Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide 1-methylimidazole-2-carboxamide netropsin.

Abstract

The designed peptide 1-methyliaole-2-carboxamide netropsin (2-ImN) binds specifically to the sequence 5'-TGACT-3'. Direct evidence from NMR spectroscopy is presented that this synthetic ligand binds DNA as a 2:1 complex, which reveals that the structure is an antiparallel dimer in the minor groove of DNA. This is in contrast to the 1:1 complexes usually seen with most crescent-shaped minor groove binding molecules targeted toward A+T-rich tracts but reminiscent of a dimeric motif found for distamycin at high concentrations. These results suggest that sequence-dependent groove width may play an important role in allowing an expanded set of DNA binding motifs for synthetic peptides.

Stoichiometry and structure of complexes of DNA oligomers with microgonotropens and distamycin by 1H NMR spectroscopy and molecular modeling.

“…(dsDNA)(L)2 complexes the species L [L = Dm (2), 1-methyl imidazole-2-carboxamide netropsin (3), 2-imidazole distamycin, and Dm plus 2-imidazole distamycin (4)] have an antiparallel geometry. These agents all target the A-T-rich region of the minor groove.…”

NMR studies of DNA oligomers and their interactions with minor groove binding ligands

“…NOESY spectra of the ligand:DNA complexes in D2O and/or H2O enabled assignment of the DNA and ligand resonances (Hare et al, 1983;Wuthrich, 1986; Pelton base protons and sugar HI", H2', H2", and H3' protons were assigned, extending to the the cross peaks in the D2O NOESY spectra acquired at a mixing time of 200 msec as described previously Mrksich et al, 1992). The cross peak volumes were classified semi-quantitatively into three categories: strong (1.8 to 2.8 A), medium The model refinements were performed in two steps.…”

“…There has been significant success in the development of distamycin analogs in which one or more of the pyrrole rings are substituted with an imidazole ring (lexitropsins) (Lown et al, 1986;Wade & Dervan, 1987;Wade et al, 1993;Lown, 1994). Lexitropsins utilize the side-by-side 2:1 binding mode to target the minor groove of mixed G,C-and A,T-containing sites, with the imidazole nitrogen targeting the guanine 2-amino group (Mrksich et al, 1992;Geierstanger et al, 1994a;Geierstanger et al, 1994b). The design of sequence-specific minor groove binding ligands requires consideration of sequence-dependent groove width as a major determinant of binding motif, as well as specific hydrogen bonds to the floor of the minor groove by pyrrolecarboxamides and imidazolecarboxamides.…”

“…Several lexitropsin:DNA complexes have been characterized structurally, and have been found to bind in the predicted fashion to their target DNA sites (e.g. Dwyer et al, 1992;Mrksich et al, 1992;Geierstanger et al, 1994a (Kim et al, 1993a;Kim et al, 1993b), LEF-1 (for lymphoid enhancer-binding factor) (Love et al, 1995), SRY (for sex-determining region Y) (Werner et al, 1995), and purine repressor (PurR) (Schumacher et al, 1994). The wide range of sequence specificity, or lack of it, exhibited by these and other minor groove-binding proteins can be better understood in the context of our knowledge of small molecule minor groove binders.…”

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

“…[3][4][5][6] These molecules bind to specific sequences in the minor groove of DNA. 4,5,[7][8][9][10][11] Polyamides have been employed to both repress and activate the expression of specific genes. 4,[12][13][14][15][16][17][18][19] They also have interesting antiviral [20][21][22][23][24] and anticancer 12,13,[25][26][27][28][29][30] properties.…”