Cyclohexanyl Peptide Nucleic Acids (chPNAs) for Preferential RNA Binding:  Effective Tuning of Dihedral Angle β in PNAs for DNA/RNA Discrimination

Abstract

[structures: see text] A serious drawback of peptide nucleic acids (PNAs) from an application perspective that has not been adequately dealt with is nondiscrimination of identical DNA and RNA sequences. An analysis of the available X-ray and NMR solution structures of PNA complexes with DNA and RNA suggested that it might be possible to rationally impart DNA/RNA duplex binding selectivity by tuning the dihedral angle beta of the flexible ethylenediamine part of the PNA backbone (II) via suitable chemical modifications. Cyclohexanyl PNAs (chPNAs) with beta approximately = 65 degrees were designed on the basis of this rationale. The chPNAs introduced remarkable differences in duplex stabilities among their DNA and RNA complexes, with melting temperatures (deltaTm(RNA-DNA) = +16-50 degrees C) depending on the number of modifications and the stereochemistry. This is a highly significant, exceptional binding selectivity of a mix sequence of PNA to RNA over the same DNA sequence as that seen to date. In contrast, cyclopentanyl PNAs (cpPNAs) with beta approximately = 25 degrees hybridize to DNA/RNA strongly without discrimination because of the ring puckering of the cyclopentane ring. The high affinity of chPNAs to bind to RNA without losing base specificity will have immediate implications in designing improved PNAs for therapeutic and diagnostic applications.

Chirality as a tool in nucleic acid recognition: Principles and relevance in biotechnology and in medicinal chemistry

“…In other words, a ; (i) (1S,2R)-cis-cyclopentyl PNA (cpPNA). 173,175 mixture of enthalpic and entropic effect is expected when considering the influence of cyclic modifications of the PNA structure on the DNA and RNA binding abilities. Again, to fulfill the requirements proposed by the model in Figure 10a, substituents in the ring should be placed in a position which is able to produce the correct helical preorganization.…”

“…18h) with b 6 658 were therefore subsequently designed. 173 The chPNAs expressed remarkable differences in duplex stability with their DNA and RNA counterparts, depending on a number of modifications and stereochemistry. A highly significant preference to form a duplex with RNA as compared to DNA was observed.…”

Pyrrolidinyl peptide nucleic acid with α/β-peptide backbone

“…[15][16][17][18][19][20][21] It has been argued that the binding properties should be improved if one could restrict the conformational flexibility of the PNA backbone, for example, by locking the PNA backbone into cyclic structures [15][16][17][18] or by adding one or more substituents at a specific position of the aegPNA backbone. [19][20][21] In addition to improving binding affinity and specificity, conformational restriction should offer a possibility to selectively recognize different types of nucleic acids.…”

“…While aegPNA has been shown to bind marginally more strongly to RNA over DNA, the selectivity towards RNA has been improved by incorporating one or more cyclohexane rings into the PNA backbone. 16,17 Kinetic selectivity in RNA recognition over DNA has been observed in some pyrrolidinyl PNA variants, 22,23 although this behavior seems to be highly sequencedependent. 24,25 In a much fewer instances, preference for DNA binding over RNA has also been reported.…”

“…16,17,22,23 It is interesting to note that while the original aegPNA showed a preference for binding to RNA over DNA, substitution at the γ-position of the PNA backbone by a methyl group increased the stability of the DNA hybrids considerably more than the corresponding RNA hybrid, leading to a lower discrimination between DNA and RNA. 19 The present acpcPNA system and its aza-analog described previously by our group, 31 as well as a chimeric (aeg-pyrrolidine)PNA developed by Kumar,26 are among a few examples of PNA that show a preference for DNA binding.…”