Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties

Asanuma, Hiroyuki; Kashida, Hiromu; Murayama, Keiji

doi:10.1039/d1cc05868a

Cited by 18 publications

(9 citation statements)

References 96 publications

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“…1 . While the present work was performed with PNA, the findings should translate to other oligonucleotide backbones such as aTNA or SNA. , Finally, the demonstration that a G-clamp leads to a significant reduction in hybridization to N7-G but a higher affinity to unmodified G suggests that probes could be designed to detect this natural post-transcriptional modification by competitive binding of oligomers bearing or not a G-clamp.…”

Section: Discussionmentioning

confidence: 99%

Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection)

López-Tena

Farrera-Soler

Barluenga

et al. 2023

JACS Au

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Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2–4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.

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Section: Discussionmentioning

confidence: 99%

Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection)

López-Tena

Farrera-Soler

Barluenga

et al. 2023

JACS Au

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“…Also, there are some limitations with respect to the design of PNAs. 22 Although various artificial nucleic acids have been developed, 23 their synthesis remains limited and commercially inaccessible. Each artificial nucleic acid shows unique behaviors, which make it difficult to choose the right one.…”

Section: ■ Introductionmentioning

confidence: 99%

Oligoribonucleotide-Mediated Blockade of DNA Extension by Taq DNA Polymerases Increases Specificity and Sensitivity for Detecting Single-Nucleotide Differences

2023

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Blocking PCR is a method that inhibits amplification of DNA possessing a nucleotide sequence complementary to that of a blocker; the method can be used to suppress amplification of target wild-type DNA while amplifying mutated DNA. Previously, we demonstrated that an oligoribonucleotide (ORN) functions as a cost-effective and sequence-specific blocker. This blocking PCR system, named ORN interference-PCR (ORNi-PCR), is compatible with DNA polymerases lacking 5′–3′ exonuclease activity but not with those possessing the activity (e.g., Taq DNA polymerase), which can remove a hybridized ORN during DNA extension. Here, we demonstrate that under specific experimental conditions, an intact or phosphorothioated ORN strongly suppresses extension of target DNA by Taq DNA polymerases. This method was applied successfully to real-time ORNi-PCR and one-step real-time reverse transcription-ORNi-PCR using a dual-labeled fluorescent probe to detect a single-nucleotide mutation in DNA and RNA in a sequence-specific manner. The results reaffirm the utility of blocking PCR and provide technical hints for its improvement.

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“…For example, cyanuric acid triggers the assembly of polyadenine DNA into long fibers (Figure F) . While DNA benefits from streamlined synthesis by commercial vendors, other platforms based on alternative backbones also deserve attention for the benefit they can bring to the hardware of algorithm design . Peptide nucleic acid (PNA) , has been shown to undergo HCRs as efficiently as DNA but with shorter sequences owing to the higher thermal stability of the PNA homoduplexes .…”

Section: Introductionmentioning

confidence: 99%

Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits

2022

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The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.

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Xeno nucleic acids (XNAs) having non-ribose scaffolds with unique supramolecular properties

Abstract: DNA and RNA have significance as a genetic materials, therapeutic potential, and supramolecular properties. Advances in nucleic acid chemistry have enabled large-scale synthesis of DNA and RNA oligonucleotides and oligomers...

Cited by 18 publications

References 96 publications

Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection)

Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection)

Oligoribonucleotide-Mediated Blockade of DNA Extension by Taq DNA Polymerases Increases Specificity and Sensitivity for Detecting Single-Nucleotide Differences

Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits

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