Design, synthesis, biophysical and primer extension studies of novel acyclic butyl nucleic acid (BuNA)

Kumar, Vipin; Gore, Kiran R.; Pradeepkumar, P. I.; Kesavan, Venkitasamy

doi:10.1039/c3ob41244j

Cited by 24 publications

(20 citation statements)

References 70 publications

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“…Lately, there has been an explosion in the number of investigated candidates [4–7]. We have recently reported on the base-pairing properties of isoGNA, an isomer of glycerol derived nucleic acid (Fig.…”

Section: Introductionmentioning

confidence: 99%

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Kim¹,

Punna²,

Karri³

et al. 2014

Beilstein J. Org. Chem.

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SummaryIsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.

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Section: Introductionmentioning

confidence: 99%

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Kim¹,

Punna²,

Karri³

et al. 2014

Beilstein J. Org. Chem.

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“…As some polymerases are known to display this activity in the presence of manganese at the expense of fidelity (Myers and Gelfand 1991;Grabko et al 1996), the Bst DNA polymerase does not require any special buffer conditions and is, therefore, useful in amplification reactions with RNA templates. In addition, it has been found that the Bst DNA polymerase can accept a very wide range of unusual nucleic acids as templates (Chaput et al 2003;Jackson et al 2019) and incorporates modified nucleotides (Kumar et al 2013;R€ othlisberger et al 2017). The great impact in isothermal amplification methods of the Bst DNA polymerase, and thus its commercial success, has led to the development of modified versions comprising useful features such as "warm start", improved thermal stability, and reverse transcriptase activity (Lee et al 2016).…”

Section: Dna Polymerasesmentioning

confidence: 99%

Isothermal amplifications – a comprehensive review on current methods

Glökler

Lim

Ida

et al. 2021

Critical Reviews in Biochemistry and Molecular Biology

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The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.

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“…Kumar et al. designed butyl nucleic acid (BuNA), another isomer of GNA [38] . The C2 linker of the main chain in GNA is extended to a C3 linker in BuNA, corresponding to the number of atoms in the ribose scaffold in DNA and RNA (Figure 5).…”

Section: Negatively Charged Acyclic Xna Oligomersmentioning

confidence: 99%

Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers

Murayama

Asanuma

2021

ChemBioChem

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Xeno nucleic acids (XNAs) are analogues of DNA and RNA that have a non‐ribose artificial scaffold. XNAs are possible prebiotic genetic carriers as well as alternative genetic systems in artificial life. In addition, XNA oligomers can be used as biological tools. Acyclic XNAs, which do not have cyclic scaffolds, are attractive due to facile their synthesis and remarkably high nuclease resistance. To maximize the performance of XNAs, a negatively charged backbone is preferable to provide sufficient water solubility; however, acyclic XNAs containing polyanionic backbones suffer from high entropy cost upon duplex formation, because of the high flexibility of the acyclic nature. Herein, we review the relationships between the structure and duplex hybridization properties of various acyclic XNA oligomers with polyanion backbones.

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Design, synthesis, biophysical and primer extension studies of novel acyclic butyl nucleic acid (BuNA)

Cited by 24 publications

References 70 publications

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid

Isothermal amplifications – a comprehensive review on current methods

Design and Hybridization Properties of Acyclic Xeno Nucleic Acid Oligomers

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