ArticleNucleic acids research2017
Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Comparative investigation of uridine and Hachimoji RNA base interaction with single-walled carbon nanotube.Journal of molecular modeling · 2026Article
- Engineering and Assay of Enzymes for Expanded Genetic Alphabet Replication.Biochemistry · 2025Article
- Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA.Scientific reports · 2023Article
- High-Order Quantum-Mechanical Analysis of Hydrogen Bonding in Hachimoji and Natural DNA Base Pairs.Journal of chemical information and modeling · 2023Article
- Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study.Computational and structural biotechnology journal · 2021Article
- Building better polymerases: Engineering the replication of expanded genetic alphabets.The Journal of biological chemistry · 2020Review
- The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Review
- Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase.Protein science : a publication of the Protein Society · 2020Article
- Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide.Nucleic acids research · 2018Article
- Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).ACS synthetic biology · 2017Article
- Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.Accounts of chemical research · 2017Review
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Z: Little is known about the influence of multiple consecutive 'non-standard' ( , 6-amino-5-nitro-2(1H)-pyridone, and , 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one) nucleobase pairs on the structural parameters of duplex DNA. nucleobase pairs follow standard rules for Watson-Crick base pairing but have rearranged hydrogen bonding donor and acceptor groups. Using the X-ray crystal structure as a starting point, we have modeled the motions of a DNA duplex built from a self-complementary oligonucleotide (5΄-CTTATPPPZZZATAAG-3΄) in water over a period of 50 μs and calculated DNA local parameters, step parameters, helix parameters, and major/minor groove widths to examine how the presence of multiple, consecutive nucleobase pairs might impact helical structure. In these simulations, the -containing DNA duplex exhibits a significantly wider major groove and greater average values of stagger, slide, rise, twist and h-rise than observed for a 'control' oligonucleotide in which nucleobase pairs are replaced by . The molecular origins of these structural changes are likely associated with at least two differences between and . First, the electrostatic properties of differ from in terms of density distribution and dipole moment. Second, differences are seen in the base stacking of pairs in dinucleotide steps, arising from energetically favorable stacking of the nitro group in with π-electrons of the adjacent base.
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