Ultra‐fast adenosine 5′‐triphosphate,adenosine 5′‐diphosphate and adenosine 5′‐monophosphate detection by pressure‐assisted capillary electrophoresis UV detection

Herein, we report a new CE method to measure adenine nucleotides adenosine 5′‐triphosphate, adenosine 5′‐diphosphate, and adenosine 5′‐monophosphate in red blood cells. For this purpose, 20 mmol/L sodium acetate buffer at pH 3.80 was used as running electrolyte, and the separation was performed by the simultaneous application of a CE voltage of 25 kV and an overimposed pressure of 0.2 psi from inlet to outlet. A rapid separation of these analytes in less than 1.5 min was obtained with a good reproducibility for intra‐ and inter‐assay (CV<4 and 8%, respectively) and an excellent analytical recovery (from 98.3 to 99%). The applicability of our method was proved by measuring adenine nucleotides in red blood cells.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

An Fe2+‐ and α‐Ketoglutarate‐Dependent Halogenase Acts on Nucleotide Substrates

While halogenated nucleosides are used as common anticancer and antiviral drugs, naturally occurring halogenated nucleosides are rare. Adechlorin (ade) is a 2′‐chloro nucleoside natural product first identified from Actinomadura sp. ATCC 39365. However, the installation of chlorine in the ade biosynthetic pathway remains elusive. Reported herein is a Fe²⁺‐α‐ketoglutarate halogenase AdeV that can install a chlorine atom at the C2′ position of 2′‐deoxyadenosine monophosphate to afford 2′‐chloro‐2′‐deoxyadenosine monophosphate. Furthermore, 2′,3′‐dideoxyadenosine‐5′‐monophosphate and 2′‐deoxyinosine‐5′‐monophosphate can also be converted, albeit 20‐fold and 2‐fold, respectively, less efficiently relative to the conversion of 2′‐deoxyadenosine monophosphate. AdeV represents the first example of a Fe²⁺‐α‐ketoglutarate‐dependent halogenase that converts nucleotides into chlorinated analogues.     

Development and validation of a rapid and sensitive HPLC method for the quantification of 5‐fluorocytosine and its metabolites

To study the intracellular metabolism of the prodrug 5‐fluorocytosine (5FC), we developed a novel reverse‐phase high‐performance liquid chromatography method to simultaneously detect 5FC and its four major anabolic metabolites: 5‐fluorouracil, 5‐fluorouridine, 5‐fluorouridine‐monophosphate and 5‐fluoro‐2′deoxyuridine‐5′‐monophosphate. Separation of each compound was accomplished under isocratic conditions using a C₁₈ column and mobile phase of formic acid–water (1 : 99 v/v). The method was validated for both accuracy and reproducibility in cell culture media. Additionally, metabolites were assessed for stability at ambient temperatures and following freeze–thaw cycles. Calibration curves were linear over a range of 1–200 μg/mL. Limit of quantification for four of the five compounds was 1 μg/mL in cell culture media (RSD < 11%). This method was successfully used to monitor intracellular conversion of 5FC to its metabolic products over a 24h period. Copyright © 2009 John Wiley & Sons, Ltd.     

Cyclic‐Disulfide‐Based Prodrugs for Cytosol‐Specific Drug Delivery

The cytosolic conversion of therapeutically relevant nucleosides into bioactive triphosphates is often hampered by the inefficiency of the first kinase‐mediated step. Nucleoside monophosphate prodrugs can be used to bypass this limitation. Herein we describe a novel cyclic‐disulfide class of nucleoside monophosphate prodrugs with a cytosol‐specific, reductive release trigger. The key event, a charge‐dissipating reduction‐triggered cyclodeesterification leads to robust cytosolic production of the cyclic 3′,5′‐monophosphate for downstream enzymatic processing. The antiviral competence of the platform was demonstrated with an O‐benzyl‐1,2‐dithiane‐4,5‐diol ester of 2′‐C‐methyluridine‐3′,5′‐phosphate. Both in vitro and in vivo comparison with the clinically efficacious ProTide prodrug of 2′‐deoxy‐2′‐α‐fluoro‐β‐C‐methyluridine is provided. The cytosolic specificity of the release allows for a wide range of potential applications, from tissue‐targeted drug delivery to intracellular imaging.     

Semiempirical studies on the interactions of dialkyldi(aquo)tin cations, [R2Sn(H2O)2]2+, with selected nucleotides

Semiempirical calculations have been carried out on the interactions of [R₂Sn(H₂O)₂]²⁺, [R = H(CH₂)_n: n = 1–8], mainly with five nucleotides, 5′‐adenosine monophosphate (5′‐AMP), but also with guanosine 5′‐monophosphate (5′‐GMP), cytidine 5′‐monophosphate (5′‐CMP), uridine‐5′‐monophosphate (5′‐UMP) and inosine 5′‐monophosphate (5′‐IMP). The preferred sites of interaction were calculated to be the ribose O2 and O3 hydroxyl oxygens and/or the phosphate oxygens, with the nitrogen sites in the bases the least attractive to the tin compounds. This is in general agreement with experimental findings. Structures of the 1:1 coordination complexes vary from distorted tetrahedral, to distorted trigonal pyramidal to distorted octahedral geometries. Copyright © 2007 John Wiley & Sons, Ltd.     

Synthesis and Pairing Properties of 3′‐Deoxyribopyranose (4′→2′)‐Oligonucleotides (‘p‐DNA')

The preparation and the pairing properties of the new 3′‐deoxyribopyranose (4′→2′)‐oligonucleotide (=p‐DNA) pairing system, based on 3′‐deoxy‐β‐D ‐ribopyranose nucleosides is presented. D ‐Xylose was efficiently converted to the prefunctionalized 3‐deoxyribopyranose derivative 4‐O‐[(tert‐butyl)dimethylsilyl]‐3‐deoxy‐D ‐ribopyranose 1,2‐diacetate 8 (obtained as a 4 : 1 mixture of α‐ and β‐D ‐anomers; Scheme 1). From this sugar building block, the corresponding, appropriately protected thymine, guanine, 5‐methylcytosine, and purine‐2,6‐diamine nucleoside phosphoramidites 29 – 32 were prepared in a minimal number of steps (Schemes 2–4). These building blocks were assembled on a DNA synthesizer, and the corresponding p‐DNA oligonucleotides were obtained in good yields after a one‐step deprotection under standard conditions, followed by HPLC purification (Scheme 5 and Table 1). Qualitatively, p‐DNA shows the same pairing behavior as p‐RNA, forming antiparallel, exclusively Watson‐Crick‐paired duplexes that are much stronger than corresponding DNA duplexes. Duplex stabilities within the three related (i.e., based on ribopyranose nucleosides) oligonucleotide systems p‐RNA, p‐DNA, and 3′‐O‐Me‐p‐RNA were compared with each other (Table 2). Intrinsically, p‐RNA forms the strongest duplexes, followed by p‐DNA, and 3′‐O‐Me‐p‐RNA. However, by introducing the nucleobases purine‐2,6‐diamine (D) and 5‐methylcytosine (M) instead of adenine and cytosine, a substantial increase in stability of corresponding p‐DNA duplexes was observed.     

Preparation of a Hyper‐cross‐linked Polymer Monolithic Column and Its Application to the Sensitive Determination of Genomic DNA Methylation

A hyper‐cross‐linked polymer monolithic column, poly(methacrylatoethyl trimethyl ammonium‐co‐vinylbenzene chloride‐co‐divinylbenzene) (MATE‐co‐VBC‐co‐DVB) with phenyl and quaternary ammonium groups was successfully prepared in the current study. The prepared monolith possesses large specific surface area, narrow mesopore size distribution and high column efficiency. The poly(MATE‐co‐VBC‐co‐DVB) monolithic column was demonstrated to have strong anion exchange/reversed‐phase (SAX/RP) mixed‐mode retention for analytes on capillary liquid chromatography (cLC). By using this monolithic column, we developed a rapid and sensitive method for the detection of DNA methylation. Our results showed that six nucleobases (adenine, guanine, cytosine, thymine, uracil, and 5‐methylcytosine (5‐mC)) can be baseline separated within 15 min by electrostatic repulsion and hydrophobic interactions between nucleobases and the monolithic stationary phase. The limit of detection (LOD, signal/noise=3) of 5‐mC is 0.014 pmol and endogenous 5‐mC can be distinctly detected by using only 10 ng genomic DNA, which is comparable to that obtained by mass spectrometry analysis. Furthermore, by using the method developed here, we found that DNA methylation inhibitor 5‐azacytidine (5‐aza‐C) and 5‐aza‐2′‐deoxycytidine (5‐aza‐CdR) could induce a significant decrease of genome‐wide DNA methylation in human lung carcinoma cells (A549) and cervical carcinoma cells (HeLa).     

A Facile and Cost‐effective Electroanalytical Strategy for the Quantification of Deoxyguanosine and Deoxyadenosine in Oligonucleotides Using Screen‐printed Graphite Electrodes

The development of electroanalytical methods for the detection and quantification of nucleotides in DNA offers vital implications in assessing the degree of oxidation or epigenetic modification in DNA. Unfortunately, the electrochemical response of oligonucleotides is strongly influenced by the size, composition and nucleic base sequence. In this article, an optimized analytical procedure for the enzymatically breakdown of the oligonucleotides to their corresponding nucleotides for the evaluation of the electrochemical response through the use of square wave voltammetry (SWV) is presented. Enzymatic digestion of oligonucleotides has been optimized in terms of buffer composition, digestion time, strategy for stopping the enzymatic reaction and filtration requirement for enzyme removal, and then compared to an established protocol. Under the optimized protocol SWV response of a number of untreated and enzymatically digested six‐mer oligonucleotides, namely 5′‐GGGGGG‐3′, 5′‐AAAAAA‐3′, 5′‐CGCGCG‐3′ and 5′‐AAACGC‐3′ have been analysed, providing a higher sensitivity for the determination of guanosine and adenosine monophosphate species under digestion conditions with a more facile and cost effective procedure. The novel strategy for the enzymatically treated oligonucleotides in combination with the SWV response provides a proof of principle for feasible applications in the diagnosis of methylated guanosine in DNA as a potential biomarker due to its relation with cancer.     

The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions

The role of adenine (A) derivatives in DNA damage is scarcely studied due to the low electron affinity of base A. Experimental studies demonstrate that low‐energy electron (LEE) attachment to adenine derivatives complexed with amino acids induces barrier‐free proton transfer producing the neutral N₇‐hydrogenated adenine radicals rather than conventional anionic species. To explore possible DNA lesions at the A sites under physiological conditions, probable bond ruptures in two models—N₇‐hydrogenated 2′‐deoxyadenosine‐3′‐monophosphate (3′‐dA(N7H)MPH) and 2′‐deoxyadenosine‐5′‐monophosphate (5′‐dA(N7H)MPH), without and with LEE attachment—are studied by DFT. In the neutral cases, DNA backbone breakage and base release resulting from C_3′?O_3′ and N₉?C_1′ bond ruptures, respectively, by an intramolecular hydrogen‐transfer mechanism are impossible due to the ultrahigh activation energies. On LEE attachment, the respective C_3′?O_3′ and N₉?C_1′ bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions via a pathway of intramolecular proton transfer (PT) from the C_2′ site of 2′‐deoxyribose to the C₈ atom of the base moiety become effective, and this indicates that substantial DNA backbone breaks and base release can occur at non‐3′‐end A sites and the 3′‐end A site of a single‐stranded DNA in the physiological environment, respectively. In particular, compared to the results of previous theoretical studies, not only are the electron affinities of 3′‐dA(N7H)MPH and 5′‐dA(N7H)MPH comparable to those of hydrogenated pyrimidine derivatives, but also the lowest energy requirements for the C_3′?O_3′ and N₉‐glycosidic bond ruptures in [3′‐dA(N7H)MPH]^? and [5′‐dA(N7H)MPH]^? anions, respectively, are comparable to those for the C_3′?O_3′ and N₁‐glycosidic bond cleavages in corresponding anionic hydrogenated pyrimidine derivatives. Thus, it can be concluded that the role of adenine derivatives in single‐stranded DNA damage is equally important to that of pyrimidine derivatives in an irradiated cellular environment.     

Type I Photosensitization of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) by Biopterin and its Photoproduct Formylpterin

Biopterin (Bip) and its photoproducts 6‐formylpterin (Fop) and 6‐carboxypterin (Cap) accumulate in the skin of patients suffering from vitiligo, a chronic depigmentation disorder where the protection against UV radiation fails because of the lack of melanin. These compounds absorb in the UV‐A inducing a potential photosensitizing action that can cause damage to DNA and other biomolecules. In this work, we have investigated the capability of these pterin derivatives (Pt) to act as photosensitizers under UV‐A irradiation for the degradation of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) in aqueous solutions, as model DNA target. Steady‐state and time‐resolved experiments were performed and the effect of pH was evaluated. The results showed that photosensitized degradation of 5′‐dAMP was only observed under acidic conditions, and a mechanistic analysis revealed the participation of the triplet excited state of the pterin derivatives (³Pt*) by electron transfer yielding the corresponding pair of radical ions (Pt^?? and 5′‐dAMP^?+), with successive photosensitizer recovery by electron transfer from Pt^?? to O₂. Finally, 5′‐dAMP^?+ participates in subsequent reactions to yield degradation products.     

Syntheses of 5′‐Nucleoside Monophosphate Derivatives with Unique Aminal,Hemiaminal, and Hemithioaminal Functionalities: A New Class of 5′‐Peptidyl Nucleotides

A number of synthetically useful transformations have been developed to generate novel 5′‐peptidyl nucleoside monophosphate analogues that incorporate sensitive phosphoaminal, ‐hemiaminal or ‐hemithioaminal functionalities. The strategies adopted entailed the coupling between dipeptides, which enclose a reactive Cα‐functionalized glycine residue and phosphate or phosphorothioate moieties. These developments led to potentially powerful and general methodologies for the preparation of α‐phosphorylated pseudopeptides as well as nucleoside monophosphate mimics. The resulting conjugates are of interest for a variety of important applications, which range from drug development to synthetic biology, as pronucleotides or artificial building blocks for the enzymatic synthesis of xenobiotic information systems. The potential of all dipeptide‐TMP conjugates as pyrophosphate mimics in the DNA polymerization reaction was tested, and the influence of the nature of the linker was evaluated by in vitro chain elongation assay in the presence of wild‐type microbial DNA polymerases.     

Preferential 5‐Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten–eleven translocation) family proteins oxidize 5‐methylcytosine (mC) to 5‐hydroxymethylcytosine (hmC), 5‐formylcytosine (fC), and 5‐carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG‐methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.     

Sensitive and validated LC‐MS/MS methods to evaluate mycophenolic acid pharmacokinetics and pharmacodynamics in hematopoietic stem cell transplant patients

Monitoring of pharmacodynamics in addition to pharmacokinetics is one of strategies to individualize mycophenolate mofetil therapy. The purpose of this study was to develop sensitive liquid chromatography–tandem mass spectrometry (LC‐MS/MS) methods for evaluation of the pharmacokinetics and pharmacodynamics of mycophenolic acid (MPA). Concentrations of mycophenolic acid glucuronide (MPAG), mycophenolic acid acyl‐glucuronide, as well as unbound MPA and MPAG, were determined, and inosine‐5′‐monophosphate dehydrogenase activity was calculated by measuring concentrations of produced xanthosine‐5′‐monophosphate (XMP) and intracellular adenosine‐5′‐monophosphate after incubation of peripheral blood mononuclear cell (PBMC) lysates. A metal‐free Mastro^TM column and two gradient patterns were used to improve the quantification limit of XMP to 0.1 μm . In the clinical MPA concentration range, the linearity of the calibration curve, inter‐ and intra‐day precision and accuracy satisfied the relevant US Food and Drug Administration guidelines. The MPA concentrations in hematopoietic stem cell transplant (HSCT) patients determined by the enzyme assay and the present LC‐MS/MS method showed a good correlation (r² = 0.95, p < 0.001). In this study, we report sensitive and validated LC‐MS/MS methods to evaluate the pharmacokinetics and pharmacodynamics of MPA, which are sufficiently sensitive to assess small quantities of PBMC lysates collected shortly after HSCT. Copyright © 2015 John Wiley & Sons, Ltd.     

Convenient Synthesis of Nucleoside‐5′‐Diphosphates from the Corresponding Ribonucleoside‐5′‐phosphoroimidazole

The reaction of ribonucleoside‐5′‐phosphoroimidazolide with a tributylammonium orthophosphate in anhydrous dimethylformamide at room temperature provides a general method for the synthesis of nucleoside‐5′‐diphosphates. The novelty of the approach is to use the triethylammonium salt of 5′‐monophosphate nucleoside derivative prior to the imidazolate reaction with imidazole, triphenylphosphine, and 2,2′‐dithiodipyridine. Deprotection, followed by displacement of the imidazole moiety using tributylammonium orthophosphate and a catalytic amount of zinc chloride in dimethylformamide gave the desired 5′‐diphosphate products. The triethyl ammonium salt of 5′‐diphosphate nucleosides was purified by flash chromatography using DEAE (diethylaminoethyl weak anion exchange resin) Sepharosa fast flow packed in an XK 50/60 column on an Akta FPLC (Fast Protein Liquid Chromatography). Synthesis procedures are reported for adenosine‐5′‐diphosphate, uridine‐5′‐diphosphate, cytidine‐5′‐diphosphate, and guanosine‐5′‐diphosphate. Yields for the displacement reactions ranged from 95 to 97%. Thus, this method offers the advantages of shorter reaction time, greater product yield, and a more cost‐effective synthetic route.     

碳链长度对芳香异羟肟酸二烃基锡配合物与5’-AMP或DNA相互作用的影响

选择体外筛选活性强的Bu₂Sn(4-FC₆H₄C(O)NHO)₂和活性弱的有机锡化合物Me₂Sn(4-FC₆H₄C(O)NHO)₂为模型,利用高分辨¹H NMR和³¹P NMR 技术比较研究这两个有代表性的有机锡化合物与DNA的基本组成单元5’-AMP在不同时间、不同条件下的作用模式并用紫外法进一步研究其与DNA的相互作用。结果显示,具有不同碳链的有机锡化合物与5’-AMP相互作用明显不同,含较长碳链的Bu₂Sn(4-FC₆H₄C(O)NHO)₂与5’-AMP的作用明显强于Me₂Sn(4-FC₆H₄C(O)NHO)₂,Me₂Sn(4-FC₆H₄C(O)NHO)₂分子可能只与5’-AMP的磷酸骨架静电结合,与整个分子作用较弱,而含丁基的Bu₂Sn(4-FC₆H₄C(O)NHO)₂可能除了与磷酸骨架静电结合,也与疏水碱基具有超分子相互作用而更有利于与5’-AMP稳定结合。Bu₂Sn(4-FC₆H₄C(O)NHO)₂的长链有机配体在与DNA的作用模式上发挥了重要作用。     

Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization

We report a rapid and sensitive electrochemical strategy for the detection of gene‐specific 5‐methylcytosine DNA methylation. Magnetic beads (MBs) modified with an antibody for 5‐methylcytosines (5‐mC) are used for the capture of any 5‐mC methylated single‐stranded (ss)DNA sequence. A flanking region next to the 5‐mCs of the captured methylated ssDNA is recognized by hybridization with a synthetic biotinylated DNA sequence. Amperometric transduction at disposable screen‐printed carbon electrodes (SPCEs) is employed. The developed biosensor has a dynamic range from 3.9 to 500 pm and a limit of detection of 1.2 pm for the methylated synthetic sequence of the tumor suppressor gene O‐6‐methylguanine‐DNA methyltransferase (MGMT) promoter region. The method is applied in the 45‐min analysis of specific methylation in the MGMT promoter region directly in raw spiked human serum samples and in genomic DNA extracted from U‐87 glioblastoma cells and paraffin‐embedded brain tumor tissues without any amplification and pretreatment step.     

Enzymatic Conversion of Cypridina Luciferyl Sulfate to Cypridina Luciferin with Coenzyme A as a Sulfate Acceptor in Cypridina (Vargula) hilgendorfii

In the luminous ostracod Cypridina (presently Vargula) hilgendorfii, Cypridina luciferyl sulfate (3‐enol sulfate of Cypridina luciferin) is converted to Cypridina luciferin by a sulfotransferase with 3′‐phosphoadenosine‐5′‐phosphate (PAP) as a sulfate acceptor. The resultant Cypridina luciferin is used for the luciferase–luciferin reaction of Cypridina to emit blue light. The luminescence stimulation with major organic cofactors was examined using the crude extracts of Cypridina specimens, and we found that the addition of coenzyme A (CoA) to the crude extracts significantly stimulated luminescence intensity. Further, the light‐emitting source in the crude extracts stimulated with CoA was identified as Cypridina luciferyl sulfate, and we demonstrated that CoA could act as a sulfate acceptor from Cypridina luciferyl sulfate. In addition, the sulfate group of Cypridina luciferyl sulfate was also transferred to adenosine 5′‐monophosphate (5′‐AMP) and adenosine 3′‐monophosphate (3′‐AMP) by a sulfotransferase. The sulfated products corresponding to CoA, 5′‐AMP and 3′‐AMP were identified using mass spectrometry. This is the first report that CoA can act as a sulfate acceptor in a sulfotransferase reaction.     

Synthesis and Anti‐HIV Activity of Triazolo‐Fused 3′,5′‐Cyclic Nucleoside Analogues Derived from an Intramolecular Huisgen 1,3‐Dipolar Cycloaddition

Triazolo‐fused 3′,5′‐cyclic nucleoside analogues were synthesized by an intramolecular 1,3‐dipolar cycloaddition of nucleoside‐derived azido‐alkynes in a regio‐ and stereospecific manner. The thymine nucleoside base in these target compounds was transformed successfully into the corresponding 5‐methylcytosine component. The synthesized compounds were examined in a MAGI assay for exploring the anti‐HIV activity and in a H9 T lymphocytes assay for measuring the cell toxicity.