View in 3Dmol.js

List of 6 G-tetrads

 1 glyco-bond=---- sugar=3333 groove=---- planarity=0.420 type=other  nts=4 gggg A.LCG2,C.LCG2,D.LCG2,B.LCG2
 2 glyco-bond=---- sugar=3333 groove=---- planarity=0.454 type=other  nts=4 gggg A.LCG3,C.LCG3,D.LCG3,B.LCG3
 3 glyco-bond=---- sugar=3333 groove=---- planarity=0.319 type=other  nts=4 gggg A.LCG4,C.LCG4,D.LCG4,B.LCG4
 4 glyco-bond=---- sugar=3333 groove=---- planarity=0.434 type=other  nts=4 gggg E.LCG2,G.LCG2,H.LCG2,F.LCG2
 5 glyco-bond=---- sugar=3333 groove=---- planarity=0.454 type=other  nts=4 gggg E.LCG3,G.LCG3,H.LCG3,F.LCG3
 6 glyco-bond=---- sugar=3333 groove=---- planarity=0.330 type=other  nts=4 gggg E.LCG4,G.LCG4,H.LCG4,F.LCG4

List of 2 G4-helices

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrad layers, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG2,D.LCG2,B.LCG2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG3,D.LCG3,B.LCG3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG4,D.LCG4,B.LCG4 step#1 pm(>>,forward) area=12.80 rise=3.45 twist=31.2 step#2 pm(>>,forward) area=14.11 rise=3.56 twist=26.4 strand#1 --- glyco-bond=--- sugar=333 nts=3 ggg A.LCG2,A.LCG3,A.LCG4 strand#2 --- glyco-bond=--- sugar=333 nts=3 ggg C.LCG2,C.LCG3,C.LCG4 strand#3 --- glyco-bond=--- sugar=333 nts=3 ggg D.LCG2,D.LCG3,D.LCG4 strand#4 --- glyco-bond=--- sugar=333 nts=3 ggg B.LCG2,B.LCG3,B.LCG4 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG2,D.LCG2,B.LCG2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG3,D.LCG3,B.LCG3 step#1 pm(>>,forward) area=12.80 rise=3.45 twist=31.2 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG3,D.LCG3,B.LCG3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG4,D.LCG4,B.LCG4 step#2 pm(>>,forward) area=14.11 rise=3.56 twist=26.4 Download PDB file Interactive view in 3Dmol.js

Helix#2, 3 G-tetrad layers, inter-molecular, with 1 stem

	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG2,G.LCG2,H.LCG2,F.LCG2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG3,G.LCG3,H.LCG3,F.LCG3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG4,G.LCG4,H.LCG4,F.LCG4 step#1 pm(>>,forward) area=12.79 rise=3.40 twist=31.7 step#2 pm(>>,forward) area=14.26 rise=3.62 twist=26.1 strand#1 --- glyco-bond=--- sugar=333 nts=3 ggg E.LCG2,E.LCG3,E.LCG4 strand#2 --- glyco-bond=--- sugar=333 nts=3 ggg G.LCG2,G.LCG3,G.LCG4 strand#3 --- glyco-bond=--- sugar=333 nts=3 ggg H.LCG2,H.LCG3,H.LCG4 strand#4 --- glyco-bond=--- sugar=333 nts=3 ggg F.LCG2,F.LCG3,F.LCG4 Download PDB file Interactive view in 3Dmol.js
2 stacking diagrams
	1 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG2,G.LCG2,H.LCG2,F.LCG2 2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG3,G.LCG3,H.LCG3,F.LCG3 step#1 pm(>>,forward) area=12.79 rise=3.40 twist=31.7 Download PDB file Interactive view in 3Dmol.js
	2 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG3,G.LCG3,H.LCG3,F.LCG3 3 glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG4,G.LCG4,H.LCG4,F.LCG4 step#2 pm(>>,forward) area=14.26 rise=3.62 twist=26.1 Download PDB file Interactive view in 3Dmol.js

List of 2 G4-stems

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 3 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG2,C.LCG2,D.LCG2,B.LCG2
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG3,C.LCG3,D.LCG3,B.LCG3
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg A.LCG4,C.LCG4,D.LCG4,B.LCG4
  step#1  pm(>>,forward)  area=12.80 rise=3.45 twist=31.2
  step#2  pm(>>,forward)  area=14.11 rise=3.56 twist=26.4
  strand#1  U --- glyco-bond=--- sugar=333 nts=3 ggg A.LCG2,A.LCG3,A.LCG4
  strand#2  U --- glyco-bond=--- sugar=333 nts=3 ggg C.LCG2,C.LCG3,C.LCG4
  strand#3  U --- glyco-bond=--- sugar=333 nts=3 ggg D.LCG2,D.LCG3,D.LCG4
  strand#4  U --- glyco-bond=--- sugar=333 nts=3 ggg B.LCG2,B.LCG3,B.LCG4

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Interactive view in 3Dmol.js

Stem#2, 3 G-tetrad layers, 0 loops, inter-molecular, UUUU, parallel, parallel(4+0)

 1  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG2,G.LCG2,H.LCG2,F.LCG2
 2  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG3,G.LCG3,H.LCG3,F.LCG3
 3  glyco-bond=---- sugar=3333 groove=---- WC-->Major nts=4 gggg E.LCG4,G.LCG4,H.LCG4,F.LCG4
  step#1  pm(>>,forward)  area=12.79 rise=3.40 twist=31.7
  step#2  pm(>>,forward)  area=14.26 rise=3.62 twist=26.1
  strand#1  U --- glyco-bond=--- sugar=333 nts=3 ggg E.LCG2,E.LCG3,E.LCG4
  strand#2  U --- glyco-bond=--- sugar=333 nts=3 ggg G.LCG2,G.LCG3,G.LCG4
  strand#3  U --- glyco-bond=--- sugar=333 nts=3 ggg H.LCG2,H.LCG3,H.LCG4
  strand#4  U --- glyco-bond=--- sugar=333 nts=3 ggg F.LCG2,F.LCG3,F.LCG4