Comparative analysis of inosine-substituted duplex DNA by circular dichroism and X-ray crystallography
Autor: | Martin Egli, L. James Maher, Ewa A. Kowal, Pradeep S. Pallan, Justin P. Peters |
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Jazyk: | angličtina |
Rok vydání: | 2017 |
Předmět: |
0301 basic medicine
Models Molecular Circular dichroism Stereochemistry Stacking Oligonucleotides Base analog Crystal structure 010402 general chemistry Crystallography X-Ray 01 natural sciences Article 03 medical and health sciences chemistry.chemical_compound Structural Biology Molecular Biology Oligonucleotide Circular Dichroism General Medicine DNA Inosine 0104 chemical sciences Crystallography 030104 developmental biology chemistry Duplex (building) X-ray crystallography Nucleic Acid Conformation Thermodynamics |
Popis: | 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. |
Databáze: | OpenAIRE |
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