1K8N

NMR structure of the XBY2 DNA duplex, an analog of CK14 containing phosphorodithioate groups at C22 and C24

Summary for 1K8N

• Entry DOI: 10.2210/pdb1k8n/pdb
• Related: 1K8J 1K8L
• NMR Information: BMRB: 5716,5717,5718
• Descriptor: FIRST STRAND OF CK14 DNA DUPLEX, SECOND STRAND OF CK14 DNA DUPLEX (2 entities in total)
• Functional Keywords: phosphorodithioate, ck14, ck1, nf-kb, xby6, xby2, thiophosphate, dna
• Total number of polymer chains: 2
• Total formula weight: 8625.84

Authors

Volk, D.E.,Yang, X.,Fennewald, S.M.,King, D.J.,Bassett, S.E.,Venkitachalam, S.,Herzog, N.,Luxon, B.A.,Gorenstein, D.G. (deposition date: 2001-10-24, release date: 2003-04-15, Last modification date: 2024-05-22)

Primary citation

Volk, D.E.,Yang, X.,Fennewald, S.M.,King, D.J.,Bassett, S.E.,Venkitachalam, S.,Herzog, N.,Luxon, B.A.,Gorenstein, D.G.
Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB
Bioorg.Chem., 30:396-419, 2002

PubMed Abstract: A variety of monothio- and dithiosubstituted duplex aptamers targeting NF-kappaB have been synthesized and designed. The specificity and affinity of the dithioate aptamers of p50 and RelA(p65) NF-kappaB homodimers was determined by gel shift experiments. The NMR solution structures for several unmodified and dithioate backbone modified 14-base paired duplex aptamers have been determined by a hybrid, complete matrix (MORASS)/restrained molecular dynamics method. Structural perturbations of the dithioate substitutions support our hypothesis that the dithioate binds cations less tightly than phosphoryl groups. This increases the electrostatic repulsion across the B-form narrow minor groove and enlarges the minor groove, similar to that found in A-form duplexes. Structural analysis of modeled aptamer complexes with NF-kappaB homo- and heterodimers suggests that the dithioate backbone substitution can increase the aptamer's relative affinity to basic groups in proteins such as NF-kappaB by helping to "strip" the cations from the aptamer backbone.

PubMed: 12642125
DOI: 10.1016/S0045-2068(02)00510-2

Experimental method

SOLUTION NMR