Topology Variation and Loop Structural Homology in Crystal
and Simulated Structures of a Bimolecular DNA Quadruplex
Pascale Hazel
Gary N. Parkinson
Stephen Neidle
10.1021/ja058577+.s001
https://acs.figshare.com/articles/journal_contribution/Topology_Variation_and_Loop_Structural_Homology_in_Crystal_and_Simulated_Structures_of_a_Bimolecular_DNA_Quadruplex/3372286
The topology of DNA quadruplexes depends on the nature and number of the nucleotides linking
G-quartet motifs. To assess the effects of a three-nucleotide TTT linker, the crystal structure of the DNA
sequence d(G<sub>4</sub>T<sub>3</sub>G<sub>4</sub>) has been determined at 1.5 Å resolution, together with that of the brominated analogue
d(G<sub>4</sub><sup>Br</sup>UTTG<sub>4</sub>) at 2.4 Å resolution. Both sequences form bimolecular intermolecular G-quadruplexes with
lateral loops. d(G<sub>4</sub><sup>Br</sup>UTTG<sub>4</sub>) crystallized in the monoclinic space group <i>P</i>2<sub>1</sub> with three quadruplex molecules
in the asymmetric unit, two associating together as a head-to-head stacked dimer, and the third as a single
head-to-tail dimer. The head-to-head dimers have two lateral loops on the same G-quadruplex face and
form an eight-G-quartet stack, with a linear array of seven K<sup>+</sup> ions between the quartets. d(G<sub>4</sub>T<sub>3</sub>G<sub>4</sub>)
crystallized in the orthorhombic space group <i>C</i>222 and has a structure very similar to the head-to-tail dimer
in the <i>P</i>2<sub>1</sub> unit cell. The sequence studied here is able to form several different folds; however, all four
quadruplexes in the two structures have lateral loops, in contrast to the diagonal loops reported for the
analogous quadruplex with T<sub>4</sub> loops. A total of seven independent T<sub>3</sub> loops were observed in the two
structures. These can be classified into two discrete conformational classes, suggesting that these represent
preferred loop conformations that are independent of crystal-packing forces.
2006-04-26 00:00:00
DNA quadruplexes
space group C 222
quadruplex molecules
T 4 loops
1.5 Å resolution
brominated analogue
dimer
Topology Variation
Bimolecular DNA Quadruplex
sequences form
TTT
UTTG
Loop Structural Homology
DNA sequence
crystal structure
T 3 loops
P 2 1 unit cell
space group P 2 1
2.4 Å resolution
Simulated Structures
loop conformations