Rnahybrid online dating

Where ANA contains a hydroxyl group, 2′F-ANA contains fluorine (Figure 1A).The most extensive structural studies of ANA•RNA and 2′F-ANA•RNA duplexes to date, performed on short hairpins with modified stems, observed no major conformational differences between them—neither in sugar pucker nor hydrogen bonding nor steric effects (1,2).This duplex is ideal for studying the origin of the difference in thermal stability between ANA•RNA and 2′F-ANA•RNA because it is representative of prototypical hybrids and because the difference in ) to ensure the highest applicability of the current study to the field of antisense therapeutics.Oligonucleotides were synthesized from phosphoramidite precursors using standard solid-phase methods. Purification of oligonucleotides was carried out using denaturing PAGE and ion-pairing HPLC.Assignment of baselines was very clear in most cases.Curves with flaws in the baseline were discarded without analysis.

All UV spectroscopy was carried out in a Cary 300 or Cary 5000 UV spectrophotometer (Varian).For the lower-melting samples at low salt concentrations, baselines were of necessity short and somewhat ambiguous, and we chose a lower baseline that was parallel to the long upper baseline for the sake of consistency.For other curves, if there was ambiguity about the lower baseline, we chose the lowest linear region or in severe cases, discarded the run.No dramatic differences are found in terms of relative hydration for the two hybrids, but the ANA•RNA duplex showed lower uptake of counterions than its 2′F-ANA•RNA counterpart.Finally, while the two hybrid duplexes are of similar rigidities, 2′F-ANA single strands may be more suitably preorganized for duplex formation.

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Comparison between the solution structure of 2′F-ANA•RNA and ANA•RNA hybrids indicates that the increased binding affinity of 2′F-ANA is related to several subtle differences, most importantly a favorable pseudohydrogen bond (2′F–purine H8) which contrasts with unfavorable 2′-OH–nucleobase steric interactions in the case of ANA.

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