Category: 452-06-2

Czernecki, Dariusz; Hu, Haidai; Romoli, Filippo; Delarue, Marc published the artcile< Structural dynamics and determinants of 2-aminoadenine specificity in DNA polymerase DpoZ of vibriophage ϕVC8>, Electric Literature of 452-06-2, the main research area is Thermus DNA polymerase DpoZ vibriophage 2 aminoadenine.

All genetic information in cellular life is stored in DNA copolymers composed of four basic building blocks (ATGC-DNA). In contrast, a group of bacteriophages belonging to families Siphoviridae and Podoviridae has abandoned the usage of one of them, adenine (A), replacing it with 2-aminoadenine (Z). The resulting ZTGC-DNA is more stable than its ATGC-DNA counterpart, owing to the addnl. hydrogen bond present in the 2-aminoadenine:thymine (Z:T) base pair, while the addnl. amino group also confers resistance to the host endonucleases. Recently, two classes of replicative proteins found in ZTGC-DNA-containing phages were characterized and one of them, DpoZ from DNA polymerase A (PolA) family, was shown to possess significant Z-vs-A specificity. Here, we present the crystallog. structure of the apo form of DpoZ of vibriophage ϕVC8, composed of the 3-5 exonuclease and polymerase domains. We captured the enzyme in two conformations that involve the tip of the thumb subdomain and the exonuclease domain. We highlight insertions and mutations characteristic of ϕVC8 DpoZ and its close homologues. Through mutagenesis and functional assays we suggest that the preference of ϕVC8 DpoZ towards Z relies on a polymerase backtracking process, more efficient when the nascent base pair is A:T than when it is Z:T.

Nucleic Acids Research published new progress about Crystal structure. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Electric Literature of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Stachelska-Wierzchowska, Alicja; Wierzchowski, Jacek; Gorka, Michal; Bzowska, Agnieszka; Stolarski, Ryszard; Wielgus-Kutrowska, Beata published the artcile< Tricyclic nucleobase analogs and their ribosides as substrates and inhibitors of purine-nucleoside phosphorylases III. Aminopurine derivatives>, Formula: C5H5N5, the main research area is NMR; chemo-enzymatic synthesis; enzyme-substrate complexes; fluorescence; nucleobase/nucleoside analogs; purine nucleoside phosphorylase.

Etheno-derivatives of 2-aminopurine, 2-aminopurine riboside, and 7-deazaadenosine (tubercidine) were prepared and purified using standard methods. 2-Aminopurine reacted with aqueous chloroacetaldehyde to give two products, both exhibiting substrate activity towards bacterial (E. coli) purine-nucleoside phosphorylase (PNP) in the reverse (synthetic) pathway. The major product of the chem. synthesis, identified as 1,N2-etheno-2-aminopurine, reacted slowly, while the second, minor, but highly fluorescent product, reacted rapidly. NMR anal. allowed identification of the minor product as N2,3-etheno-2-aminopurine, and its ribosylation product as N2,3-etheno-2-aminopurine-N2-β-D-riboside. Ribosylation of 1,N2-etheno-2-aminopurine led to analogous N2-β-d-riboside of this base. Both enzymically produced ribosides were readily phosphorolyzed by bacterial PNP to the resp. bases. The reaction of 2-aminopurine-N9-β-D-riboside with chloroacetaldehyde gave one major product, clearly distinct from that obtained from the enzymic synthesis, which was not a substrate for PNP. A tri-cyclic 7-deazaadenosine (tubercidine) derivative was prepared in an analogous way and shown to be an effective inhibitor of the E. coli, but not of the mammalian enzyme. Fluorescent complexes of amino-purine analogs with E. coli PNP were observed

Molecules published new progress about 452-06-2. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Formula: C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Madaoui, Mimouna; Datta, Dhrubajyoti; Wassarman, Kelly; Zlatev, Ivan; Egli, Martin; Ross, Bruce S.; Manoharan, Muthiah published the artcile< A Chemical Approach to Introduce 2,6-Diaminopurine and 2-Aminoadenine Conjugates into Oligonucleotides without Need for Protecting Groups>, Computed Properties of 452-06-2, the main research area is .

We report a simple, postsynthetic strategy for synthesis of oligonucleotides containing 2,6-diaminopurine nucleotides and 2-aminoadenine conjugates using 2-fluoro-6-amino-adenosine. The strategy allows introduction of 2,6-diaminopurine and other 2-amino group-containing ligands. The strongly electroneg. 2-fluoro deactivates 6-NH2 obviating the need for any protecting group on adenine, and simple aromatic nucleophilic substitution of fluorine makes reaction with aqueous NH3 or R-NH2 feasible at the 2-position.

Organic Letters published new progress about 452-06-2. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Computed Properties of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Cristofalo, Matteo; Kovari, Daniel; Corti, Roberta; Salerno, Domenico; Cassina, Valeria; Dunlap, David; Mantegazza, Francesco published the artcile< Nanomechanics of Diaminopurine-Substituted DNA>, Related Products of 452-06-2, the main research area is diaminopurine double strand DNA nanomechanics.

2,6-Diaminopurine (DAP) is a nucleobase analog of adenine. When incorporated into double-stranded DNA (dsDNA), it forms three hydrogen bonds with thymine. Rare in nature, DAP substitution alters the phys. characteristics of a DNA mol. without sacrificing sequence specificity. Here, we show that in addition to stabilizing double-strand hybridization, DAP substitution also changes the mech. and conformational properties of dsDNA. Thermal melting experiments reveal that DAP substitution raises melting temperatures without diminishing sequence-dependent effects. Using a combination of at. force microscopy (AFM), magnetic tweezer (MT) nanomech. assays, and CD spectroscopy, we demonstrate that DAP substitution increases the flexural rigidity of dsDNA yet also facilitates conformational shifts, which manifest as changes in mol. length. DAP substitution increases both the static and dynamic persistence length of DNA (measured by AFM and MT, resp.). In the static case (AFM), in which tension is not applied to the mol., the contour length of DAP-DNA appears shorter than wild-type (WT)-DNA; under tension (MT), they have similar dynamic contour lengths. At tensions above 60 pN, WT-DNA undergoes characteristic overstretching because of strand separation (tension-induced melting) and spontaneous adoption of a conformation termed S-DNA. Cyclic overstretching and relaxation of WT-DNA at near-zero loading rates typically yields hysteresis, indicative of tension-induced melting; conversely, cyclic stretching of DAP-DNA showed little or no hysteresis, consistent with the adoption of the S-form, similar to what has been reported for GC-rich sequences. However, DAP-DNA overstretching is distinct from GC-rich overstretching in that it happens at a significantly lower tension. In physiol. salt conditions, evenly mixed AT/GC DNA typically overstretches around 60 pN. GC-rich sequences overstretch at similar if not slightly higher tensions. Here, we show that DAP-DNA overstretches at 52 pN. In summary, DAP substitution decreases the overall stability of the B-form double helix, biasing toward non-B-form DNA helix conformations at zero tension and facilitating the B-to-S transition at high tension.

Biophysical Journal published new progress about Conformational transition. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Related Products of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Schroeder, Griffin M.; Dutta, Debapratim; Cavender, Chapin E.; Jenkins, Jermaine L.; Pritchett, Elizabeth M.; Baker, Cameron D.; Ashton, John M.; Mathews, David H.; Wedekind, Joseph E. published the artcile< Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation>, Recommanded Product: 7H-Purin-2-amine, the main research area is turnip yellow mosaic virus preQ1I riboswitch nucleobase gene regulation.

Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this mol. framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallog.-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biol. function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

Nucleic Acids Research published new progress about 3′-Untranslated region Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Recommanded Product: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Zhu, Jinbo; Yan, Zhiqiang; Boskovic, Filip; Haynes, Cally J. E.; Kieffer, Marion; Greenfield, Jake L.; Wang, Jin; Nitschke, Jonathan R.; Keyser, Ulrich F. published the artcile< FeII4L4 tetrahedron binds and aggregates DNA Gquadruplexes>, Product Details of C5H5N5, the main research area is iron ligand tetrahedron metal organic cage DNA G quadruplex.

Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biol. processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA-cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5′ end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, CD and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease.

Chemical Science published new progress about Absorption spectra. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Product Details of C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Hornum, Mick; Stendevad, Julie; Sharma, Pawan K.; Kumar, Pawan; Nielsen, Rasmus B.; Petersen, Michael; Nielsen, Poul published the artcile< Base-Pairing Properties of Double-Headed Nucleotides>, Electric Literature of 452-06-2, the main research area is base pair double headed nucleotide DNA duplex; 2,6-diaminopurine; double-headed nucleotides; hypoxanthine; oligonucleotides.

Nucleotides that contain two nucleobases (double-headed nucleotides) have the potential to condense the information of two sep. nucleotides into one. This presupposes that both bases must successfully pair with a cognate strand. Here, double-headed nucleotides that feature cytosine, guanine, thymine, adenine, hypoxanthine, and diaminopurine linked to the C2′-position of an arabinose scaffold were developed and examined in full detail. These monomeric units were efficiently prepared by convergent synthesis and incorporated into DNA oligonucleotides by means of the automated phosphoramidite method. Their pairing efficiency was assessed by UV-based melting-temperature anal. in several contexts and extensive mol. dynamics studies. Altogether, the results show that these double-headed nucleotides have a well-defined structure and invariably behave as functional dinucleotide mimics in DNA duplexes.

Chemistry – A European Journal published new progress about DNA-DNA hybridization. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Electric Literature of 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Hao, Xueyu; Wang, Chunyu; Wang, Yu; Li, Chunjie; Hou, Jingwei; Zhang, Feng; Kang, Chuanqing; Gao, Lianxun published the artcile< Topological conversion of human telomeric G-quadruplexes from hybrid to parallel form induced by naphthalene diimide ligands>, Name: 7H-Purin-2-amine, the main research area is naphthalene diimide G quadruplex telomere regulation; G-quadruplex; Human telomere; Naphthalene diimide; Topological conversion.

G-quadruplexes (GQs) have become promising anti-cancer therapeutic targets, which are formed by the folding of a guanine-rich repeat DNA/RNA sequence at human telomeres or oncogene promoters. Polymorphism has been observed for the folding topologies of intramol. GQs. Here we report the topol. conversion of human telomeric GQ induced by naphthalene diimide (NDI) ligands in K+ solution The ligands selectively induce metastable hybrid-type GQs to highly stable parallel-type GQ at physiol. temperature (37°C) in dilute aqueous solutions and under crowding conditions that mimic cellular bioenvironment. According to spectroscopic analyses, the topol. conversion is speculated to undergo stepwise unfolding of hybrid-type GQ through intermediate states to parallel-type GQ. The results will prompt further studies on the designs of ligands with GQ conformation regulation functions and nanotechnol. systems based on nucleic acids with dynamic regulation of GQ conformation.

International Journal of Biological Macromolecules published new progress about Animal gene, c-myc Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Name: 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Li, Xianming; Yang, Hang; He, Jialun; Yang, Bin; Zhao, Yi; Wu, Peng published the artcile< Full liberation of 2-Aminopurine with nucleases digestion for highly sensitive biosensing>, Application of C5H5N5, the main research area is aminopurine nuclease digestion fluorescence biosensor lifetime DNA transformation; 2-Aminopurine; Fluorescence lifetime; Multiple labelling; Nuclease digestion.

2-Aminopurine (2-AP), a fluorescent isomer of adenine, is a popular fluorescent tag for DNA-based biosensors. The fluorescence of 2-AP is highly dependent on its microenvironment, i.e., almost non-fluorescent and merely fluorescent in dsDNA and ssDNA, resp., but can be greatly brightened as mononucleotide. In most 2-AP-based biosensors, DNA transformation from dsDNA to ssDNA was employed, while selective digestion of 2-AP-labeled DNA with nucleases represents an appealing approach for improving the biosensor sensitivity. However, some detailed fundamental information, such as the reason for nuclease digestion, the influence of the labeling site, neighboring bases, or the label number of 2-AP for final signal output, are still largely unknown, which greatly limits the utility of 2-AP-based biosensors. In this work, using both steady- and excited-state fluorescence (lifetime), we demonstrated that nuclease digestion resulted in almost full liberation of 2-AP mononucleotides, and was free from labeling site and neighboring bases. Furthermore, we also found that nuclease digestion could lead to multiplexed sensitivity from increasing number of 2-AP labeling, but was not achievable for the conventional biosensors without full liberation of 2-AP. Considering the popularity of 2-AP in biosensing and other related applications, the above obtained information in sensitivity boosting is fundamentally important for future design of 2-AP-based biosensors.

Biosensors & Bioelectronics published new progress about Biological digestion. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Application of C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Martinez-Fernandez, Lara; Arslancan, Serra; Ivashchenko, Dmytro; Crespo-Hernandez, Carlos E.; Corral, Ines published the artcile< Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine>, Safety of 7H-Purin-2-amine, the main research area is photostability purine nucleobase photophysics oxopurine.

This work scrutinizes the relaxation mechanism of 2-oxopurine. Contrary to its ancestor, purine, which is a UVC chromophore, 2-oxopurine shows a red-shifted absorption spectrum centered in the UVA region. In 2-oxopurine, relaxation along the ππ* spectroscopic state directs the population from the Franck-Condon (FC) region towards a min., which acts as a crossroad for the further decay of the system either to triplet states or, alternatively, to the ground state through a C6-puckered S1/S0 funnel. A comparison of the optical properties and excited state potential energy surfaces of purine, 2-oxopurine, 2-aminopurine, 6-oxopurine and adenine, allows establishing how the position and nature of substituent tune the photophysics of purine. For this series, we conclude that both C2 and C6 substitution red shift the absorption spectrum of purine, with 2-oxo substitution exhibiting the largest shift. An important exception is the canonical nucleobase adenine, which presents a blue shifted absorption spectrum. The topog. of purine’s ππ* potential energy surface experiences major changes when functionalized at the C6 position. In particular, the disappearance of the min. along the ππ* potential energy surface efficiently funnels the excited state population from the FC region to the ground state and increases the photostability of 6-aminopurine (adenine) and 6-oxopurine (hypoxanthine) nucleobases.

Physical Chemistry Chemical Physics published new progress about Absorption spectra. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Safety of 7H-Purin-2-amine.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem