5J3F

NMR solution structure of [Rp, Rp]-PT dsDNA

Summary for 5J3F

• Entry DOI: 10.2210/pdb5j3f/pdb
• Related: 5J3G 5J3I
• NMR Information: BMRB: 30052
• Descriptor: DNA (5'-D(*CP*GP*(RSG)P*CP*CP*GP*CP*CP*GP*A)-3'), DNA (5'-D(*TP*CP*GP*GP*CP*GP*(RSG)P*CP*CP*G)-3') (2 entities in total)
• Functional Keywords: dna, [rp, rp]-pt dsdna
• Biological source: Streptomyces lividans; More
• Total number of polymer chains: 2
• Total formula weight: 6125.10

Authors

Lan, W.,Hu, Z.,Cao, C. (deposition date: 2016-03-30, release date: 2016-11-16, Last modification date: 2024-05-15)

Primary citation

Lan, W.,Hu, Z.,Shen, J.,Wang, C.,Jiang, F.,Liu, H.,Long, D.,Liu, M.,Cao, C.
Structural investigation into physiological DNA phosphorothioate modification
Sci Rep, 6:25737-25737, 2016

PubMed Abstract: DNA phosphorothioate (PT) modification, with sulfur replacing a nonbridging phosphate oxygen in a sequence and stereo specific manner, is a novel physiological variation in bacteria. But what effects on DNA properties PT modification has is still unclear. To address this, we prepared three double-stranded (ds) DNA decamers, d(CG(PX)GCCGCCGA) with its complementary strand d(TCGGCG(PX)GCCG) (where X = O or S, i.e., PT-free dsDNA, [Sp, Sp]-PT dsDNA or [Rp, Rp]-PT dsDNA) located in gene of Streptomyces lividans. Their melting temperature (Tm) measurement indicates that [Rp, Rp]-PT dsDNA is most unstable. Their electron transfer potential detection presents an order of anti-oxidation properties: Sp-PT DNA > Rp-PT DNA > PT-free DNA. Their NMR structures demonstrate that PT modification doesn't change their B-form conformation. The sulfur in [Rp, Rp]-PT dsDNA locates in the major groove, with steric effects on protons in the sugar close to modification sites, resulting in its unstability, and facilitating its selectively interactions with ScoMcrA. We thought that PT modification was dialectical to the bacteria. It protects the hosting bacteria by working as antioxidant against H2O2, and acts as a marker, directing restriction enzyme observed in other hosts, like ScoMcrA, to correctly cleave the PT modified DNA, so that bacteria cannot spread and survive.

PubMed: 27169778
DOI: 10.1038/srep25737

Experimental method

SOLUTION NMR