PDBsum entry 2plb

DNA

PDB id

2plb

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Contents

			DNA/RNA

			Ligands

					SPM

			Waters ×76

PDB id:

2plb

Links

Name:

DNA

Title:

D(gtatacc) under hydrostatic pressure of 1.39 gpa

Structure:

5'-d( Dgp Dgp Dtp Dap Dtp Dap Dcp Dc)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: synthetic DNA octamer

Resolution:

1.60Å

R-factor:

0.219

R-free:

0.222

Authors:

T.Prange,E.Girard,R.Kahn,R.Fourme

Key ref:

E.Girard et al. (2007). Adaptation of the base-paired double-helix molecular architecture to extreme pressure. Nucleic Acids Res, 35, 4800-4808. PubMed id: 17617642

Date:

19-Apr-07

Release date:

24-Jul-07

	Headers

	References

DNA/RNA chains

		G-G-T-A-T-A-C-C 8 bases
		G-G-T-A-T-A-C-C 8 bases

	Nucleic Acids Res 35:4800-4808 (2007)
PubMed id: 17617642

Adaptation of the base-paired double-helix molecular architecture to extreme pressure.
E.Girard, T.Prangé, A.C.Dhaussy, E.Migianu-Griffoni, M.Lecouvey, J.C.Chervin, M.Mezouar, R.Kahn, R.Fourme.

ABSTRACT

The behaviour of the d(GGTATACC) oligonucleotide has been investigated by X-ray crystallography at 295 K in the range from ambient pressure to 2 GPa (approximately 20,000 atm). Four 3D-structures of the A-DNA form (at ambient pressure, 0.55, 1.09 and 1.39 GPa) were refined at 1.60 or 1.65 A resolution. In addition to the diffraction pattern of the A-form, the broad meridional streaks previously explained by occluded B-DNA octamers within the channels of the crystalline A-form matrix were observed up to at least 2 GPa. This work highlights an important property of nucleic acids, their capability to withstand very high pressures, while keeping in such conditions a nearly invariant geometry of base pairs that store and carry genetic information. The double-helix base-paired architecture behaves as a molecular spring, which makes it especially adapted to very harsh conditions. These features may have contributed to the emergence of a RNA World at prebiotic stage.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21169687

R.Fourme, E.Girard, A.C.Dhaussy, K.Medjoubi, T.Prangé, I.Ascone, M.Mezouar, and R.Kahn (2011).
A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results.

J Synchrotron Radiat, 18, 31-36.

21220280

S.C.Morris (2011).
Predicting what extra-terrestrials will be like: and preparing for the worst.

Philos Transact A Math Phys Eng Sci, 369, 555-571.

20483346

E.Girard, S.Marchal, J.Perez, S.Finet, R.Kahn, R.Fourme, G.Marassio, A.C.Dhaussy, T.Prangé, M.Giffard, F.Dulin, F.Bonneté, R.Lange, J.H.Abraini, M.Mezouar, and N.Colloc'h (2010).
Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.

Biophys J, 98, 2365-2373.

PDB code:

3f2m

19497630

A.Aertsen, F.Meersman, M.E.Hendrickx, R.F.Vogel, and C.W.Michiels (2009).
Biotechnology under high pressure: applications and implications.

Trends Biotechnol, 27, 434-441.

19476496

M.Ztouti, H.Kaddour, F.Miralles, C.Simian, J.Vergne, G.Hervé, and M.C.Maurel (2009).
Adenine, a hairpin ribozyme cofactor - high-pressure and competition studies.

FEBS J, 276, 2574-2588.

19416064

R.Fourme, E.Girard, R.Kahn, A.C.Dhaussy, and I.Ascone (2009).
Advances in high-pressure biophysics: status and prospects of macromolecular crystallography.

Annu Rev Biophys, 38, 153-171.

18515837

D.J.Wilton, M.Ghosh, K.V.Chary, K.Akasaka, and M.P.Williamson (2008).
Structural change in a B-DNA helix with hydrostatic pressure.

Nucleic Acids Res, 36, 4032-4037.

PDB codes:

2vah 2vai

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.