Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

Abstract

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability.

Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions

“…In fact, the adenine-adenine trans Hoogsteen/Hoogsteen edge base pair is the most common of all the types of adenineadenine pairs present in the non-redundant set of RNA structures (http://ndbserver.rutgers.edu/ndbmodule/services/ BPCatalog/bpCatalog.html): around 300 instances of this studied base pair were noted. For example, the studied pair is the only one present in the parallel double helix formed by two polyadenylic acid (poly A) chains (Gleghorn et al, 2016;Ke et al, 2009;Copp et al, 2017;Petrovic & Polavarapu, 2005Kim et al, 2011;Safaee et al, 2013). Moreover, the existence of the pair in its protonated form in the double helix, exactly as in the studied crystals, with phosphate groups in the position of chlorides and with a water molecule in the same place, is well proven in acidic media.…”

Above the Epitranscriptome: RNA Modifications and Stem Cell Identity

“…In this chapter, are reported the latest findings describing the chemical modifications influencing the structure and the function of the different RNA classes: coding RNAs and noncoding-RNAs. Modifications are designed based on the type of chemical changes: N6-methyladenosine (m 6 A) [ 37 , 38 , 39 , 40 ]; Pseudouridine (Ψ), 5-methylcytosine (m 5 C) [ 41 ]; 5-hydroxymethylcytidine (hm 5 C) [ 42 , 43 , 44 ], N1-methyladenosine (m 1 A) [ 45 , 46 ], and A-to-I editing [ 47 , 48 , 49 ]. The mechanism of each modification is described in the mRNA section, as this is the first in this review.…”

Parallel poly(A) homo- and hetero-duplex formation detection with an adapted DNA nanoswitch technique

“…Although there are examples of antiparallel A-A pairing in the context of helices stabilized by other pairing or stabilizing molecules (Baeyens et al 1996;Persil et al 2004;Xing et al 2005;Jain et al 2008;Joung et al 2009;Devi et al 2015), when nucleic acid strands are only poly(A), only the parallel orientation is known to form a duplex. Copp et al (2017) have analyzed strand interactions in poly(rA) parallel duplexes when the component strands were identical in nucleic acid sequence and length. They used UV-melting and native gel analyses at different pH values to test for homo-duplex formation when modified sugars were placed in key locations of the strand (Copp et al 2017).…”

“…Copp et al (2017) have analyzed strand interactions in poly(rA) parallel duplexes when the component strands were identical in nucleic acid sequence and length. They used UV-melting and native gel analyses at different pH values to test for homo-duplex formation when modified sugars were placed in key locations of the strand (Copp et al 2017). In that study, duplex stability was enhanced in acidic conditions when 2 ′ -O-methylated sugars of adenosine (Fig.…”