Loop and Backbone Modifications of Peptide Nucleic Acid Improve G-Quadruplex Binding Selectivity

Abstract

Targeting guanine (G) quadruplex structures is an exciting new strategy with potential for controlling gene expression and designing anticancer agents. Guanine-rich peptide nucleic acid (PNA) oligomers bind to homologous DNA and RNA to form hetero-G-quadruplexes but can also bind to complementary cytosine-rich sequences to form heteroduplexes. In this study, we incorporated backbone modifications into G-rich PNAs to improve the selectivity for quadruplex vs duplex formation. Incorporation of abasic sites as well as chiral modifications to the backbone were found to be effective strategies for improving selectivity as shown by UV-melting and surface plasmon resonance measurements. The enhanced selectivity is due primarily to decreased affinity for complementary sequences, since binding to the homologous DNA to form PNA-DNA heteroquadruplexes retains high affinity. The improved selectivity of these PNAs is an important step toward using PNAs for regulating gene expression by G quadruplex formation.

Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures

“…An alternative strategy relies on sequence-based recognition, where complementary C-rich oligonucleotides bind via Watson-Crick base pairing to form heteroduplexes [7][8][9][10] or homologous G-rich oligonucleotides bind via Hoogsteen-based G-tetrad formation to yield heteroquadruplexes. [11][12][13][14][15] Peptide nucleic acid (PNA) probes can bind to G-quadruplexes by either of these mechanisms, leading to stable hybrid structures.…”

“…Our recent focus has been on PNA-DNA/RNA heteroquadruplex formation, based on the high affinity (low nanomolar K d s) of the PNA for its homologous DNA 11,13,14 and RNA 12,16 targets, as well as excellent sequence discrimination for homologous versus complementary targets that can be achieved through PNA backbone modification. 14 Short PNAs consisting of two G 2…”

Chemistry Can Make Strict and Fuzzy Controls for Bio-Systems: DNA Nanoarchitectonics and Cell-Macromolecular Nanoarchitectonics

“…Incorporation of abasic sites to γ-PNA was useful to improve the selectivity of G-quadruplex formation vs. duplex formation. 194 It is interesting that, even with conventional PNA (the left in Figure 4a), only one PNA strand can invade double-stranded DNA when it is conjugated with a positively charged nuclear localization signal peptide (a PKKKRKV peptide is attached to the terminus of PNA). 152 The conjugate is easily transfected into cells without any transfection agent and preferentially localized in nuclei there.…”

Nucleotides and nucleic acids; oligo- and polynucleotides

“…57 PNA oligomers have been used to stabilise G-quadruplex structures by targeting the PNA to the cytidine-rich complementary regions of the G-quadruplex, 58 as well as by formation of hetero-G-quadruplexes. 59 Other applications to which PNA has been applied include the templatedirected formation of oligosaccharide constructs using oligosaccharide-PNA conjugates to attempt to mimic the HIV carbohydrate epitope. 60 Charge transport has been investigated in PNA oligomers using PNAferrocene conjugates attached to a gold electrode; it was shown that charge transport through PNA follows the same pattern as found in DNA which is dependent on the oxidation potential of the nucleobases.…”

“…279 Kool and coworkers have synthesised two sets of benzohomologated nucleosides; the four size-expanded (dxN) nucleosides, e.g. dxC (59) and dxG (60) were individually incorporated into M13 phage and the replication measured in E.coli where it was found that, in spite of the increased size of the nucleobases, they were efficiently replicated. 280 The second set are widened nucleosides (dyN), such as dyA (61) and dyT (62) which have been assayed for polymerase extension opposite their natural nucleobases with Klenow fragment and the repair enzyme Dpo4.…”