Arginine Arrangement of Bacteriophage λ N‐Peptide Plays a Role as a Core Motif in GNRA Tetraloop RNA Binding

Abstract

A simple α-helical N-model-peptide was designed to investigate the role of the arginine-rich motif of bacteriophage λ N-peptide in selective binding with boxB RNA. The five-arginine arrangement of native N-peptide was retained; all other residues were replaced with alanine. In vitro selection of RNA (30 random-nucleotide region) was carried out with N-model-peptide immobilized on a 27 MHz quartz-crystal microbalance (QCM). Selected RNAs were evaluated on the same QCM plate to obtain binding constants (Ka =10(7) -10(8) M(-1) ). Many selected RNAs contained GNR(N)A-type loops (similar to the boxB RNA motif recognized by the native N-peptide). Fragments and minimal RNAs containing the GNRA-type loop also bound to N-model-peptide (Ka =10(6) -10(7) M(-1) ). The RNA recognition specificity of the peptide was studied by changing the "closing" U-A base pair and one base in the tetraloop of the RNA aptamers, and by peptide mutations (18th residue of N-model-peptide). It was concluded that the five-arginine arrangement of the peptide performs selective recognition of the GNRA tetraloop and GNR(N)A pentaloop RNA structures, and that substitution of another functional amino acid residue at the 18th position in N-peptide adds the recognition ability for a loop-RNA sequence.

Introducing Structure–Energy Concepts of RNA at the Undergraduate Level: Nearest Neighbor Thermodynamics and NMR Spectroscopy of a GAGA Tetraloop

“…The GNRA tetraloop acts primarily as a building block to stitch together distant elements of RNA structure; thus, it is a tertiary motif that helps “shape” the function of RNA . Given their importance in biology, the physicochemical properties of GNRA tetraloops have been well-studied. − Several complete NMR chemical shift data sets of GNRA tetraloops have been published, , from which signature spectroscopic features can be deduced.…”

Corroboration of Zn(ii)–Mg(ii)-tertiary structure interplays essential for the optimal catalysis of a phosphorothiolate thiolesterase ribozyme

“…In addition to the integral roles of metal ions in RNA folding and its catalytic function, the tertiary RNA structure and function can be further supported by long-range interactions between RNA hairpins capped by GNRA (where N represents any nucleotide; R is a purine) tetraloops and their receptors, 19–21 including RNA motifs 19,22 and proteins. 23 GNRA tetraloops were first identified in ribosomal RNA (rRNA) and are frequently used to cap RNA duplexes in rRNA. 24 Thus, GNRA tetraloop–receptor interactions can be critical to optimizing the conformations and catalytic functions of ribozymes.…”