AC-motif: a DNA motif containing adenine and cytosine repeat plays a role in gene regulation

i-Motifs as regulatory switches: Mechanisms and implications for gene expression

i-Motifs, cytosine-tetrads, or C-quadruplexes are intercalated structures formed by base pairing between cytosine and protonated cytosine. These structures demonstrate increased stability in acidic environments due to the presence of the latter cytosinium group (i.e., the protonated cytosine). Research has shown that i-motifs are typically disrupted or destabilized at physiological pH levels (7.0-7.4), which makes their potential formation in the nucleus and their biological relevance uncertain. However, in 2018, it was demonstrated that i-motifs exist within the nucleus under physiological conditions, with various intracellular factors contributing to their stability. Identification of i-motifs in the nucleus and their association with gene promoters-particularly with those of proto-oncogenes-has generated significant interest in their potential regulatory functions. Additionally, recent studies suggest that i-motifs may function as switches for gene expression, influencing gene regulation through their folding and stabilization or unfolding and destabilization. This review aims to delve into these mechanisms to improve our understanding of the physiological significance of i-motifs.

Excited state relaxation mechanisms and tautomerism effects in 2,6-Diamino-8-Azapurine

The photochemistry of 9H-2,6-diamino-8-azapurine (9H-8AZADAP), a promising fluorescent probe, was investigated using the Multi-State Complete-Active-Space Second-Order Perturbation Theory (MS-CASPT2) quantum chemical method, along with the Average Solvent Electrostatic Configuration and Free Energy Gradient (ASEC-FEG) and Polarizable Continuum Model (PCM) to take into account water solvation effects. For both isolated and solvated species, the main photochemical event is initiated by the absorption of light from ground-state to the bright 1(ππ* La) state, which undergoes barrierless evolution to its minimum energy region (1(ππ* La)min) without crossing any other potential energy surface (PES). Subsequently, the excess of energy is released through fluorescence. From the 1(ππ* La)min region, two radiationless decay pathways back to the initial ground state, mediated by two distinct conical intersections between the ground and 1(ππ* La) states, are found to be unlikely due to the presence of high energy barriers in both environments. Our results also indicate that the solvation effects are more pronounced when using the ASEC-FEG method, which predicts larger structural and energy changes, especially concerning energetic barriers. Based on the free energy perturbation theory (FEP), a hypothetical thermodynamic cycle was devised, from which we infer that in an aqueous environment the N3 site is the most favorable for protonation. We also conclude that the 8H-8AZADAP tautomer is responsible for the fluorescent band observed experimentally at 410 nm and elucidates the mechanism of phototautomerism.

Synechococsins: Lanthipeptides acting as defensive signals to disarm offensive competitors?

Synechococsins represent a diverse group of class II lanthipeptides from the prochlorosin family, produced by the marine picocyanobacterium Synechococcus. A single strain can produce multiple SyncA peptides through modification by SyncM, a bifunctional lanthipeptide synthetase. Despite the prevalence of these lanthipeptides in nature, their biological functions remain elusive, even for the most studied group, Prochlorococcus MIT9313. This study investigated the transcriptomic response of the marine SyncA-producing strain Synechococcus sp. RS9116 to the characterized and purified SyncA6 peptide from Synechococcus sp. MITS9509. Intriguingly, the analysis of gene expression revealed a strong down-regulation of genes that encode putative ribosomally produced antimicrobial peptides, such as coculture-responsive genes (CCRG-2) and microcin-C-like bacteriocins. This study suggests a potential biological role for synechococsins as interspecific gene modulators, improving the fitness of the producing strain in a competitive and resource-limited environment.

Multimodal separation and cross fusion network based on Raman spectroscopy and FTIR spectroscopy for diagnosis of thyroid malignant tumor metastasis

The diagnosis of cervical lymph node metastasis from thyroid cancer is an essential stage in the progression of thyroid cancer. The metastasis of cervical lymph nodes directly affects the prognosis and survival rate of patients. Therefore, timely and early diagnosis is crucial for effective treatment and can significantly improve patients' survival rate and quality of life. Traditional diagnostic methods, such as ultrasonography and radionuclide scanning, have limitations, such as complex operations and high missed diagnosis rates. Raman spectroscopy and FTIR spectroscopy can well reflect the molecular information of samples, have characteristics such as sensitivity and specificity, and are simple to operate. They have been widely used in clinical research in recent years. With the development of intelligent medical diagnosis technology, medical data shows a multi-modal trend. Compared with single-modal data, multi-modal data fusion can achieve complementary information, provide more comprehensive and valuable diagnostic information, significantly enhance the richness of data features, and improve the modeling effect of the model, helping to achieve better results. Accurate disease diagnosis. Existing research mostly uses cascade processing, ignoring the important correlations between multi-modal data, and at the same time not making full use of the intra-modal relationships that are also beneficial to prediction. We developed a new multi-modal separation cross-fusion network (MSCNet) based on deep learning technology. This network fully captures the complementary information between and within modalities through the feature separation module and feature cross-fusion module and effectively integrates Raman spectrum and FTIR spectrum data to diagnose thyroid cancer cervical lymph node metastasis accurately. The test results on the serum vibrational spectrum data set of 99 cases of cervical lymph node metastasis showed that the accuracy and AUC of a single Raman spectrum reached 63.63% and 63.78% respectively, and the accuracy and AUC of a single FTIR spectrum reached 95.84% respectively and 96%. The accuracy and AUC of Raman spectroscopy combined with FTIR spectroscopy reached 97.95% and 98% respectively, which is better than existing diagnostic technology. The omics correlation verification obtained correlation pairs of 5 Raman frequency shifts and 84 infrared spectral bands. This study provides new ideas and methods for the early diagnosis of cervical lymph node metastasis of thyroid cancer.

A folding motif formed with an expanded genetic alphabet

Adding synthetic nucleotides to DNA increases the linear information density of DNA molecules. Here we report that it also can increase the diversity of their three-dimensional folds. Specifically, an additional nucleotide (dZ, with a 5-nitro-6-aminopyridone nucleobase), placed at twelve sites in a 23-nucleotides-long DNA strand, creates a fairly stable unimolecular structure (that is, the folded Z-motif, or fZ-motif) that melts at 66.5 °C at pH 8.5. Spectroscopic, gel and two-dimensional NMR analyses show that the folded Z-motif is held together by six reverse skinny dZ-:dZ base pairs, analogous to the crystal structure of the free heterocycle. Fluorescence tagging shows that the dZ-:dZ pairs join parallel strands in a four-stranded compact down-up-down-up fold. These have two possible structures: one with intercalated dZ-:dZ base pairs, the second without intercalation. The intercalated structure would resemble the i-motif formed by dC:dC+-reversed pairing at pH ≤ 6.5. This fZ-motif may therefore help DNA form compact structures needed for binding and catalysis.

Modulation of the tetrameric I-motif folding of C-rich Tetrahymena telomeric sequences by hexitol nucleic acid (HNA) modifications

I-motifs are non-canonical DNA structures consisting of two parallel strands held together by hemiprotonated cytosine-cytosine+ base pairs, which intercalate to form a ordered column of stacked base pairs. This unique structure covers potential relevance in various fields, including gene regulation and biotechnological applications. A unique structural feature of I-motifs (iM), is the presence of sugar-sugar interactions through their extremely narrow minor grooves. Consistently, oligonucleotides containing pentose derivatives such as ribose, 2'-deoxyribose, arabinose, and 2'-deoxy-2'-fluoroarabinose highlighted a very different attitude to fold into iM. On the other hand, there is significant attention focused on exploring sugar-modifications that can increase nucleic acids resistance to nuclease degradation, a crucial requirement for therapeutic applications. An interesting example, not addressed in the iM field yet, is represented by hexitol nucleic acid (HNA), a metabolically stable six-membered ring analogue compatible with A-like double helix formation. Herein, we selected two DNA C-rich Tetrahymena telomeric sequences whose tetrameric iMs were already resolved by NMR and we investigated the iM folding of related HNA and RNA oligonucleotides by circular dichroism, differential scanning calorimetry and NMR. The comparison of their behaviours vs the DNA counterparts provided interesting insights into the influence of the sugar on iM folding. In particular, ribose and hexitol prevented iM formation. However, by clustering the hexitol-containing residues at the 3'-end, it was possible to modulate the distribution of the different topological species described for the DNA iMs. These data open new avenues for the exploitation of sugar modifications for I-motif characterization and applications.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A⁺/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A⁺/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pK_a, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.

DNA-guided self-assembly in living cells

Self-assembly processes exist widely in life systems and play essential roles in maintaining life activities. It is promising to explore the molecular fundamentals and mechanisms of life systems through artificially constructing self-assembly systems in living cells. As an excellent self-assembly construction material, deoxyribonucleic acid (DNA) has been widely used to achieve the precise construction of self-assembly systems in living cells. This review focuses on the recent progress of DNA-guided intracellular self-assembly. First, the methods of intracellular DNA self-assembly based on the conformational transition of DNA are summarized, including complementary base pairing, the formation of G-quadruplex/i-motif, and the specific recognition of DNA aptamer. Next, The applications of DNA-guided intracellular self-assembly on the detection of intracellular biomolecules and the regulation of cell behaviors are introduced, and the molecular design of DNA in the self-assembly systems is discussed in detail. Ultimately, the challenges and opportunities of DNA-guided intracellular self-assembly are commented.

The Full Cytosine-Cytosine Base Paring: Self-Assembly and Crystal Structure

The synthesis of self-assembly systems that can mimic partial biological behaviours require ingenious and delicate design. For decades, scientists are committed to exploring new base pairing patterns using hydrogen bonds directed self-assembly of nucleotides. A fundamental question is the adaptive circumstance of the recognition between base pairs, namely, how solvent conditions affect the domain of base pairs. Towards this question, three nucleotide complexes based on 2'-deoxycytidine-5'-monophosphate (dCMP) and cytidine-5'-monophosphate (CMP) were synthesized in different solvents and pH values, and an unusual cytosine-cytosine base paring pattern (named full C : C base pairing) has been successfully obtained. Systematic single crystal analysis and ¹ H NMR titration spectra have been performed to explore factors influencing the formation of base paring patterns. Moreover, supramolecular chirality of three complexes were studied using circular dichroism (CD) spectroscopy in solution and solid-state combined with crystal structure analysis.

Non-canonical DNA structures: Diversity and disease association

A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.