PDBsum entry 2fij

DNA

PDB id

2fij

Loading ...

Contents

			DNA/RNA

			Ligands

					NCO ×3

			Metals

					_CL

			Waters ×128

PDB id:

2fij

Links

Name:

DNA

Title:

Crystal structure analysis of the a-DNA decamer gcgt-2'omea-au-acgc, with incorporated 2'-o-methylated-adenosine (2'omea) and arabino- uridine (au)

Structure:

5'-d( Gp Cp Gp Tp (A2m)p (Uar)p Ap Cp Gp C)-3'. Chain: a, b. Engineered: yes. Mutation: yes

Source:

Synthetic: yes

Biol. unit:

Dimer (from PQS)

Resolution:

1.19Å

R-factor:

0.159

R-free:

0.169

Authors:

M.Egli,F.Li

Key ref:

F.Li et al. (2006). 2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H. Biochemistry, 45, 4141-4152. PubMed id: 16566588 DOI: 10.1021/bi052322r

Date:

29-Dec-05

Release date:

23-May-06

	Headers

	References

DNA/RNA chains

		G-C-G-T-A2M-UAR-A-C-G-C 10 bases
		G-C-G-T-A2M-UAR-A-C-G-C 10 bases

DOI no: 10.1021/bi052322r	Biochemistry 45:4141-4152 (2006)
PubMed id: 16566588

2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.
F.Li, S.Sarkhel, C.J.Wilds, Z.Wawrzak, T.P.Prakash, M.Manoharan, M.Egli.

ABSTRACT

2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21183463

P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, and M.Egli (2011).
Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.

Nucleic Acids Res, 39, 3482-3495.

PDB codes:

3p4a 3p4b 3p4c 3p4d

20071751

J.K.Watts, N.Martín-Pintado, I.Gómez-Pinto, J.Schwartzentruber, G.Portella, M.Orozco, C.González, and M.J.Damha (2010).
Differential stability of 2'F-ANA*RNA and ANA*RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility.

Nucleic Acids Res, 38, 2498-2511.

PDB codes:

2kp3 2kp4

20087997

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

Chem Biodivers, 7, 60-89.

19333476

P.S.Pallan, T.P.Prakash, F.Li, R.L.Eoff, M.Manoharan, and M.Egli (2009).
A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution.

Chem Commun (Camb), (), 2017-2019.

PDB codes:

3ey1 3ey2 3ey3

17277445

L.V.Loukachevitch, and M.Egli (2007).
Crystallization and preliminary X-ray analysis of Escherichia coli RNase HI-dsRNA complexes.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 84-88.

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.

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.