pH-controlled DNA- and RNA-templated assembly of short oligomers

Barbeyron, Renaud; Vasseur, Jean‐Jacques; Smietana, Michaël

doi:10.1039/c4sc03028a

Cited by 23 publications

(22 citation statements)

References 52 publications

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“…Hence, in the presence of a 3 0 -ended ribonucleotide partner, the dynamic and reversible formation of a boronic ester internucleoside linkage provided an efficient means to covalently link the two ODN partners (Scheme 40). [358][359][360] The linkage can be reversibly directed by controlling the pH, temperature or anion concentration. Melting temperature experiments showed that the presence of the bn linkage induced a strong destabilization compared to the analogous non-modified duplex.…”

Section: Rsc Chemical Biology Reviewmentioning

confidence: 99%

Modified internucleoside linkages for nuclease-resistant oligonucleotides

et al. 2021

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Section: Rsc Chemical Biology Reviewmentioning

confidence: 99%

Modified internucleoside linkages for nuclease-resistant oligonucleotides

et al. 2021

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“…A note on the use of borate for nucleoside assembly. While borate has been proposed to have played a role in the selection of ribose,56 and to link nucleic acids together,57 the use of borate in our study of TAP nucleosides and cyanuric acid was borne out of necessity to form water‐soluble assemblies. As we learned from our initial rosette assembly study,50 the formation of water‐soluble noncovalent linear structures requires steric blocking of one face of TAP, obtained by ribose coupling, and the incorporation of a solubilizing charge.…”

Section: Consideration Of Alternative Base Pairs In Proto‐rnamentioning

confidence: 99%

Was a Pyrimidine‐Pyrimidine Base Pair the Ancestor of Watson‐Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA

Cafferty

Hud

2015

Israel Journal of Chemistry

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Uncovering the origin of RNA is essential for understanding the origins of life. The persistent inability of chemists to identify a plausible prebiotic route to RNA polymers, along with the seemingly optimal structure of RNA for its functions in extant life, argue in favor of the hypothesis that RNA is a product of chemical or biological evolution. To understand the origin of RNA, we must consider which molecules could have originally acted in place of RNA’s substructures (i.e., nucleobases (the recognition units), ribose (a trifunctional connector), and phosphate (an ionized linker)) in the oldest ancestor of RNA (or proto‐RNA). Major challenges to uncovering the chemical structure of proto‐RNA include finding molecules that would have spontaneously undergone molecular selection and covalent assembly into an RNA‐like polymer, within the complex mixture of the “prebiotic soup” and without the aid of enzymes. In this review, we discuss progress towards identifying the recognition units of proto‐RNA and mechanisms by which the ancestral nucleobases might have been originally selected and incorporated into polymers. We consider possible proto‐nucleobases within the chemical space of the heterocycles defined by the purines and pyrimidines that have H, NH2, or O as exocyclic groups (which includes the extant nucleobases). Taking into account the results of numerous experiments that have explored nucleic acids with alternative backbones and noncanonical nucleobases, we are able to remove about half of these 81 molecules from candidacy as ancestral nucleobases. A particularly encouraging result of this approach is the identification of two molecules, 2,4,6‐triaminopyrimidine and barbituric acid, which look very promising as possible nucleobases of proto‐RNA.

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“…Even autotemplated duplex self-assembly representing a model of sequence-defined synthetic polymers has been examined by borononucleic acids. 22 …”

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DNA-Templated N(Me)-Alkoxyamine Glycosylation

2018

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The potential of N(Me)-alkoxyamine glycosylation as a DNA-templated ligation has been studied. On a hairpin stem-template model, a notable rate enhancement and an increased equilibrium yield are observed compared to the corresponding reaction without a DNA catalyst. The N-glycosidic connection is dynamic at pH 5, whereas it becomes irreversible at pH 7. The N(Me)-alkoxyamine glycosylation may hence be an attractive pH controlled reaction for the assembly of DNA-based dynamic products.

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pH-controlled DNA- and RNA-templated assembly of short oligomers

Abstract: A stimuli-responsive enzyme-free and activator-free DNA- and RNA-templated assembly of bifunctional short oligonucleotides is reported.

Cited by 23 publications

References 52 publications

Modified internucleoside linkages for nuclease-resistant oligonucleotides

Modified internucleoside linkages for nuclease-resistant oligonucleotides

Was a Pyrimidine‐Pyrimidine Base Pair the Ancestor of Watson‐Crick Base Pairs? Insights from a Systematic Approach to the Origin of RNA

DNA-Templated N(Me)-Alkoxyamine Glycosylation

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