DNA binding and recognition by synthetic peptides and metallopeptides

Xiaofen Huang, Purdue University

Abstract

DNA recognition by synthetic peptides and metallopeptides was investigated. Two different classes of structured peptides were examined. First, the unnatural amino acid L-2-quinoxalylalanine was synthesized and incorporated into peptide motifs containing a high population of tandem β-turns derived from the carboxy-terminal domain of RNA polymerase II. The resulting quinoxaline-containing peptides structurally resemble the quinoxaline antitumor antibiotics triostin A and echinomycin, however, these hybrid peptides were found to bind to A/T-rich regions in the minor groove of the DNA helix in comparison to the G/C preference of the quinoxaline antibiotics. These modified peptides also likely adopt a partial intercalation mode of DNA binding. The β-turn peptide backbone, instead of the intercalative quinoxaline ring, plays an important role in the interaction with DNA and quite possibly, is the dominant force in the DNA sequence-selective interaction. Metallopeptides of the general form Ni(II)•Xaa-Xaa-His, which can induce DNA strand scission via a minor groove interaction upon activation, were systematically investigated using a positional scanning combinatorial procedure employing naturally-occurring L-α-amino acids. Substitutions at both Xaa positions of the metallopeptides with a certain set of amino acids, specifically, Arg/Lys/Met/Pro at the N-terminal position and Arg/Lys/Met/Ser/Thr at the second position, can enhance their DNA cleavage ability. These enhanced metallopeptides remain bound within the minor groove and initiate DNA cleavage via a C4′-H abstraction mechanism. The increased DNA cleavage ability of the combinatorially-derived peptides is probably due to a subtle positioning of metallopeptides within the minor groove in relationship to the C4′-H target. In addition, while amino acid substitutions result in some differences in sequence selectivity, these metallopeptides maintained their preference for A/T-rich regions, most likely due to interactions that occur between the pyrrole N-H of the imidazole of His and the O2 and N-3 of T and A, respectively. Interestingly, most amino acids selected combinatorially (Pro/Arg/Lys/Ser/Thr) to enhance DNA cleavage were also found in many DNA minor groove binding motifs. Studies of these two peptide systems have furthered our understanding of peptide-DNA, protein-DNA interactions and, could assist in the future rational design or redesign of DNA binding agents.

Degree

Ph.D.

Advisors

Long, Purdue University.

Subject Area

Biochemistry|Organic chemistry

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