Targeting G-Quadruplexes with PNA Oligomers
The growing interest in G-quadruplex (G4) structure and function is motivating intense efforts to develop G4-binding ligands. This chapter describes the design and testing of peptide nucleic acid (PNA) oligomers, which can bind to G4 DNA or RNA in two dis
- PDF / 368,553 Bytes
- 13 Pages / 504.567 x 720 pts Page_size
- 42 Downloads / 183 Views
1
Introduction With each passing year, our understanding of the complexity of genome structure and the mechanisms by which gene expression is regulated continues to grow. The guanine quadruplex (G4) [1] is a non-duplex DNA and RNA structure that is believed to play important regulatory roles at all stages of gene expression, including transcription, splicing, mRNA export and localization, translation and miRNA maturation [2–4]. The increased scrutiny of G4 biology is motivating intense efforts to design and synthesize molecules capable of binding G-quadruplexes and modulating their function. Molecular recognition of G4 structures can be approached from either a shape- or sequence-based perspective (Fig. 1). Small molecules and proteins (e.g., antibodies) recognize the threedimensional shape of a quadruplex, finding potential elements of complementarity in the planar tetrad surfaces, the concave grooves and the loops that connect adjacent corners of the structure. The challenge of shape-based recognition, particularly via small molecules, is generalization: once a small molecule has been identified that can bind a particular quadruplex with high affinity and selectivity, translating that result to a different quadruplex is not necessarily straightforward [5].
Danzhou Yang and Clement Lin (eds.), G-Quadruplex Nucleic Acids: Methods and Protocols, Methods in Molecular Biology, vol. 2035, https://doi.org/10.1007/978-1-4939-9666-7_20, © Springer Science+Business Media, LLC, part of Springer Nature 2019
333
334
Bruce A. Armitage
Fig. 1 Recognition modes for G-quadruplexes. Small molecules bind via shape-based recognition, whereas oligonucleotides bind via sequence-based recognition and can form either complementary heteroduplexes or homologous heteroquadruplexes
In contrast, sequence-based recognition requires that the G4 structure be disrupted in order to “read” the H-bonding groups on the individual nucleotides. There are actually two sequence-based approaches to recognizing G4s: complementary oligonucleotides can bind via standard Watson-Crick base pairing to form heteroduplexes, whereas homologous oligonucleotides can form heteroquadruplexes, via G-tetrad formation. In principle, any synthetic oligonucleotide can be designed to recognize G4s by either complementary or homologous hybridization. This chapter highlights our work with peptide nucleic acid (PNA) oligomers, which can successfully invade folded G4 structures via both binding modes. The presence of a stable quadruplex fold in the target nucleic acid imposes kinetic and thermodynamic barriers to hybridization by synthetic oligonucleotides. The lack of a negative charge on the PNA backbone and the documented high affinity of PNA [6, 7] and, even more so, its second generation analogue γPNA [8, 9] (Chart 1), allows oligomers based on these backbones to successfully target G4s to form stable heteroduplex and heteroquadruplex structures. In fact, both complementary and homologous PNAs have been shown to invade stable DNA and RNA G4s with low nanomolar KD v
Data Loading...
