Probing the DNA structural requirements for facilitated diffusion

Mark Hedglin, Yaru Zhang, Patrick J. O'Brien

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

DNA glycosylases perform a genome-wide search to locate damaged nucleotides among a great excess of undamaged nucleotides. Many glycosylases are capable of facilitated diffusion, whereby multiple sites along the DNA are sampled during a single binding encounter. Electrostatic interactions between positively charged amino acids and the negatively charged phosphate backbone are crucial for facilitated diffusion, but the extent to which diffusing proteins rely on the double-helical structure DNA is not known. Kinetic assays were used to probe the DNA searching mechanism of human alkyladenine DNA glycosylase (AAG) and to test the extent to which diffusion requires B-form duplex DNA. Although AAG excises εA lesions from single-stranded DNA, it is not processive on single-stranded DNA because dissociation is faster than N-glycosidic bond cleavage. However, the AAG complex with single-stranded DNA is sufficiently stable to allow for DNA annealing when a complementary strand is added. This observation provides evidence of nonspecific association of AAG with single-stranded DNA. Single-strand gaps, bubbles, and bent structures do not impede the search by AAG. Instead, these flexible or bent structures lead to the capture of a nearby site of damage that is more efficient than that of a continuous B-form duplex. The ability of AAG to negotiate these helix discontinuities is inconsistent with a sliding mode of diffusion but can be readily explained by a hopping mode that involves microscopic dissociation and reassociation. These experiments provide evidence of relatively long-range hops that allow a searching protein to navigate around DNA binding proteins that would serve as obstacles to a sliding protein.

Original languageEnglish (US)
Pages (from-to)557-566
Number of pages10
JournalBiochemistry
Volume54
Issue number2
DOIs
StatePublished - Jan 20 2015

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3-methyladenine-DNA glycosylase
Facilitated Diffusion
Single-Stranded DNA
DNA
Nucleotides
B-Form DNA
DNA Glycosylases
Humulus
Proteins
DNA Probes
DNA-Binding Proteins
Coulomb interactions
Static Electricity
Assays
Genes
Phosphates

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Medicine(all)

Cite this

Hedglin, Mark ; Zhang, Yaru ; O'Brien, Patrick J. / Probing the DNA structural requirements for facilitated diffusion. In: Biochemistry. 2015 ; Vol. 54, No. 2. pp. 557-566.
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Probing the DNA structural requirements for facilitated diffusion. / Hedglin, Mark; Zhang, Yaru; O'Brien, Patrick J.

In: Biochemistry, Vol. 54, No. 2, 20.01.2015, p. 557-566.

Research output: Contribution to journalArticle

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