Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography

Justin P. Peters, Ewa A. Kowal, Pradeep S. Pallan, Martin Egli, L James Maher III

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Leveraging structural biology tools, we report the results of experiments seeking to determine if the different mechanical properties of DNA polymers with base analog substitutions can be attributed, at least in part, to induced changes from classical B-form DNA. The underlying hypothesis is that different inherent bending and twisting flexibilities may characterize non-canonical B-DNA, so that it is inappropriate to interpret mechanical changes caused by base analog substitution as resulting simply from ‘electrostatic’ or ‘base stacking’ influences without considering the larger context of altered helical geometry. Circular dichroism spectra of inosine-substituted oligonucleotides and longer base-substituted DNAs in solution indicated non-canonical helical conformations, with the degree of deviation from a standard B-form geometry depending on the number of I⋅C pairs. X-ray diffraction of a highly inosine-substituted DNA decamer crystal (eight I⋅C and two A⋅T pairs) revealed an A-tract-like conformation with a uniformly narrow minor groove, reduced helical rise, and the majority of sugars adopting a C1′-exo (southeastern) conformation. This contrasts with the standard B-DNA geometry with C2′-endo sugar puckers (south conformation). In contrast, the crystal structure of a decamer with only four I⋅C pairs has a geometry similar to that of the reference duplex with eight G⋅C and two A⋅T pairs. The unique crystal geometry of the inosine-rich duplex is noteworthy given its unusual CD signature in solution and the altered mechanical properties of some inosine-containing DNAs.

Original languageEnglish (US)
Pages (from-to)1-20
Number of pages20
JournalJournal of Biomolecular Structure and Dynamics
DOIs
StateAccepted/In press - Sep 3 2017

Fingerprint

Inosine
X Ray Crystallography
Circular Dichroism
DNA
B-Form DNA
Static Electricity
Oligonucleotides
X-Ray Diffraction
Polymers

Keywords

  • A-tracts
  • B-DNA
  • circular dichroism
  • DNA topology
  • inosine
  • metal ion coordination
  • sequence-dependent helix geometry
  • X-ray crystallography

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography. / Peters, Justin P.; Kowal, Ewa A.; Pallan, Pradeep S.; Egli, Martin; Maher III, L James.

In: Journal of Biomolecular Structure and Dynamics, 03.09.2017, p. 1-20.

Research output: Contribution to journalArticle

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