Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

Abstract

Discerning the structural building blocks of macromolecules is essential for understanding their folding and function. For a new generation of modified nucleic acid ligands (called slow off-rate modified aptamers or SOMAmers), we previously observed essential functions of hydrophobic aromatic side chains in the context of well-known nucleic acid motifs. Here we report a 2.45-Å resolution crystal structure of a SOMAmer complexed with nerve growth factor that lacks any known nucleic acid motifs, instead adopting a configuration akin to a triangular prism. The SOMAmer utilizes extensive hydrophobic stacking interactions, non-canonical base pairing and irregular purine glycosidic bond angles to adopt a completely non-helical, compact S-shaped structure. Aromatic side chains contribute to folding by creating an unprecedented intercalating zipper-like motif and a prominent hydrophobic core. The structure provides compelling rationale for potent inhibitory activity of the SOMAmer and adds entirely novel motifs to the repertoire of structural elements uniquely available to SOMAmers.

Conformational Rigidity within Plasticity Promotes Differential Target Recognition of Nerve Growth Factor

“…Also available are the structures of NGF bound to its receptors (Wiesmann et al, 1999; He and Garcia, 2004; Wehrman et al, 2007; Feng et al, 2010), neutralizing antibodies (Covaceuszach et al, 2008; La Porte et al, 2014), and small ligands, such as lysophospholipids (Tong et al, 2012; Sun and Jiang, 2015) and DNA-aptamers (Jarvis et al, 2015). These studies have led to an emerging picture of the binding determinants on NGF to its key receptors.…”

“…The N-terminus in recombinant human NGF (hNGF) or mouse proNGF in complex with p75 NTR are not defined (He and Garcia, 2004; Feng et al, 2010). Only in the hNGF/TrkA complex (Wiesmann et al, 1999; Wehrman et al, 2007) and in one of the two protomers of a complex with a DNA aptamer (Jarvis et al, 2015), is the N-terminus defined and folded in an α-helix. The generally accepted view is thus that the N-terminus is disordered in the NGF unbound state (Settanni et al, 2003; Berrera et al, 2006).…”

Customised nucleic acid libraries for enhanced aptamer selection and performance

“…In these, the artificial nucleotides largely contribute to the interaction with the respective target protein [17,20]. The amide linker has been observed to contribute to the folding of SOMAmers and to the interaction with the target protein, that is by hydrogen-bonding [18,20,21 ].…”

“…In contrast to other SOMAmer structures, only a few modified nucleotides interact directly with the protein. Most of them are involved in forming hydrophobic clusters (Figure 2a,b) [21 ].…”

The expanding world of DNA and RNA

“…This question has been elegantly addressed by SomaLogic Inc., who has structurally characterized three “SOMAmers” (Slow Off-rate Modified Aptamers) which were selected against PDGF [23], IL-6 [24] or NGF [25] and where each dT is replaced by dU analogs with simple aromatic rings (typically benzyl rings) attached to the 5 position via carboxamide linkers. Mutational analysis revealed that the 8 to 10 appended aromatic rings in each SOMAmer are generally required for binding, and structural analysis revealed that they nucleate the formation of clusters that present optimal surfaces for target recognition or that act as hydrophobic cores that support unique structure formation (Figure 3).…”