4DKZ

Hairpin structure of a DNA dodecamer containing North-methanocarba-2'-deoxythymidine

Summary for 4DKZ

Entry DOI	10.2210/pdb4dkz/pdb
Descriptor	Synthetic DNA dodecamer containg North-methanocarba-2'-deoxythymidine (N-MCdT) (2 entities in total)
Functional Keywords	north-methanocarba-2'-deoxythymidine, n-mcdt, x-ray crystal structure, tetra-loop hairpin, c4'-exo pucker, hairpin dna, dna
Total number of polymer chains	2
Total formula weight	7366.94
Authors	Egli, M.,Pallan, P.S. (deposition date: 2012-02-05, release date: 2012-03-28, Last modification date: 2024-02-28)
Primary citation	Pallan, P.S.,Marquez, V.E.,Egli, M. The Conformationally Constrained N-Methanocarba-dT Analogue Adopts an Unexpected C4'-exo Sugar Pucker in the Structure of a DNA Hairpin. Biochemistry, 51:2639-2641, 2012 Cited by PubMed Abstract: Incorporation of a bicyclo[3.1.0]hexane scaffold into the nucleoside sugar was devised to lock the embedded cyclopentane ring in conformations that mimic the furanose North and South sugar puckers. To analyze the effects of North-methanocarba-2'-deoxythymidine (N-MCdT) on the B-form DNA, we crystallized d(CGCGAA[mcTmcT]CGCG) with two N-MCdTs. Instead of a duplex, the 12mer forms a tetraloop hairpin, whereby loop N-MCdTs adopt the C4'-exo pucker (NE; P = 50°). Thus, the bicyclic framework does not limit the pucker to the anticipated C2'-exo range (NNW; P = -18°). PubMed: 22409313 DOI: 10.1021/bi300215k PDB entries with the same primary citation
Experimental method	X-RAY DIFFRACTION (1.8 Å)

Structure validation