Nichtkanonische Basen im Genom: die regulative Informationsebene in der DNA

Carell, Thomas; Kurz, Matthias; Müller, Markus; Rossa, Martin; Spada, Fabio

doi:10.1002/ange.201708228

Cited by 15 publications

(3 citation statements)

References 270 publications

(335 reference statements)

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“…They release oxidative lesions yielding AP within duplex. For guanine‐oxidation, OGG1 is the gatekeeper of AP, while 5 mC oxidation by four electrons to 5‐formylcytosine (5 fC) or six electrons to 5‐carboxylcytosine (5caC) are the substrates for TDG to yield AP [103] . AP provides the thermodynamic drive allowing duplex→GQ/i‐motif switch because AP significantly compromises duplex stability (>15 °C) but does not decrease the thermal stability of the tetra‐stranded folds due to its presence in the loop (Figure 4).…”

Section: Requisites Of Simultaneous or Mutually Exclusive Formation O...mentioning

confidence: 99%

The Molecular Tête‐à‐Tête between G‐Quadruplexes and the i‐motif in the Human Genome

2021

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G‐Quadruplex (GQ) and i‐motif structures are the paradigmatic examples of nonclassical tetrastranded nucleic acids having multifarious biological functions and widespread applications in therapeutics and material science. Recently, tetraplexes emerged as promising anticancer targets due to their structural robustness, gene‐regulatory roles, and predominant distribution at specific loci of oncogenes. However, it is arguable whether the i‐motif evolves in the complementary single‐stranded region after GQ formation in its opposite strand and vice versa. In this review, we address the prerequisites and significance of the simultaneous and/or mutually exclusive formation of GQ and i‐motif structures at complementary and sequential positions in duplexes in the cellular milieu. We discussed how their dynamic interplay Sets up cellular homeostasis and exacerbates carcinogenesis. The review gives insights into the spatiotemporal formation of GQ and i‐motifs that could be harnessed to design different types of reporter systems and diagnostic platforms for potential bioanalytical and therapeutic intervention.

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Section: Requisites Of Simultaneous or Mutually Exclusive Formation O...mentioning

confidence: 99%

The Molecular Tête‐à‐Tête between G‐Quadruplexes and the i‐motif in the Human Genome

2021

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“…Despite this remarkable progress, the four‐letter genetic alphabet does not provide the complete mechanism governing gene regulation. The discovery of epigenetic bases has shed further light on disease and development; [2] however, their effective sequencing has presented new challenges. Most epigenetic sequencing methodology has been developed for use in conjunction with short‐read “next‐generation” sequencing (NGS) platforms; however, the advent of third‐generation sequencing and its potential for greater accuracy, direct access and convenience has the potential to expedite research surrounding this secondary information layer in DNA.…”

Section: Introductionmentioning

confidence: 99%

Third‐Generation Sequencing of Epigenetic DNA

et al. 2023

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The discovery of epigenetic bases has revolutionised the understanding of disease and development. Among the most studied epigenetic marks are cytosines covalently modified at the 5 position. In order to gain insight into their biological significance, the ability to determine their spatiotemporal distribution within the genome is essential. Techniques for sequencing on “next‐generation” platforms often involve harsh chemical treatments leading to sample degradation. Third‐generation sequencing promises to further revolutionise the field by providing long reads, enabling coverage of highly repetitive regions of the genome or structural variants considered unmappable by next generation sequencing technology. While the ability of third‐generation platforms to directly detect epigenetic modifications is continuously improving, at present chemical or enzymatic derivatisation presents the most convenient means of enhancing reliability. This Review presents techniques available for the detection of cytosine modifications on third‐generation platforms.

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“…1 This has motivated many previous and ongoing studies on the effects of base pair methylation. 2,3 The most frequently observed methylated nucleotide is cytosine, [4][5][6][7] and, hence, it has been thoroughly studied by different numerical, theoretical, and experimental approaches. 8,9 Nonetheless, it is well known that methylation can also occur on another DNA basis.…”

Section: Introductionmentioning

confidence: 99%

Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

2023

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The TATA box is a promoter sequence able to interact directly with the components of the basal transcription initiation machinery. We investigate the changes in the electronic and magnetic properties of a TATA-DNA sequence when functionalized with different chemical groups; using the first-principles density functional theory specifically, the TATA-DNA sequences were functionalized with methyl groups (CH 3 , methylation), amino groups (NH 2 , amination), imine groups (NH, imination), chloroamine groups (NCl 2 , chloramination), H-adatom (hydrogenation), and Cl-adatom (chlorination). The functional groups were anchored at nitrogen atoms from adenine and oxygen atoms from thymine at sites pointed as reactive regions. We demonstrated that chemical functionalization induces significant changes in charge transfer, hydrogen bond distance, and hydrogen bond energy. The hydrogenation and imination increased the hydrogen bond energy. Results also revealed that the chemical functionalization of DNA molecules exhibit a ferromagnetic ground state, reaching magnetization up to 4.665 μ B and complex magnetic ordering. We further demonstrated that the functionalization could induce tautomerism (proton migration in the base pair systems). The present study provides a theoretical basis for understanding the functionalization further into DNA molecules and visualizing possible future applications.

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Nichtkanonische Basen im Genom: die regulative Informationsebene in der DNA

Cited by 15 publications

References 270 publications

The Molecular Tête‐à‐Tête between G‐Quadruplexes and the i‐motif in the Human Genome

The Molecular Tête‐à‐Tête between G‐Quadruplexes and the i‐motif in the Human Genome

Third‐Generation Sequencing of Epigenetic DNA

Electronic and magnetic properties of TATA‐DNA sequence driven by chemical functionalization

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