ISDA

Deposition Date 2015-07-28

Release Date 2016-07-20

Last Version Date 2024-03-20

Entry Detail

PDB ID:

5AXF

Keywords:

DNA

Title:

Crystal Structure Analysis of DNA Duplexes containing sulfoamide-bridged nucleic acid (SuNA-NMe)

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.13 Å

R-Value Free:

0.14

R-Value Work:

0.13

R-Value Observed:

0.13

Space Group:

P 21 21 21

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Macromolecular Entities

Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(*GP*CP*GP*TP*AP*(LSM)P*AP*CP*GP*C)-3')
Chain IDs:A, B
Chain Length:10
Number of Molecules:2
Biological Source:synthetic construct

Primary Citation

Effect of an N-substituent in sulfonamide-bridged nucleic acid (SuNA) on hybridization ability and duplex structure.

Mitsuoka, Y, Aoyama, H, Kugimiya, A, Fujimura, Y, Yamamoto, T, Waki, R, Wada, F, Tahara, S, Sawamura, M, Noda, M, Hari, Y, Obika, S.Show

Org.Biomol.Chem. 14 6531 6538 (2016)

PMID: 27296230 DOI: 10.1039/c6ob01051b

Abstact

A sulfonamide-bridged nucleic acid without an N-substituent (SuNA[NH]) was successfully synthesized. A comparison of the SuNA[NMe]- and SuNA[NH]-modified oligonucleotides revealed that the duplex-forming abilities of the SuNA[NMe]-modified oligonucleotides with complementary DNA and RNA were higher than those of the SuNA[NH]-modified oligonucleotides. The crystal structures of DNA duplexes containing a SuNA[NR] revealed that the helical structures of the two duplexes and hydration patterns around the bridge moiety were different. These results provide insights into hydration patterns and rationale for the high RNA affinity of SuNA-modified oligonucleotides.

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Primary Citation of related structures