2KOW

Structure of a two-G-tetrad basket-type intramolecular G-quadruplex formed by Giardia telomeric repeat d(TAGGG)4 in K+ solution (with G18-to-INO substitution)

Summary for 2KOW

• Entry DOI: 10.2210/pdb2kow/pdb
• Related: 2KF7 2KF8 2KM3
• Descriptor: DNA (5'-D(*TP*AP*GP*GP*GP*TP*AP*GP*GP*GP*TP*AP*GP*GP*GP*TP*AP*IP*GP*G)-3') (1 entity in total)
• Functional Keywords: telomere, g-quadruplex, g.(a-g) triad, taggg repeat, dna, giardia
• Total number of polymer chains: 1
• Total formula weight: 6360.10

Authors

Hu, L.,Lim, K.W.,Bouaziz, S.,Phan, A.T. (deposition date: 2009-10-02, release date: 2009-11-17, Last modification date: 2024-05-29)

Primary citation

Hu, L.,Lim, K.W.,Bouaziz, S.,Phan, A.T.
Giardia Telomeric Sequence d(TAGGG)(4) Forms Two Intramolecular G-Quadruplexes in K(+) Solution: Effect of Loop Length and Sequence on the Folding Topology.
J.Am.Chem.Soc., 131:16824-16831, 2009

PubMed Abstract: Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

PubMed: 19874015
DOI: 10.1021/ja905611c

Experimental method

SOLUTION NMR