A short DNA sequence confers strong bleomycin binding to hairpin DNAs

Chenhong Tang, Ananya Paul, Mohammad P. Alam, Basab Roy, W. David Wilson, Sidney Hecht

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Bleomycins A5and B2were used to study the structural features in hairpin DNAs conducive to strong BLM-DNA interaction. Two members of a 10-hairpin DNA library previously found to bind most tightly to these BLMs were subsequently noted to share the sequence 5′-ACGC (complementary strand sequence 5′-GCGT). Each underwent double-strand cleavage at five sites within, or near, an eight base pair region of the DNA duplex which had been randomized to create the original library. A new hairpin DNA library was selected based on affinity for immobilized Fe(III)·BLM A5. Two of the 30 newly identified DNAs also contained the sequence 5′-ACGC/5′-GCGT. These DNAs bound to the Fe(II)·BLMs more tightly than any DNA characterized previously. Surface plasmon resonance confirmed tight Fe(III)·BLM B2binding and gave an excellent fit for a 1:1 binding model, implying the absence of significant secondary binding sites. Fe(II)·BLM A5was used to assess sites of double-strand DNA cleavage. Both hairpin DNAs underwent double-strand cleavage at five sites within or near the original randomized eight base region. For DNA 12, four of the five double-strand cleavages involved independent single-strand cleavage reactions; DNA 13 underwent double-strand DNA cleavage by independent single-strand cleavages at all five sites. DNA 14, which bound Fe·BLM poorly, was converted to a strong binder (DNA 15) by insertion of the sequence 5′-ACGC/5′-GCGT. These findings reinforce the idea that tighter DNA binding by Fe·BLM leads to increased double-strand cleavage by a novel mechanism and identify a specific DNA motif conducive to strong BLM binding and cleavage.

Original languageEnglish (US)
Pages (from-to)13715-13726
Number of pages12
JournalJournal of the American Chemical Society
Volume136
Issue number39
DOIs
StatePublished - Sep 4 2014

Fingerprint

DNA sequences
Bleomycin
DNA
DNA Cleavage
Gene Library
Nucleotide Motifs
Surface Plasmon Resonance
Insertional Mutagenesis
Base Pairing
Libraries
Surface plasmon resonance
Binding sites
Binding Sites
Binders

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

A short DNA sequence confers strong bleomycin binding to hairpin DNAs. / Tang, Chenhong; Paul, Ananya; Alam, Mohammad P.; Roy, Basab; Wilson, W. David; Hecht, Sidney.

In: Journal of the American Chemical Society, Vol. 136, No. 39, 04.09.2014, p. 13715-13726.

Research output: Contribution to journalArticle

Tang, Chenhong ; Paul, Ananya ; Alam, Mohammad P. ; Roy, Basab ; Wilson, W. David ; Hecht, Sidney. / A short DNA sequence confers strong bleomycin binding to hairpin DNAs. In: Journal of the American Chemical Society. 2014 ; Vol. 136, No. 39. pp. 13715-13726.
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