The Conformationally Constrained <i>N</i>-Methanocarba-dT Analogue Adopts an Unexpected C4′-<i>exo</i> Sugar Pucker in the Structure of a DNA Hairpin

Pallan, Pradeep S.; Márquez, Víctor E.; Egli, Martin

doi:10.1021/bi300215k

Cited by 19 publications

(19 citation statements)

References 36 publications

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“…Although a recent study shows that North -methanocarbathymidine is flexible and it can also adopt a North / East (C4′- exo ) conformation when present in a DNA loop. 50 …”

Section: Resultsmentioning

confidence: 99%

The effect on quadruplex stability of North-nucleoside derivatives in the loops of the thrombin-binding aptamer

Aviñó

Mazzini

Ferreira

et al. 2012

Bioorganic & Medicinal Chemistry

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Modified thrombin-binding aptamers (TBAs) carrying uridine (U), 2′-deoxy-2′-fluorouridine (FU) and North-methanocarbathymidine (NT) residues in the loop regions were synthesized and analyzed by UV thermal denaturation experiments and CD spectroscopy. The replacement of thymidines in the TGT loop by U and FU results in an increased stability of the antiparallel quadruplex structure described for the TBA while the presence of NT residues in the same positions destabilizes the antiparallel structure. The substitution of the thymidines in the TT loops for U, FU and NT induce a destabilization of the antiparallel quadruplex, indicating the crucial role of these positions. NMR studies on TBAs modified with uridines at the TGT loop also confirm the presence of the antiparallel quadruplex structure. Nevertheless, replacement of two Ts in the TT loops by uridine gives a more complex scenario in which the antiparallel quadruplex structure is present along with other partially unfolded species or aggregates.

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“…Although a recent study shows that North -methanocarbathymidine is flexible and it can also adopt a North / East (C4′- exo ) conformation when present in a DNA loop. 50 …”

Section: Resultsmentioning

confidence: 99%

The effect on quadruplex stability of North-nucleoside derivatives in the loops of the thrombin-binding aptamer

Aviñó

Mazzini

Ferreira

et al. 2012

Bioorganic & Medicinal Chemistry

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“…Substantial experimental evidence for both ribo-and deoxyribo-MC nucleotides in a wide variety of contexts supports the assumption that these modifications do not perturb oligonucleotide structure beyond the intended restriction to a particular region of the pseudorotation cycle (Marquez et al 1997(Marquez et al , 1998(Marquez et al , 2004Maderia et al 2007;Terrazas et al 2011;Ketkar et al 2012a,b). In a 1.8 Å crystal structure of two north-methanocarba-thymidine (N-MCT) nucleotides incorporated into a self-complementary DNA dodecamer, however, an unexpected left-handed stem-loop formed, with the N-dMCT residues located within the loop and taking up pseudorotation angles of 48°-52° (Pallan et al 2012). The structural context of these nucleotides varies from the present study in important ways, including the lack of the 2 ′ -hydroxyl group on both the methanocarba and native nucleotides and the presence of the unusual left-handed structural motif.…”

Section: Discussionmentioning

confidence: 99%

Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme

White

Sumita

Márquez

et al. 2018

RNA

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In common with other self-cleaving RNAs, the lead-dependent ribozyme (leadzyme) undergoes dynamic fluctuations to a chemically activated conformation. We explored the connection between conformational dynamics and self-cleavage function in the leadzyme using a combination of NMR spin-relaxation analysis of ribose groups and conformational restriction via chemical modification. The functional studies were performed with a -methanocarbacytidine modification that prevents fluctuations to C2'-endo conformations while maintaining an intact 2'-hydroxyl nucleophile. Spin-relaxation data demonstrate that the active-site Cyt-6 undergoes conformational exchange attributed to sampling of a minor C2'-endo state with an exchange lifetime on the order of microseconds to tens of microseconds. A conformationally restricted species in which the fluctuations to the minor species are interrupted shows a drastic decrease in self-cleavage activity. Taken together, these data indicate that dynamic sampling of a minor species at the active site of this ribozyme, and likely of related naturally occurring motifs, is strongly coupled to catalytic function. The combination of NMR dynamics analysis with functional probing via conformational restriction is a general methodology for dissecting dynamics-function relationships in RNA.

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“…In contrast, the cyclohexenyl ring in F-CeNA is more flexible and was shown to assume either the DNA- or RNA-like sugar conformation depending on the sequence context on its incorporation 24 . The 3.1.0 ring system in F-NMC is locked in the RNA-like C3′- endo conformation 25 . In this report, we show that introducing fluorinated modifications within the gap region can modulate the cleavage of the ASO-RNA heteroduplexes by human RNase H1, and that this can produce profound changes in allele selectivity when targeting SNPs with gapmer ASOs.…”

Section: Introductionmentioning

confidence: 99%

Fluorinated Nucleotide Modifications Modulate Allele Selectivity of SNP-Targeting Antisense Oligonucleotides

Østergaard

Nichols

Dwight

et al. 2017

Molecular Therapy - Nucleic Acids

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Antisense oligonucleotides (ASOs) have the potential to discriminate between subtle RNA mismatches such as SNPs. Certain mismatches, however, allow ASOs to bind at physiological conditions and result in RNA cleavage mediated by RNase H. We showed that replacing DNA nucleotides in the gap region of an ASO with other chemical modification can improve allele selectivity. Herein, we systematically substitute every position in the gap region of an ASO targeting huntingtin gene (HTT) with fluorinated nucleotides. Potency is determined in cell culture against mutant HTT (mtHTT) and wild-type HTT (wtHTT) mRNA and RNase H cleavage intensities, and patterns are investigated. This study profiled five different fluorinated nucleotides and showed them to have predictable, site-specific effects on RNase H cleavage, and the cleavage patterns were rationalized from a published X-ray structure of human RNase H1. The results herein can be used as a guide for future projects where ASO discrimination of SNPs is important.

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The Conformationally Constrained N-Methanocarba-dT Analogue Adopts an Unexpected C4′-exo Sugar Pucker in the Structure of a DNA Hairpin

Cited by 19 publications

References 36 publications

The effect on quadruplex stability of North-nucleoside derivatives in the loops of the thrombin-binding aptamer

The effect on quadruplex stability of North-nucleoside derivatives in the loops of the thrombin-binding aptamer

Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme

Fluorinated Nucleotide Modifications Modulate Allele Selectivity of SNP-Targeting Antisense Oligonucleotides

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