5′- <i>vs.</i> 3′-end sugar conformational control in shaping up dinucleotides

Jakhlal, Jouda; Castex, Stéphanie; Denhez, Clément; Petermann, Christian; Martinez, Agathe; Harakat, Dominique; Guillaume, Dominique; Clivio, Pascale

doi:10.1039/c5cc04212g

Cited by 7 publications

(14 citation statements)

References 44 publications

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“…Our results are also discussed to the light of the NS-dilocked dinucleotide T LN pT LS ( 5 ) (Fig. 2) 20 whose 3′-end is totally in a S-freezed conformation.…”

Section: Introductionmentioning

confidence: 71%

“…The synthesis of dinucleotides T LN pT ( 3 ) and TpT LN ( 4 ) has been previously reported. 20 The synthesis of T LN pT LS ( 5 ) made use of the two known locked thymine nucleosides T LN ( 6 ) and T LS ( 7 ) previously prepared by the Vorbrüggen method. 21,22 Nucleoside 6 has also been synthesized from a locked uridine nucleoside through C5 methylation.…”

Section: Resultsmentioning

confidence: 99%

“…Nucleoside 6 afforded the known phosphoramidite 10 following literature procedures. 21 b Dimethoxytritylation of 7 afforded 11 (54% yield) that, upon a quantitative acetylation/detritylation procedure, 20 gave rise to the 2′-acetyl derivative 12 . Then phosphoramidite 10 and alcohol 12 were condensed in the presence of 5-(ethylthio)-1 H -tetrazole and the resulting phosphite triester intermediate was oxidized and fully deprotected 20 affording dinucleotide 5 with 8% yield (four steps) after HPLC purification (Scheme 2, conditions).…”

Section: Resultsmentioning

confidence: 99%

“…In order to identify the location(s) of S puckered-sugar(s) suitable for (6–4) PP formation, here we report the photochemical behavior of the two hemilocked dinucleotides T LN pT ( 3 ) and TpT LN ( 4 ) (Fig. 2), 20 in which one sugar residue is locked in the disfavorable N conformation whereas the other can freely populate N and S conformation(s). Our results are also discussed to the light of the NS-dilocked dinucleotide T LN pT LS ( 5 ) (Fig.…”

Section: Introductionmentioning

confidence: 99%

“…The known CD-derived stacking of 3–5 20 will be important to consider with regard to the photochemical results.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

SN- and NS-puckered sugar conformers are precursors of the (6–4) photoproduct in thymine dinucleotide

et al. 2022

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“…Our results are also discussed to the light of the NS-dilocked dinucleotide T LN pT LS ( 5 ) (Fig. 2) 20 whose 3′-end is totally in a S-freezed conformation.…”

Section: Introductionmentioning

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…The known CD-derived stacking of 3–5 20 will be important to consider with regard to the photochemical results.…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

SN- and NS-puckered sugar conformers are precursors of the (6–4) photoproduct in thymine dinucleotide

et al. 2022

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Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine

Vishwakarma,

Ravi,

Mittal

2023

ChemPhysChem

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Remdesivir (RDV) emerged as an effective drug against the SARS‐CoV‐2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson‐Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H‐bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06‐2X/cc‐pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red‐shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC‐type H‐bonds. The relative strength of these two H‐bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non‐equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.

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C2′-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level

et al. 2018

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Fluorine configuration at C2' of the bis(2'-fluorothymidine) dinucleotide is demonstrated to drive intramolecular base stacking. 2'-β F-Configuration drastically reduces stacking compared to the 2'-α series. Hence, base stacking emerges as being tunable by the C2'-F stereoconfiguration through dramatic puckering variations scrutinized by NMR and natural bond orbital analysis. Accordingly, 2'-β F-isomer photoreactivity is significantly reduced compared to that of the 2'-α F-isomer.

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5′- vs. 3′-end sugar conformational control in shaping up dinucleotides

Cited by 7 publications

References 44 publications

SN- and NS-puckered sugar conformers are precursors of the (6–4) photoproduct in thymine dinucleotide

SN- and NS-puckered sugar conformers are precursors of the (6–4) photoproduct in thymine dinucleotide

Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine

C2′-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level

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