PDBsum entry 1vro

DNA

PDB id

1vro

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Contents

			DNA/RNA

			Ligands

					SPM

			Metals

					_MG

			Waters ×73

PDB id:

1vro

Links

Name:

DNA

Title:

Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for mad phasing of a DNA structure

Structure:

5'-d( Cp (Gms)p Cp Gp Cp G)-3'. Chain: a, b. Engineered: yes

Source:

Synthetic: yes. Other_details: synthesized with a solid-phase oligonucleotide synthesizer using DNA phosphoramidites and potassium selenocyanide for introducing the phosphoroselenoate linkage

Resolution:

1.10Å

R-factor:

0.097

R-free:

0.129

Authors:

C.J.Wilds,R.Pattanayek,C.Pan,Z.Wawrzak,M.Egli

Key ref:

C.J.Wilds et al. (2002). Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure. J Am Chem Soc, 124, 14910-14916. PubMed id: 12475332 DOI: 10.1021/ja021058b

Date:

14-Apr-05

Release date:

19-Apr-05

Supersedes:

1n6s

	Headers

	References

DNA/RNA chains

		C-GMS-C-G-C-G 6 bases
		C-GMS-C-G-C-G 6 bases

DOI no: 10.1021/ja021058b	J Am Chem Soc 124:14910-14916 (2002)
PubMed id: 12475332

Selenium-assisted nucleic acid crystallography: use of phosphoroselenoates for MAD phasing of a DNA structure.
C.J.Wilds, R.Pattanayek, C.Pan, Z.Wawrzak, M.Egli.

ABSTRACT

The combination of synchrotron radiation and a variety of atoms or ions (either covalently attached to the biomolecule prior to crystallization or soaked into crystals) that serve as anomalous scatterers constitutes a powerful tool in the X-ray crystallographer's repertoire of structure determination techniques. Phosphoroselenoates in which one of the nonbridging phosphate oxygens in the backbone is replaced by selenium offer a simplified means for introducing an anomalous scatterer into oligonucleotides by conventional solid-phase synthesis. Unlike other methods that are used to derivatize DNA or RNA by covalent attachment of a heavy atom (i.e., bromine at the C5 position of pyrimidines), tedious synthesis of specialized nucleosides is not required. Introduction of selenium is readily accomplished in solid-phase oligonucleotide synthesis by replacing the standard oxidation agent with a solution of potassium selenocyanide. This results in a diastereomeric mixture of phosphoroselenoates that can be separated by strong anion-exchange HPLC. As a test case, all 10 DNA hexamers of the sequence CGCGCG containing a single phosphoroselenoate linkage (PSe) were prepared. Crystals were grown for a subset of them, and the structure of [d(C(PSe)GCGCG)](2) was determined by the multiwavelength anomalous dispersion technique and refined to 1.1 A resolution.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20397215

J.Sheng, and Z.Huang (2010).
Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies.

Chem Biodivers, 7, 753-785.

20087997

M.Egli, and P.S.Pallan (2010).
Crystallographic studies of chemically modified nucleic acids: a backward glance.

Chem Biodivers, 7, 60-89.

20517991

M.Egli (2010).
Diffraction techniques in structural biology.

Curr Protoc Nucleic Acid Chem, (), Unit 7.13.

19739194

J.Kowalska, M.Lukaszewicz, J.Zuberek, E.Darzynkiewicz, and J.Jemielity (2009).
Phosphoroselenoate dinucleotides for modification of mRNA 5' end.

Chembiochem, 10, 2469-2473.

19318208

Y.Brudno, and D.R.Liu (2009).
Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers.

Chem Biol, 16, 265-276.

18357549

J.Caton-Williams, and Z.Huang (2008).
Biochemistry of selenium-derivatized naturally occurring and unnatural nucleic acids.

Chem Biodivers, 5, 396-407.

19325748

J.Sheng, and Z.Huang (2008).
Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography.

Int J Mol Sci, 9, 258-271.

17630326

E.Ennifar, S.Bernacchi, P.Wolff, and P.Dumas (2007).
Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding.

RNA, 13, 1445-1452.

17169989

J.Jiang, J.Sheng, N.Carrasco, and Z.Huang (2007).
Selenium derivatization of nucleic acids for crystallography.

Nucleic Acids Res, 35, 477-485.

PDB codes:

1z7i 2dlj 2gpx 2h05

17263541

J.Sheng, J.Jiang, J.Salon, and Z.Huang (2007).
Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study.

Org Lett, 9, 749-752.

17173143

M.Egli, P.Lubini, and P.S.Pallan (2007).
The long and winding road to the structure of homo-DNA.

Chem Soc Rev, 36, 31-45.

17288535

M.Egli, and P.S.Pallan (2007).
Insights from crystallographic studies into the structural and pairing properties of nucleic acid analogs and chemically modified DNA and RNA oligonucleotides.

Annu Rev Biophys Biomol Struct, 36, 281-305.

17406625

P.S.Pallan, and M.Egli (2007).
Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures.

Nat Protoc, 2, 640-646.

16846240

G.Brandt, N.Carrasco, and Z.Huang (2006).
Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography.

Biochemistry, 45, 8972-8977.

16304655

N.Carrasco, J.Caton-Williams, G.Brandt, S.Wang, and Z.Huang (2005).
Efficient enzymatic synthesis of phosphoroselenoate RNA by using adenosine 5'-(alpha-P-seleno)triphosphate.

Angew Chem Int Ed Engl, 45, 94-97.

15556400

M.Egli (2004).
Nucleic acid crystallography: current progress.

Curr Opin Chem Biol, 8, 580-591.

15007109

N.Carrasco, Y.Buzin, E.Tyson, E.Halpert, and Z.Huang (2004).
Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion.

Nucleic Acids Res, 32, 1638-1646.

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 codes are shown on the right.