Insight into the High Duplex Stability of the Simplified Nucleic Acid GNA

Abstract

More than 50 years after Watson and Crick unraveled the secondary structure of the canonical B-form DNA duplex, the function of the pyrimidine-purine nucleobase pairing and the importance of the charged phosphodiester backbone are well established.[1] However, the chemical and evolutionary necessity for the rather complicated deoxyribose and ribose moiety in the backbone of DNA and RNA, respectively, is still uncertain.[2] To address this question, researchers have investigated nucleic acids with alternative sugar residues. [3][4][5] In the course of searching for structurally simplified nucleic acid backbones, we discovered recently that a glycol nucleic acid (GNA) with an acyclic propylene glycol phosphodiester backbone can form stable antiparallel duplexes in a Watson-Crick fashion. [6][7][8][9] The constitution of the GNA backbone as well as a newly published GNA-duplex structure are shown in Figure 1.[9] The glycol nucleotide building blocks contain just three carbon atoms and one stereocenter, and are connected by phosphodiester bonds. GNA combines structural simplicity and atom economy with a high duplex stability that significantly exceeds the stabilities of analogous duplexes of DNA and RNA. These features not only make GNA a possible genetic molecule for initial life on Earth but also an interesting scaffold for nucleic acid derived nanotechnology.For almost the last two decades, it had been widely assumed that nucleic acid analogues containing a phosphodiester backbone need to be cyclic to produce the required conformational preorganization of the individual strands for the formation of a stable duplex. [10,11] The high duplex stability of GNA therefore appears very surprising. In fact, GNA is to date the only known phosphodiester-based nucleic acid with an acyclic backbone that is capable of forming stable duplexes. Herein we present data that resolve this apparent discrepancy between the acyclic nature of the GNA backbone and the high stability of GNA duplexes.To gain insight into the reason for the high duplex stability of GNA, we began by determining the thermodynamic parameters of duplex formation. Accordingly, the values of DG (Gibbs free energy), DH (change in enthalpy), and DS (change in entropy)were obtained from vant Hoff plots by charting the reciprocal of the melting temperature, T m , against the natural logarithm of varying duplex concentrations for three GNA duplexes and comparison with DNA duplexes with the same sequences ( Table 1). As expected, the higher thermal stabilities of GNA duplexes correlate with higher thermodynamic stabilities (298 K).[8] However, surprisingly, for all three duplexes we found that GNA-duplex formation is less exothermic than DNA-duplex formation, but at the same time entropically significantly less unfavorable. This entropic advantage is counterintuitive, since one would expect that an acyclic backbone is more flexible and thus entropically unfavorable for duplex formation. ÀT DS (298 K) [b] [kcal mol À1

Differential stability of 2′F-ANA•RNA and ANA•RNA hybrid duplexes: roles of structure, pseudohydrogen bonding, hydration, ion uptake and flexibility

“…The dramatic stability difference between these two very similar hybrids is therefore caused by the cumulative influence of multiple effects. Indeed, thermal stability can often be a surprisingly complex property ( 59–62 ). While it is difficult to rationally design an oligonucleotide analogue to optimize so many factors at once, keeping these factors in mind can be informative as new analogues are developed.…”

GNA/aegPNA Chimera Loaded with RNA Binding Preference

“…On the other hand, glycol nucleic acid (GNA) is a structurally simplified oligonucleotide mimic, in which the negatively charged phosphate backbone is intact, but the C5 cyclic sugar ring has been replaced by C3 acyclic chiral propylene glycol (Figure 1 b). 5a Homooligomers of GNA are known to pair very well with themselves through Watson–Crick base paring, but do not cross‐pair with either RNA or DNA 5b,c…”

Synthesis of the Phosphoramidite Units for Benzene‐Glycol Nucleic Acid

“…Conversely, Meggers et al. reported on oligonucleotides consisting of acyclic nucleoside and composed of glycol nucleic acid (GNA) (Zhang, Peritz, & Meggers, , ; Schlegel et al., ; Schlegel et al., ). The oligonucleotides can form stable duplex with complementary RNA, but DNA‐GNA chimeras show lower thermal stability than native DNA oligomer (Schlegel et al., ).…”