The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures

Mir, B.; Solés, X.; González, Carlos; Escaja, Núria

doi:10.1038/s41598-017-02723-y

Cited by 12 publications

(8 citation statements)

References 46 publications

(51 reference statements)

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“…Mir et al. studied the effect of pseudoiso-deoxycytidine (psC) (Figure 2A ) on the stability of head-to-head and head-to-tail dimeric i-motif structures ( 34 ). An increase of the stability of the studied i-motif structures was observed when the neutral psC:C base pair was located at the end of a C:C + stack.…”

Section: Factors Affecting the Stability Of I-motif Structuresmentioning

confidence: 99%

i-Motif DNA: structural features and significance to cell biology

Assi

Garavís

González

et al. 2018

Nucleic Acids Research

290

292

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The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.

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Section: Factors Affecting the Stability Of I-motif Structuresmentioning

confidence: 99%

i-Motif DNA: structural features and significance to cell biology

Assi

Garavís

González

et al. 2018

Nucleic Acids Research

290

292

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show abstract

“…Several decades of research on the broader functionality of the human genome have established that the structure of the genetic material is mostly polymorphic, and, among other components, comprises repetitive nucleic acid sequences that occur in abundance throughout the genome. , Under physiological conditions, the B-form double helical structure of DNA characterized by Watson–Crick base pairing is the most thermodynamically stable and commonly known. , The Watson–Crick duplex can fold into a variety of alternative noncanonical DNA polymorphs whose biochemistry is dominated by noncovalent interactions. , The i -motif is one special class of noncanonical DNA secondary structures that has garnered extensive research interest among laboratories around the world. Nucleic acid sequences that are cytosine (Cyt) rich have the potential to fold into an i -motif structure.…”

Section: Introductionmentioning

confidence: 99%

“…1,2 Under physiological conditions, the B-form double helical structure of DNA characterized by Watson−Crick base pairing is the most thermodynamically stable and commonly known. 1,3 The Watson−Crick duplex can fold into a variety of alternative noncanonical DNA polymorphs whose biochemistry is dominated by noncovalent interactions. 1,2 The i-motif is one special class of noncanonical DNA secondary structures that has garnered extensive research interest among laboratories around the world.…”

Section: ■ Introductionmentioning

confidence: 99%

Influence of 5-Methylation and the 2′- and 3′-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities ofi-Motif Structures

2021

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Repetitive nucleic acid sequences, which occur in abundance throughout the mammalian genome, are of enormous research interest due to their potential to adopt fascinating and unusual molecular structures such as the i-motif. In remarkable contrast to the DNA double helix, i-motif conformations are stabilized by protonated cytosine base pairs, (Cyt)H + (Cyt), that are centrally located in the core of the i-motif and intercalated vertically in an antiparallel fashion. An in-depth understanding of how modifications influence the stability of i-motif conformations is a prerequisite to understanding their biological functions and the development of effective means of tuning their stability for specific medical and technological applications. Here, the influence of the 2′-and 3′-hydroxy substituents of the sugar moieties and 5-methylation of the cytosine nucleobases on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, (xCyd)H + (xCyd), are examined by complementary threshold collision-induced dissociation techniques and computational methods. The xCyd nucleosides examined include the canonical DNA and RNA cytidine nucleosides, 2′-deoxycytidine (dCyd) and cytidine (Cyd), as well as several modified cytidine nucleoside analogues, 2′,3′-dideoxycytidine (ddCyd), 5-methyl-2′-deoxycytidine (m 5 dCyd), and 5-methylcytidine (m 5 Cyd). Comparisons among these model base pairs indicate that the 2′-and 3′-hydroxy substituents of the sugar moieties have very little influence on the strength of the base-pairing interactions, whereas 5-methylation of the cytosine nucleobases is found to enhance the strength of the base-pairing interactions. The increase in stability resulting from 5-methylation is only modest but is more than twice as large for the DNA than RNA protonated cytidine base pair. Overall, present results suggest that canonical DNA i-motif conformations should be more stable than analogous RNA i-motif conformations and that 5-methylation of cytosine residues, a significant epigenetic marker, provides greater stabilization to DNA than RNA i-motif conformations.

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“…Hence, C + -based i-motifs are also pH-dependent, resulting in poor stability at physiological pH. Artificial bases such as J, 93 C-5 modification, 94−99 tC, 100 and i-Clamp 101 (Figure 2F) were developed to improve the formation of i-motifs at neutral pH.…”

Section: ■ Artificial Nucleobases To Enhance Triplex Quadruplex or I-...mentioning

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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The effect of the neutral cytidine protonated analogue pseudoisocytidine on the stability of i-motif structures

Cited by 12 publications

References 46 publications

i-Motif DNA: structural features and significance to cell biology

i-Motif DNA: structural features and significance to cell biology

Influence of 5-Methylation and the 2′- and 3′-Hydroxy Substituents on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities ofi-Motif Structures

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

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