Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids

Abstract

Regulation of genetic functions based on targeting DNA or RNA sequences with complementary oligonucleotides is especially attractive in the post-genome era. Oligonucleotides can be rationally designed to bind their targets based on simple nucleic acid base pairing rules. However, the use of natural DNA and RNA oligonucleotides as targeting probes can cause numerous off-target effects. In addition, natural nucleic acids are prone to degradation in vivo by various nucleases. To address these problems, nucleic acid mimics such as peptide nucleic acids (PNA) have been developed. They are more stable, show less off-target effects, and, in general, have better binding affinity to their targets. However, their high affinity to DNA can reduce their sequence-specificity. The formation of alternative DNA secondary structures, such as the G-quadruplex, provides an extra level of specificity as targets for PNA oligomers. PNA probes can target the loops of G-quadruplex, invade the core by forming PNA-DNA guanine-tetrads, or bind to the open bases on the complementary cytosine-rich strand. Not only could the development of such G-quadruplex-specific probes allow regulation of gene expression, but it will also provide a means to clarify the biological roles G-quadruplex structures may possess.

PPG Peptide Nucleic Acids that Promote DNA Guanine Quadruplexes

“…12 In our previous work, we discovered that short, guanine-rich PNA oligomers could invade and bind to plasmid DNA (Figure 1b). 13 We showed that invasion of duplex DNAdepends on PNA binding to its target sequence by Watson-Crick hydrogen bonding and on quadruplex formation of the displaced DNA strand. 13 Using PNA to promote quadruplex formation in this manner could work in conjunction with other strategies to target quadruplexes, such as small molecules 14 and anti-bodies for specific G-rich sequences.…”

“…13 We showed that invasion of duplex DNAdepends on PNA binding to its target sequence by Watson-Crick hydrogen bonding and on quadruplex formation of the displaced DNA strand. 13 Using PNA to promote quadruplex formation in this manner could work in conjunction with other strategies to target quadruplexes, such as small molecules 14 and anti-bodies for specific G-rich sequences. 15 Since there is a large structural diversity in DNA quadruplexes, combining strategies may also help improve specificity of targeting one type of G-quadruplex over others.…”

G-Quadruplex Formation Between G-Rich PNA and Homologous Sequences in Oligonucleotides and Supercoiled Plasmid DNA

“…Stabilization of such structures may result in alteration of gene expression and could potentially bring therapeutic benefits [3,4]. For this purpose, numerous small planar molecules that bind specifically to G-quadruplexes have been developed [5][6][7]; however, most of these small molecules bind G-tetrads via intercalation and base stacking that is nonselective among different types of quadruplexes.…”

“…Another strategy to stabilize quadruplexes involves targeting the complementary strand of G-rich sequences with short peptide nucleic acids (PNA) [8][9][10] (reviewed in [3]). This approach is based on the earlier observation that PNA invade plasmid DNA more effectively at the target sequences that can form secondary structures, such as cruciforms [11].…”

“…Nonetheless, G 4 N 4 G 4 sequences are very common among the potential quadruplex-forming sequences in human genome. We found total 8959 G [3][4][5] N [3][4][5] G [3][4][5] N [3][4][5] G [3][4][5] N [3][4][5] G [3][4][5] sequences within 2 kb of gene coding regions in human genome. Of these, 6372 contain G 4 N 4 G 4 motif; G 4 T 4 G 4 sequences are found in the GNAI3, SMARCC2, and PLA2G4D genes.…”