PDBsum entry 2kf7

DNA

PDB id: 2kf7

Contents

DNA/RNA

PDB id:

2kf7

Name:

DNA

Title:

Structure of a two-g-tetrad basket-type intramolecular g-quadruplex formed by human telomeric repeats in k+ solution (with g7-to-brg substitution)

Structure:

Human telomere DNA. Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: nucleotide synthesis

NMR struc:

10 models

Authors:

K.W.Lim,S.Amrane,S.Bouaziz,W.Xu,Y.Mu,D.J.Patel,K.N.Luu,A.T.Phan

Key ref:

K.W.Lim et al. (2009). Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc, 131, 4301-4309. PubMed id: 19271707

Date:

12-Feb-09 Release date: 24-Mar-09

DNA/RNA chain

G-G-G-T-T-A-BGM-G-G-T-T-A-G-G-G-T-T-A-G-G-G-T 22 bases

J Am Chem Soc 131:4301-4309 (2009)

PubMed id: 19271707

Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers.

K.W.Lim, S.Amrane, S.Bouaziz, W.Xu, Y.Mu, D.J.Patel, K.N.Luu, A.T.Phan.

ABSTRACT

Previously, it has been reported that human telomeric DNA sequences could adopt in different experimental conditions four different intramolecular G-quadruplexes each involving three G-tetrad layers, namely, Na(+) solution antiparallel-stranded basket form, K(+) crystal parallel-stranded propeller form, K(+) solution (3 + 1) Form 1, and K(+) solution (3 + 1) Form 2. Here we present a new intramolecular G-quadruplex adopted by a four-repeat human telomeric sequence in K(+) solution (Form 3). This structure is a basket-type G-quadruplex with only two G-tetrad layers: loops are successively edgewise, diagonal, and edgewise; glycosidic conformations of guanines are syn x syn x anti x anti around each tetrad. Each strand of the core has both a parallel and an antiparallel adjacent strands; there are one narrow, one wide, and two medium grooves. Despite the presence of only two G-tetrads in the core, this structure is more stable than the three-G-tetrad intramolecular G-quadruplexes previously observed for human telomeric sequences in K(+) solution. Detailed structural elucidation of Form 3 revealed extensive base pairing and stacking in the loops capping both ends of the G-tetrad core, which might explain the high stability of the structure. This novel structure highlights the conformational heterogeneity of human telomeric DNA. It establishes a new folding principle for G-quadruplexes and suggests new loop sequences and structures for targeting in human telomeric DNA.