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Because of this high binding affinity, and many other favorable properties, 2′F-ANA has shown promise for applications as diverse as gene silencing therapeutics, diagnostics and aptamer design (9) and a 2′F-ANA-based antisense drug has received approval to begin clinical trials (10).
The elusive origin of the difference in binding affinity is therefore of significant interest: it will deepen our understanding of nucleic acid structure and binding while potentially allowing the design of derivatives with improved properties.
Initially, it was supposed that an unfavorable steric interaction involving the 2′-OH of ANA was responsible for its low binding affinity (3,7,8).
Assignment of baselines was very clear in most cases.
Curves with flaws in the baseline were discarded without analysis.
(B) Numbering scheme of the 10-mer hybrid duplexes used for this study. The corresponding hybrids are named DR, FR and AR, respectively.
Thymines are replaced by uracils in the ANA strand.
Small triethylammonium signals were visible in the NMR spectra from the ion-pairing reagent but did not interfere with an important region of the NMR spectrum.
All UV spectroscopy was carried out in a Cary 300 or Cary 5000 UV spectrophotometer (Varian).
This allowed us to study flexibility, hydration and ion uptake together with structure and conformation, bringing together spectroscopic and computational data.
The structure of the unmodified DNA•RNA duplex has been extensively studied by NMR and restrained molecular dynamics calculations, using conventional and time averaged constraints (13).
Hybrids of RNA with arabinonucleic acids 2′F-ANA and ANA have very similar structures but strikingly different thermal stabilities.