7KZL

Cyclopentane peptide nucleic acid in complex with DNA

Summary for 7KZL

• Entry DOI: 10.2210/pdb7kzl/pdb
• Descriptor: DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3'), XDJ-XDD-XDY-XDJ-XDY-XDJ-XDD-XDY-XDD-XDV, IODIDE ION, ... (7 entities in total)
• Functional Keywords: peptide nucleic acid, pna, peptide nucleic acid-dna complex, peptide nucleic acid/dna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 6373.46

Authors

Botos, I.,Appella, D.H. (deposition date: 2020-12-10, release date: 2020-12-23, Last modification date: 2024-10-09)

Primary citation

Zheng, H.,Botos, I.,Clausse, V.,Nikolayevskiy, H.,Rastede, E.E.,Fouz, M.F.,Mazur, S.J.,Appella, D.H.
Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA.
Nucleic Acids Res., 49:713-725, 2021

PubMed Abstract: We report a series of synthetic, nucleic acid mimics with highly customizable thermodynamic binding to DNA. Incorporation of helix-promoting cyclopentanes into peptide nucleic acids (PNAs) increases the melting temperatures (Tm) of PNA+DNA duplexes by approximately +5°C per cyclopentane. Sequential addition of cyclopentanes allows the Tm of PNA + DNA duplexes to be systematically fine-tuned from +5 to +50°C compared with the unmodified PNA. Containing only nine nucleobases and an equal number of cyclopentanes, cpPNA-9 binds to complementary DNA with a Tm around 90°C. Additional experiments reveal that the cpPNA-9 sequence specifically binds to DNA duplexes containing its complementary sequence and functions as a PCR clamp. An X-ray crystal structure of the cpPNA-9-DNA duplex revealed that cyclopentanes likely induce a right-handed helix in the PNA with conformations that promote DNA binding.

PubMed: 33406227
DOI: 10.1093/nar/gkaa1249

Experimental method

X-RAY DIFFRACTION (1.3 Å)