2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Abstract

2′-Deoxy-2′-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A-and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A-and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing

“…ILF2/3 also bound an RNA-RNA duplex, as expected 34 , but not a DNA-RNA duplex. Because RNA-RNA, 2′-F ASO–RNA and 2′-MOE ASO–RNA duplexes are all A-form helices 35, 36 , whereas DNA-RNA duplexes form helices intermediate between A- and B-form 37 , the interaction of ILF2/3 with heteroduplexes is more complex than mere recognition of an A-form helix. The 2′-MOE side chain resides in the minor groove of the heteroduplex, which, together with its hydration shell, adds steric bulk 36 .…”

“…The 2′-deoxy-2′-fluoroarabinonucleic acid (2′-F-ANA) (Fig. 1a) ASO is a stereoisomer of the 2′-F ASO, with the fluorine at the 2′ position having inverted stereochemistry 37, 39 . 2′-F-ANA–RNA duplexes form helices intermediate between A- and B-form 37 .…”

“…1a) ASO is a stereoisomer of the 2′-F ASO, with the fluorine at the 2′ position having inverted stereochemistry 37, 39 . 2′-F-ANA–RNA duplexes form helices intermediate between A- and B-form 37 . Consistent with the DNA-RNA duplex data, there was a marked decrease in binding of ILF2/3 to the 2′-F-ANA ASO–RNA duplex compared to binding to the 2′-F ASO–RNA duplex (Fig.…”

Insights from Crystallographic Studies into the Structural and Pairing Properties of Nucleic Acid Analogs and Chemically Modified DNA and RNA Oligonucleotides

“…In a B-form duplex environment, FANA-T adopted an O4 -endo sugar conformation (4), and subsequent crystal structures of A-form DNA duplexes containing single ANA or FANA residues and of B-form DNA duplexes with incorporated ANA residues provided good evidence for different conformational preferences by ANA and FANA (51). Thus, sugar puckers of FANA residues are restricted to the North-East quadrant of the pseudorotation phase cycle (C3 -endo and C4 -exo in the A-form and O4 -endo in the B-form duplex environments).…”

Crystallization and preliminary X-ray analysis ofEscherichia coliRNase HI–dsRNA complexes

“…In addition, the interpretation of the large amount of functional data with regard to the dependence of E. coli or human RNase H cleavage activity on location and nature of chemical modifications in the DNA strand (Lima et al, 2004) would greatly benefit from the three-dimensional structures of enzyme-substrate and enzyme-inhibitor complexes. Our recent investigation of the conformational preferences of DNA duplexes with incorporated 2 0 -FANA residues provided evidence that this analog is unable to adopt a Southern pucker (Li et al, 2006). This observation begs the following questions: (i) does the enzyme tolerate a limited range of conformations of the DNA or AON strand paired to RNA?…”