Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

Abstract

Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure as well as the physical-chemical and pairing properties of DNA and RNA and for probing protein-nucleic acid interactions. In this article we review research conducted by our laboratory over the past two decades with a focus on crystal structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailormade properties, including pairing specificity, nuclease resistance and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids.

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

“…However, the 2′-O-Me modification of RNA leads to increased stability over unmodified RNA even though the crucial hydrogen bond donating capacity of the 2′-hydroxyl is lost. While this has been suggested to be associated with a “clathrate-like H 2 O structure 25,30 ” in the major groove the present model can be used to explain this observation. Simply, replacement of the 2′-hydroxyl proton with a methyl group makes sampling of the O3′ orientation forbidden, thereby further favoring the equilibrium towards the base orientation, leading to intrinsic stabilization of the A-form conformation of the phosphodiester backbone.…”

Molecular Modeling in Nucleic Acid‐Targeted Drug Design

“…Over the past decades, a large number of artificial oligonucleotides were synthesized with modifications occurring in the phosphodiester, sugar, or nucleobase moiety, which were shown to be resistant to chemical degradation and were able to selectively hybridize to target nucleic acids with strong affinity [57,58]. They were proved to be capable of hybridizing with the complementary DNA or RNA sequence with substantial increased thermal stabilities compared to the parent DNA: DNA or DNA: RNA duplexes, which made themselves promising candidates for clinical applications [59].…”

The many twists and turns of DNA: template, telomere, tool, and target

“…There are numerous structure determinations of CNAs and for in-depth reviews and discussion of this topic, please see the updates by Egli and Pallan [62,63•]. Recent publications of chemical modifications and studies of their structural consequences concern all basic components of DNA, sugar, phosphate and base, and we will discuss them in this order.…”