Category: 452-06-2

Majumdar, Chandrima; McKibbin, Paige L.; Krajewski, Allison E.; Manlove, Amelia H.; Lee, Jeehiun K.; David, Sheila S. published the artcile< Unique Hydrogen Bonding of Adenine with the Oxidatively Damaged Base 8-Oxoguanine Enables Specific Recognition and Repair by DNA Glycosylase MutY>, HPLC of Formula: 452-06-2, the main research area is DNA glycosylase MutY base excision repair adenine analog.

The DNA glycosylase MutY prevents deleterious mutations resulting from guanine oxidation by recognition and removal of adenine (A) misincorporated opposite 8-oxo-7,8-dihydroguanine (OG). Correct identification of OG:A is crucial to prevent improper and detrimental MutY-mediated adenine excision from G:A or T:A base pairs. Here we present a structure-activity relationship (SAR) study using analogs of A to probe the basis for OG:A specificity of MutY. We correlate observed in vitro MutY activity on A analog substrates with their exptl. and calculated acidities to provide mechanistic insight into the factors influencing MutY base excision efficiency. These data show that H-bonding and electrostatic interactions of the base within the MutY active site modulate the lability of the N-glycosidic bond. A analogs that were not excised from duplex DNA as efficiently as predicted by calculations provided insight into other required structural features, such as steric fit and H-bonding within the active site for proper alignment with MutY catalytic residues. We also determined MutY-mediated repair of A analogs paired with OG within the context of a DNA plasmid in bacteria. Remarkably, the magnitudes of decreased in vitro MutY excision rates with different A analog duplexes do not correlate with the impact on overall MutY-mediated repair. The feature that most strongly correlated with facile cellular repair was the ability of the A analogs to H-bond with the Hoogsteen face of OG. Notably, base pairing of A with OG uniquely positions the 2-amino group of OG in the major groove and provides a means to indirectly select only these inappropriately placed adenines for excision. This highlights the importance of OG lesion detection for efficient MutY-mediated cellular repair. The A analog SARs also highlight the types of modifications tolerated by MutY and will guide the development of specific probes and inhibitors of MutY.

Journal of the American Chemical Society published new progress about DNA base excision repair. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, HPLC of Formula: 452-06-2.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Tian, Meng; Li, Zhenhua; Song, Ruihong; Li, Yingxian; Guo, Chengang; Sha, Yujie; Cui, Wanling; Xu, Shicai; Hu, Guodong; Wang, Jihua published the artcile< Graphene biosensor as affinity biosensors for biorecognition between Guanine riboswitch and ligand>, Electric Literature of 452-06-2, the main research area is graphene field effect transistor biosensor guanine riboswitch ligand.

Guanine riboswitch (GR) is located in the untranslated region of mRNA that performs important biol. functions by interactions with specific ligand mols. The present standard methods for detecting mRNA has been widely used, but suffer from extra labeling steps, high cost, low throughput, low sensitivities and limited dynamic ranges. The field effect transistor (FET) biosensors showed high performance in detecting a large number of biol. analytes. However, the detection of analytes with low charge and small mol. still remains a challenge. In this paper, a label-free graphene field effect transistor (G-FET) biosensor has been developed to detect the binding interactions between GR and four purine analog ligand mols. (GUA, 6GU, 2BP, XAN). We demonstrated that the G-FET biosensor were highly sensitive in detecting the elec.-neutral and low mol. weight ligands by using GR as probe. The sensing mechanisms for elec.-neutral mol. is revealed by mol. dynamics simulation. The equilibrium dissociation constants KD and binding free energy ΔG of GR-GUA, GR-6GU, GR-2BP and GR-XAN were obtained by the G-FET biosensor, and the results are comparable with the calculated by mol. dynamics simulation and previous reports. We demonstrated that the G-FET biosensor can be used as affinity biosensors to quantify biomol. interactions.

Applied Surface Science published new progress about Aptamers (guanine riboswitch). 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

Boehnke, Hendrik; Roettger, Katharina; Ingle, Rebecca A.; Marroux, Hugo J. B.; Bohnsack, Mats; Schwalb, Nina K.; Orr-Ewing, Andrew J.; Temps, Friedrich published the artcile< Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations>, Electric Literature of 452-06-2, the main research area is electronic relaxation dynamics UV photoexcited aminopurine thymine base conformation.

The fluorescent analog 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in mol. biol. for probing DNA and RNA structures and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. Although attempts have been made to ascribe decreased excited-state lifetimes to intrastrand charge-transfer and stacking interactions, possible influences from dynamic interstrand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP·T in Watson-Crick (WC) and Hoogsteen (HS) conformations. Although the WC conformation features slowed-down, monomer-like electronic relaxation in τ ∼ 1.6 ns toward ground-state recovery and triplet formation, the dynamics associated with 2AP·T in the HS motif exhibit faster deactivation in τ ∼ 70 ps. As recent research has revealed abundant transient interstrand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramol. photophys. mechanisms are discussed in terms of a proposed excited-state double-proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.

Journal of Physical Chemistry B published new progress about Double-stranded DNA Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 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

D’Souza, Sara; Miller, Justin E.; Ahn, Jenny; Subandi, Raechel; Lozano, Daniel; Ramirez, James; Goff, Marisa; Davidian, Christina; Miller, Jeffrey H. published the artcile< The antibiotic trimethoprim displays strong mutagenic synergy with 2-aminopurine>, Name: 7H-Purin-2-amine, the main research area is antibiotic; mutagenesis; synergy; trimethoprim.

We show that trimethoprim (TMP), an antibiotic in current use, displays a strong synergistic effect on mutagenesis in Escherichia coli when paired with the base analog 2-aminopurine (2AP), resulting in a 35-fold increase in mutation frequencies in the rpoB-Rifr system. Combination therapies are often employed both as antibiotic treatments and in cancer chemotherapy. However, mutagenic effects of these combinations are rarely examined An anal. of the mutational spectra of TMP, 2AP, and their combination indicates that together they trigger a response via an alteration in deoxynucleoside triphosphate (dNTP) ratios that neither compound alone can trigger. A similar, although less strong, response is seen with the frameshift mutagen ICR191 and 2AP. These results underscore the need for testing the effects on mutagenesis of combinations of antibiotics and chemotherapeutics.

Antimicrobial Agents and Chemotherapy published new progress about 452-06-2. 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

Wang, Kai-Bo; Dickerhoff, Jonathan; Wu, Guanhui; Yang, Danzhou published the artcile< PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs>, Safety of 7H-Purin-2-amine, the main research area is vacancy G quadruplex PDGFRbeta promoter dGMP conformation guanine drug.

Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small mol. targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiol. relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic anal. elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3′- and 5′-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5′-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5′-vacancy, except for cGMP. CGMP binds both the 3′- and 5′-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiol. and pathol. processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.

Journal of the American Chemical Society published new progress about Drugs. 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

Tang, Ke; Roca, Jorjethe; Chen, Rong; Ansari, Anjum; Liang, Jie published the artcile< Thermodynamics of unfolding mechanisms of mouse mammary tumor virus pseudoknot from a coarse-grained loop-entropy model>, Category: imidazoles-derivatives, the main research area is mammary tumor virus pseudoknot thermodn entropy model; Energy landscape; Fluorescence spectroscopy; Heat capacity; Loop entropy; PK3D; Pseudoknotted RNA; RNA folding; RNA hairpin; Unfolding mechanism.

Pseudoknotted RNA mols. play important biol. roles that depend on their folded structure. To understand the underlying principles that determine their thermodn. and folding/unfolding mechanisms, we carried out a study on a variant of the mouse mammary tumor virus pseudoknotted RNA (VPK), a widely studied model system for RNA pseudoknots. Our method is based on a coarse-grained discrete-state model and the algorithm of PK3D (pseudoknot structure predictor in three-dimensional space), with RNA loops explicitly constructed and their conformational entropic effects incorporated. Our loop entropy calculations are validated by accurately capturing previously measured melting temperatures of RNA hairpins with varying loop lengths. For each of the hairpins that constitutes the VPK, we identified alternative conformations that are more stable than the hairpin structures at low temperatures and predicted their populations at different temperatures Our predictions were validated by thermodn. experiments on these hairpins. We further computed the heat capacity profiles of VPK, which are in excellent agreement with available exptl. data. Notably, our model provides detailed information on the unfolding mechanisms of pseudoknotted RNA. Anal. of the distribution of base-pairing probability of VPK reveals a cooperative unfolding mechanism instead of a simple sequential unfolding of first one stem and then the other. Specifically, we find a simultaneous “”loosening”” of both stems as the temperature is raised, whereby both stems become partially melted and co-exist during the unfolding process.

Journal of Biological Physics published new progress about Algorithm. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Category: imidazoles-derivatives.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Ilgu, Muslum; Yan, Shuting; Khounlo, Ryan M.; Lamm, Monica H.; Nilsen-Hamilton, Marit published the artcile< Common secondary and tertiary structural features of aptamer-ligand interaction shared by RNA aptamers with different primary sequences>, COA of Formula: C5H5N5, the main research area is secondary tertiary structural feature RNA aptamer ligand interaction; 2-aminopurine (2AP), molecular dynamics; aminoglycoside; isothermal titration calorimetry; neomycin-B RNA aptamer.

Aptamer selection can yield many oligonucleotides with different sequences and affinities for the target mol. Here, we have combined computational and exptl. approaches to understand if aptamers with different sequences but the same mol. target share structural and dynamical features. NEO1A, with a known NMR-solved structure, displays a flexible loop that interacts differently with individual aminoglycosides, its ligand affinities and specificities are responsive to ionic strength, and it possesses an adenosine in the loop that is critical for high-affinity ligand binding. NEO2A was obtained from the same selection and, although they are only 43% identical in overall sequence, NEO1A and NEO2A share similar loop sequences. Exptl. anal. by 1D NMR and 2-aminopurine reporters combined with mol. dynamics modeling revealed similar structural and dynamical characteristics in both aptamers. These results are consistent with the hypothesis that the target ligand drives aptamer structure and also selects relevant dynamical characteristics for high-affinity aptamer-ligand interaction. Furthermore, they suggest that it might be possible to “”migrate”” structural and dynamical features between aptamer group members with different primary sequences but with the same target ligand.

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

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Bandela, Anil Kumar; Wagner, Nathaniel; Sadihov, Hava; Morales-Reina, Sara; Chotera-Ouda, Agata; Basu, Kingshuk; Cohen-Luria, Rivka; de la Escosura, Andres; Ashkenasy, Gonen published the artcile< Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks>, Formula: C5H5N5, the main research area is functional synergy nucleopeptide network; chemical evolution; molecular networks; nucleic-acid–peptide conjugates; self-replication.

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chem. precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymic replication, a central mechanism driving early chem. evolution, have focused largely on the activity of each class of these mols. sep. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the phys. (flow) and chem. (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biol. assemblies.

Proceedings of the National Academy of Sciences of the United States of America published new progress about Autocatalysis. 452-06-2 belongs to class imidazoles-derivatives, and the molecular formula is C5H5N5, Formula: C5H5N5.

Referemce:
Imidazole – Wikipedia,
Imidazole | C3H4N2 – PubChem

Boehnke, Hendrik; Roettger, Katharina; Ingle, Rebecca A.; Marroux, Hugo J. B.; Bohnsack, Mats; Schwalb, Nina K.; Orr-Ewing, Andrew J.; Temps, Friedrich published the artcile< Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations>, Electric Literature of 452-06-2, the main research area is electronic relaxation dynamics UV photoexcited aminopurine thymine base conformation.

The fluorescent analog 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in mol. biol. for probing DNA and RNA structures and conformational dynamics. However, detailed understanding of the processes responsible for fluorescence quenching remains largely elusive on a fundamental level. Although attempts have been made to ascribe decreased excited-state lifetimes to intrastrand charge-transfer and stacking interactions, possible influences from dynamic interstrand H-bonding have been widely ignored. Here, we investigate the electronic relaxation of UV-excited 2AP·T in Watson-Crick (WC) and Hoogsteen (HS) conformations. Although the WC conformation features slowed-down, monomer-like electronic relaxation in τ ∼ 1.6 ns toward ground-state recovery and triplet formation, the dynamics associated with 2AP·T in the HS motif exhibit faster deactivation in τ ∼ 70 ps. As recent research has revealed abundant transient interstrand H-bonding in the Hoogsteen motif for duplex DNA, the established model for dynamic fluorescence quenching may need to be revised in the light of our results. The underlying supramol. photophys. mechanisms are discussed in terms of a proposed excited-state double-proton transfer as an efficient deactivation channel for recovery of the HS species in the electronic ground state.

Journal of Physical Chemistry B published new progress about Double-stranded DNA Role: BSU (Biological Study, Unclassified), BIOL (Biological Study). 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

D’Souza, Sara; Miller, Justin E.; Ahn, Jenny; Subandi, Raechel; Lozano, Daniel; Ramirez, James; Goff, Marisa; Davidian, Christina; Miller, Jeffrey H. published the artcile< The antibiotic trimethoprim displays strong mutagenic synergy with 2-aminopurine>, Name: 7H-Purin-2-amine, the main research area is antibiotic; mutagenesis; synergy; trimethoprim.

We show that trimethoprim (TMP), an antibiotic in current use, displays a strong synergistic effect on mutagenesis in Escherichia coli when paired with the base analog 2-aminopurine (2AP), resulting in a 35-fold increase in mutation frequencies in the rpoB-Rifr system. Combination therapies are often employed both as antibiotic treatments and in cancer chemotherapy. However, mutagenic effects of these combinations are rarely examined An anal. of the mutational spectra of TMP, 2AP, and their combination indicates that together they trigger a response via an alteration in deoxynucleoside triphosphate (dNTP) ratios that neither compound alone can trigger. A similar, although less strong, response is seen with the frameshift mutagen ICR191 and 2AP. These results underscore the need for testing the effects on mutagenesis of combinations of antibiotics and chemotherapeutics.

Antimicrobial Agents and Chemotherapy published new progress about 452-06-2. 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