1WV5

X-ray structure of the A-decamer GCGTATACGC with a single 2'-o-butyl thymine in place of T6, Mg-form

PDB DOI: 10.2210/pdb1WV5/pdb
NDB: AD0035

Classification: DNA
Mutation(s): No

Deposited: 2004-12-11 Released: 2005-06-28
Deposition Author(s): Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharam, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.260
R-Value Work: 0.237
R-Value Observed: 0.238

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Probing the influence of stereoelectronic effects on the biophysical properties of oligonucleotides: comprehensive analysis of the RNA affinity, nuclease resistance, and crystal structure of ten 2'-O-ribonucleic acid modifications.

Egli, M., Minasov, G., Tereshko, V., Pallan, P.S., Teplova, M., Inamati, G.B., Lesnik, E.A., Owens, S.R., Ross, B.S., Prakash, T.P., Manoharan, M.

(2005) Biochemistry 44: 9045-9057

PubMed: 15966728 Search on PubMed
DOI: 10.1021/bi050574m
Primary Citation of Related Structures:
1WV5, 1WV6, 1Y7F, 1Y84, 1Y86, 1Y8L, 1Y8V, 1Y9F, 1Y9S, 1YB9, 1YBC

PubMed Abstract:

The syntheses of 10 new RNA 2'-O-modifications, their incorporation into oligonucleotides, and an evaluation of their properties such as RNA affinity and nuclease resistance relevant to antisense activity are presented. All modifications combined with the natural phosphate backbone lead to significant gains in terms of the stability of hybridization to RNA relative to the first-generation DNA phosphorothioates (PS-DNA). The nuclease resistance afforded in particular by the 2'-O-modifications carrying a positive charge surpasses that of PS-DNA. However, small electronegative 2'-O-substituents, while enhancing the RNA affinity, do not sufficiently protect against degradation by nucleases. Similarly, oligonucleotides containing 3'-terminal residues modified with the relatively large 2'-O-[2-(benzyloxy)ethyl] substituent are rapidly degraded by exonucleases, proving wrong the assumption that steric bulk will generally improve protection against nuclease digestion. To analyze the factors that contribute to the enhanced RNA affinity and nuclease resistance we determined crystal structures of self-complementary A-form DNA decamer duplexes containing single 2'-O-modified thymidines per strand. Conformational preorganization of substituents, favorable electrostatic interactions between substituent and sugar-phosphate backbone, and a stable water structure in the vicinity of the 2'-O-modification all appear to contribute to the improved RNA affinity. Close association of positively charged substituents and phosphate groups was observed in the structures with modifications that protect most effectively against nucleases. The promising properties exhibited by some of the analyzed 2'-O-modifications may warrant a more detailed evaluation of their potential for in vivo antisense applications. Chemical modification of RNA can also be expected to significantly improve the efficacy of small interfering RNAs (siRNA). Therefore, the 2'-O-modifications introduced here may benefit the development of RNAi therapeutics.

Organizational Affiliation:

Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, USA. martin.egli@vanderbilt.edu

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(GPCPGPTPAP(2BT)PAPCPGPC)-3'	A, B	10	N/A
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction