1MYQ

An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction

Summary for 1MYQ

• Entry DOI: 10.2210/pdb1myq/pdb
• Descriptor: 5'-D(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3' (1 entity in total)
• Functional Keywords: intramolecular parallel quadruplex structure, dimeric structure, dna
• Total number of polymer chains: 2
• Total formula weight: 7683.03

Authors

Matsugami, A.,Ouhashi, K.,Kanagawa, M.,Liu, H.,Kanagawa, S.,Uesugi, S.,Katahira, M. (deposition date: 2002-10-04, release date: 2002-10-23, Last modification date: 2024-05-22)

Primary citation

Matsugami, A.,Ouhashi, K.,Kanagawa, M.,Liu, H.,Kanagawa, S.,Uesugi, S.,Katahira, M.
An intramolecular quadruplex of (GGA)(4) triplet repeat DNA with a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad, and its dimeric interaction.
J.Mol.Biol., 313:255-269, 2001

PubMed Abstract: The structure of d(GGAGGAGGAGGA) containing four tandem repeats of a GGA triplet sequence has been determined under physiological K(+) conditions. d(GGAGGAGGAGGA) folds into an intramolecular quadruplex composed of a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad. Four G-G segments of d(GGAGGAGGAGGA) are aligned parallel with each other due to six successive turns of the main chain at each of the GGA and GAGG segments. Two quadruplexes form a dimer stabilized through a stacking interaction between the heptads of the two quadruplexes. Comparison of the structure of d(GGAGGAGGAGGA) with the reported structure of d(GGAGGAN) (N=G or T) containing two tandem repeats of the GGA triplet revealed that although the two structures resemble each other to some extent, the extension of the repeats of the GGA triplet leads to distinct structural differences: intramolecular quadruplex for 12-mer versus intermolecular quadruplex for 7-mer; heptad versus hexad in the quadruplex; and three sheared G:A base-pairs versus two sheared G:A base-pairs plus one A:A base-pair per quadruplex. It was also suggested that d(GGAGGAGGAGGA) forms a similar quadruplex under low salt concentration conditions. This is in contrast to the case of d(GGAGGAN) (N=G or T), which forms a duplex under low salt concentration conditions. On the basis of these results, the structure of naturally occurring GGA triplet repeat DNA is discussed.

PubMed: 11800555
DOI: 10.1006/jmbi.2001.5047

Experimental method

SOLUTION NMR