A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson–Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15–25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35–90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.     

Extending the possibility of an N-Troc-protected sialic acid donor toward variant sialo-glycoside synthesis

The potential of an N-Troc-protected sialic acid donor, equipped with phenylsulfenyl functionality as a leaving group, has been explored. As a result, the entitled donor was proven to be highly reactive and to have broad applicability toward the synthesis of variant sialo-glycans, which have N-glycolyl, de-N-acetyl, 1,5-lactam and 8-O-sulfo sialic acid analogs.     

Recent studies on phosphorus-bridging carbonyl derivatives: organophosphorus analogs of aldehydes and ketones

Reactions of disodium tetracarbonylferrate, Na₂Fe(CO)₄, with sterically hindered dialkylaminodichlorophosphines, R₂NPCl₂ (R₂N=diisopropylamino, dicyclohexylamino, and 2,2, 6, 6-tetramethylpiperidino) in diethyl ether lead to the air-stable phosphorus-bridging carbonyl derivatives (R₂NP)₂COFe₂(CO)₆ as the major products. The phosphorus-bridging carbonyl group in (i-Pr₂NP)₂COFe₂(CO)₆ has been found to undergo the following types of reactions: 1)Reduction, 2)Acylation, 3)Extrusion of the carbonyl group. The mechanisms of the reactions have been considered.This work was presented at the Workshop «The Modern Problems of Heteroorganic Chemistry» held on the ship «Nikolai Bauman» during the period May 8–13, 1993.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1858–1867, November, 1993.     

四（对羟基苯基）卟啉—硅胶固定相的合成及在核苷酸分析中的应用

以大孔微硅胶作基体，经γ－氨丙基三乙氧基硅烷活化与间隔臂氯代环内烷反应后，再与预先合成的四（对羟基苯基）卟啉配体键合，构成电荷转移型亲和色谱固定相。以ＰＨ＝７．０的磷酸盐缓冲溶液作流动相，成功实现对一些核苷酸的高效液相亲和色谱分离。     

Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations

We present a reliable, rapid, and economical multiplex amplified product-length polymorphism (APLP) method for analyzing the haplogroup-diagnostic mitochondrial single-nucleotide polymorphisms (mtSNPs) in East Asian populations. By examining only 36 haplogroup-specific mtSNPs in the coding region by using four 9-multiplex polymerase chain reaction (PCR) and subsequent electrophoresis, we could safely assign 1815 individuals from 8 populations of Japanese, Korean, Chinese, and Germans to 45 relevant haplogroups. This multiplex APLP analysis of coding-region mtSNPs for haplogrouping is especially useful not only for molecular phylogenetic studies but also for large-scale association studies due to its rapid and economical nature. This is the first panel of mtSNPs in the coding region to be used for haplogrouping of East Asian populations.     

Synthesis of diastereomeric 3-hydroxy-4-pyrrolidinyl derivatives of nucleobases

The work deals with the synthesis of hydroxypyrrolidine analogs of nucleosides. Starting from the optically pure l- or d-tartaric acid, we improved the synthesis of enantiomeric trans-3,4-dihydroxypyrrolidines and elaborated a procedure for the synthesis of all possible diastereoisomers of 3-hydroxy-4-pyrrolidinyl derivatives of both purine and pyrimidine nucleobases. The prepared compounds were tested for cytostatic and antiviral properties but no significant activity was found.     

Aqueous Solubilities, Infinite Dilution Activity Coefficients and Octanol–Water Partition Coefficients of Tricyclic Analogs of Acyclovir

Solubilities of tricyclic analogs of acyclovir have been determined in water at 25, 35, and 45°C and in octanol, water-saturated octanol, and octanol-saturated water at 25°C. Octanol-water partition coefficients were determined at 25°C. Melting temperatures and molar enthalpies of fusion were measured. Activity coefficients in water, octanol, and in aqueous octanol solutions were determined and are discussed. The effect of hydrophilic and hydrophobic substituents in the tricyclic analogs on their thermodynamic properties are discussed. The standard Gibbs energy of transfer between the saturated phases were found to correlate with known values of the melting point of the solvents and the solubilities of the solute. For a number of the compounds examined, correlations between the minimum inhibitory concentration against the herpes simplex virus type 1 (HSV-1) and type 2 (HSV-2), varicella-zoster virus (VZV), thymidine kinase-deficient (TK^–) strains of VZV and were established. Detailed conclusions have been derived concerning the relationships between the structure and the thermodynamic parameters of the compounds examined.     

Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

A statistical method to detect chromosomal regions with DNA copy number alterations using SNP-array-based CGH data

Single nucleotide polymorphism (SNP) arrays were used to detect chromosomal regions with DNA copy number alterations. Current statistical methods for microarray-based comparative genomic hybridization (array-CGH) analysis generally assume certain relationships among adjacent markers on the same chromosome, and these assumptions may be questionable. For an SNP-array-based CGH study, multiple normal reference SNP arrays were collected. In order to utilize these normal reference SNP arrays, we derived an empirical distribution of signal ratios for each SNP marker. With an assumed threshold value for the overall error rate control and the defined signal ratio ranges for chromosomal amplification and deletion, we proposed a procedure to identify chromosomal alteration regions based on several bootstrapped one-sample t-tests and the false discovery rate control. When we have multiple arrays for different individuals with the same disease, our method can also be used to detect SNP markers for chromosomal alteration regions that are common among these individuals. We applied our method to a published SNP array data set for breast carcinoma cell lines. For an individual with breast cancer, numerous chromosomal alteration regions were identified. Compared to results of previous studies, our method identified more chromosomal alteration regions, with some being implicated in the literature to harbor genes associated with breast cancer. For multiple cancer arrays, our results suggested the existence of common chromosomal alteration regions. However, a high proportion of false positives also indicated that genetic variations among different individuals with breast cancer can be present.     

Modification of silica gel with diethylamino group by novel reaction and its characterization

1,3,5,7-Tetramethylcyclotetrasiloxane (H₄) was deposited on silica gel at 80°C by utilizing a chemical vapor deposition (CVD) method, where it was catalytically polymerized to form a surface coating of polymethylsiloxane (PMS). Treated silica gel (PMS-Si) increased in weight up to a plateau level, and there was no further increase with increasing reaction time. The film of PMS was partially cross linked; typical values of crosslinking ratio and film thickness were 2% and 0.6 nm, respectively. An anionic ion exchanger containing diethylamino groups was synthesized from PMS-Si by hydrosilylation of allyl glycidyl ether followed by treatment with diethylamine. Its structure was confirmed by¹³C and²⁹Si CP/MAS NMR spectroscopy and FT-IR spectrophotometry. Characterization of silica gel (DEA-Si) modified with diethylamino group was evaluated by a packing of the column for liquid chromatography. As a mixture of five nucleotides was completely separated, it was recognized that DEA-Si was operated by ion exchange action. Because the surface of the silica gel was covered with hydrophobic PMS, the peak heights and retention times did not change after washing of the column with alkaline solution.