title: Solution structure and design of dithiophosphate backbone aptamers targeting transcription factor NF-kappaB.
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.
authors.affiliation: Department of Human Biological Chemistry and Genetics, The University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555-1157, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Volk
authors.forename: Xianbin
authors.initials: X
authors.lastname: Yang
authors.forename: Susan M
authors.initials: SM
authors.lastname: Fennewald
authors.forename: David J
authors.initials: DJ
authors.lastname: King
authors.forename: Suzanne E
authors.initials: SE
authors.lastname: Bassett
authors.forename: Sheela
authors.initials: S
authors.lastname: Venkitachalam
authors.forename: Norbert
authors.initials: N
authors.lastname: Herzog
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Luxon
authors.forename: David G
authors.initials: DG
authors.lastname: Gorenstein
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D019281:Dimerization; D015195:Drug Design; D004926:Escherichia coli; D006801:Humans; D007202:Indicators and Reagents; D008958:Models, Molecular; D016328:NF-kappa B / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry*; D011994:Recombinant Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D012996:Solutions; D051996:Transcription Factor RelA; D014157:Transcription Factors / Q000737:chemistry
chemical_list: D017931:DNA Primers; D007202:Indicators and Reagents; D016328:NF-kappa B; D009838:Oligodeoxyribonucleotides; D010710:Phosphates; D011994:Recombinant Proteins; D012996:Solutions; D051996:Transcription Factor RelA; D014157:Transcription Factors; C083120:phosphorodithioic acid; C035638:thiophosphoric acid