Langmuir Aggregation of Thionin in Nucleic Acids and Its Application

Introduction　　Nucleicacidchemistryhasbeenattractingtheattentionofmanybiochemists.1 7Understandingtheinteractionofachromophorewithnucleicacidscanhelpustorealizethefunctionofsuchgeneticbiopolymersandanalyzethetransmis sionofthegeneticinformation .Thequantitativedeterminationofnucleicacidsisalsosignificantinclinicaltestsandlabora torypractice .However,theinteractionhasnotbeenelucidat edsatisfactorilyandearlierobservationshavenotbeenex plainedclearlyandreasonably ,e.g .,thePesaventoequa tion8an…     

Interactions of Safranin T with Nucleic Acids

The interactions of Safranin T (ST) with several nucleic acids have been investigated by electrochemical, UV‐visible and CD spectroscopic techniques. The form of the nucleic acid‐ST complexes is sensitive to the ratio of the two species. Two electrochemically inactive complexes such as, nucleic acid‐ST and nucleic acid‐2ST, were formed while ST interacts with nucleic acids. Two processes were obtained from spectral experiments: (1) at the high value of R (R is defined as the ratio of the total concentration of ST to that of nucleic acid), ST is groove‐binding with stacking, (2) at the low value of R, ST is groove‐binding without stacking. Intrinsic binding constants were obtained by spectral methods. The experiments also show that electrostatic binding plays an important role in the interaction of ST with nucleic acids.     

健那绿B的荧光猝灭研究及作为核酸测定探针的应用

用紫外可见光谱、稳态荧光发射及荧光寿命测定研究了核酸猝灭十二烷基磺酸钠胶束中的健那绿荧光。水溶液中弱的健那绿荧光在十二烷基磺酸钠胶束中被大大加强，其最大发射从425纳米移至410纳米，核酸的加入将猝灭健那绿的荧光，当健那绿浓度为2.5×10^–5 mol•L^-1时，荧光猝灭(F₀/F)分别与小牛胸腺DNA及鱼精DNA在2.4×10^–8 到 1.08×10^–7及 1.9×10^–8 到 3.8×10^–8 mol•L^-1范围内成正比, 检测限分别为1.3×10^–8 mol•L^-1 (小牛胸腺DNA)及6.3×10^–9 mol•L^-1 (鱼精DNA)。当DNA浓度较高时, 将系统偏离Stern-Volmer方程。这是因为动态猝灭和静态猝灭同时存在。方法已应用于鸡血提取液中DNA的测定, 测定结果与紫外法一致。     

Fluorescence Quenching and Binding Interaction of l0-Methylacridinium Iodide to Nucleic Acids

Interaction of 10‐methylacridinium iodide (MAI) as fluorescence probe with nucleobases, nucleosides and nucleic acids has been studied by UV‐visible absorption and fluorescence spectroscopy. It was found that fluorescence of MAI is strongly quenched by the nucleobases, nucleosides and nucleic acids, respectively. The quenching follows the Stern‐Volmer linear equation. The fluorescence quenching rate constant (k_q) was measured to be 10^9‐10¹⁰ (L/mol)/s within the range of diffusion‐controlled rate limit, indicating that the interaction between MAI and nucleic acid and their precursors is characteristic of electron transfer mechanism. In addition, the binding interaction model of MAI to calf thymus DNA (ct‐DNA) was further investigated. Apparent hypochromism in the absorption spectra of MAI was observed when MAI binds to ct‐DNA. Three spectroscopic methods, which include (1) UV spectroscopy, (2) fluorescence quenching of MAI, (3) competitive dual‐probe method of MAI and ethidium bromide (EB), were utilized to determine the affinity binding constants (K) of MAI and ct‐DNA. The binding constants K obtained from the above methods gave consistent data in the same range (1.0–5.5) × 10⁴L/mol, which lend credibility to these measurements. The binding site number was determined to be 1.9. The influence of thermal denaturation and phosphate concentration on the binding was examined. The binding model of MAI to ct‐DNA including intercalation and outside binding was investigated.     

Synthesis of New Chrial Building Blocks for Novel Peptide Nucleic Acids

N-Boc protected amino acids of analogues of peptide nucleic acid (PNA),which are a class of conformationally constrained building blocks based on 4-aminoproline backbone with chirality at 2-c and 4-c,have been synthesized.Those monomers can be used for the construction of novel peptide nucleic acid analogues.     

Interactions of Nile Blue Sulphate with Nucleic Acids as Studied by Resonance Light-Scattering Measurements and Determination of Nucleic Acids at Nanogram Levels

ABSTRACT

The interactions of nile blue sulphate (NBS) with nucleic acids, including calf thymus DNA, fish sperm DNA and yeast RNA, were characterized with resonance light-scattering (RLS) measurements by using a common spectrofluorometer. Accordingly a method for the determination of nucleic acids at nanogram levels was established. At pH's of 7.20～7.60 and ionic strengths lower than 0.012, the interactions of NBS with nucleic acids result in three characteristic RLS peaks at 293.4 nm, 349.4 nm and 560.4 nm. Mechanism study shows that these peaks are ascribed to the long range assembly of NBS on the molecular surface of nucleic acids, which depends on pH, ionic strength and the stranded structure of nucleic acids. A Scatchard plot was constructed by using the RLS data, yielding the assembly number and assembly constant being 6.4 and 7.13x10⁶ mol^?1 1 for NBS assembly on the molecular surface of calf thymus DNA. The same parameters are 6.6 and 4.58x10⁶ mol^?1 1 for the assembly on that of fish sperm DNA, 3.9 and 1.67x10⁶ mol^?1 1 on that of yeast RNA, respectively. Linear relationships were found between the enhanced RLS intensity at 293.4 nm and nucleic acid concentration. If 1.2x10^?5 mol I^?1 NBS was employed, 0～0.80 μg ml^?1 calf thymus DNA and fish sperm DNA, 0.20～0.60 μg ml^?1 yeast RNA can be determined with the determination limits being 3.2 ng ml^?1 for calf thymus DNA, 11.5 ng ml^?1 for fish sperm DNA and 38.3 ng ml^?1 for yeast RNA, respectively. Four synthetic samples were determined with satisfaction.     

Fluorescent Complexes of Nucleic Acids/8-Hydroxyquinoline/Lanthanum(III) and the Fluorometry of Nucleic Acids

Abstract

The ternary fluorescent complexes of nucleic acids/8-hydroxyquinoline/ lanthanum (III) were studied. Nucleic acids in the study involve natured and thermally denatured calf thymus DNA, fish sperm DNA and yeast RNA. In the range of pH 8.0–8.4 (controlled by NH₃-NH₄Cl buffer) ternary fluorescent complexes are formed which emit at 485.0 nm for calf thymus DNA and at 480.0 nm for yeast RNA (when excited at 267.0 nm) and emits at 483.0 nm for fish sperm DNA when excited at 265.0 nm. Based on the fluorescence reactions sensitive fluorometric methods for nucleic acids were proposed. Using optimal conditions, the calibration curves were linear in the range of 0.4–3.6 μg˙ml^?1 for calf thymus DNA, 0.4–4.0 μg-ml^?1 for fish sperm DNA and 0.4–4.0 μg˙ml^?1 for yeast RNA, respectively. The limits of determination (3σ) were 0.076 μg˙ml^?1 for calf thymus DNA, 0.068 μg˙ml^?1 for fish sperm DNA and 0.329 μg˙ml^?1 for yeast RNA, respectively. Five synthetic samples were determined with satisfaction.

     

Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds

The stabilities of duplexes formed by strands of novel artificial nucleic acids composed of acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) building blocks were compared with duplexes formed by the acyclic glycol nucleic acid (GNA), peptide nucleic acid (PNA), and native DNA and RNA. All acyclic nucleic acid homoduplexes examined in this study had significantly higher thermal stability than DNA and RNA duplexes. Melting temperatures of homoduplexes were in the order of aTNA>PNA≈GNA≥SNA?RNA>DNA. Thermodynamic analyses revealed that high stabilities of duplexes formed by aTNA and SNA were due to large enthalpy changes upon formation of duplexes compared with DNA and RNA duplexes. The higher stability of the aTNA homoduplex than the SNA duplex was attributed to the less flexible backbone due to the methyl group of D ‐threoninol on aTNA, which induced clockwise winding. Unlike aTNA, the more flexible SNA was able to cross‐hybridize with RNA and DNA. Similarly, the SNA/PNA heteroduplex was more stable than the aTNA/PNA duplex. A 15‐mer SNA/RNA was more stable than an RNA/DNA duplex of the same sequence.     

Determination of Nucleic Acids Based on their Resonance Light Scattering Enhancement Effect on Metalloporphyrin Derivatives

A new method for the determination of nucleic acids at nanogram per mL level is proposed based on the enhanced resonance light scattering (RLS) signal resulting from the interaction of metalloporphyrins with nucleic acids. Under optimum conditions, the weak RLS signal of metalloporphyrin is enhanced by nucleic acids, and the enhanced RLS intensity is proportional to the concentration of nucleic acids. The detection limits of calf thymus DNA were 3.5ngmL^–1, 2.9ngmL^–1 and 1.0ngmL^–1 for three metalloporphyrins, respectively. Synthetic samples were determined with satisfactory results.     

Intercalating Nucleic Acids Containing Insertions of Naphthalimide

In a study of linker‐length dependence, we evaluated naphthalimide (= 1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) and 4‐bromonaphthalimide as intercalating nucleic acids. We used a vicinal dihydroxy system when incorporating the six different naphthalimide monomers into DNA, and found the minimum linker‐length to be five C‐atoms. With this length of the linker, naphthalimide was discriminating between DNA and RNA – stabilizing DNA, while destabilizing RNA. Furthermore, naphthalimide showed universal base character by hybridizing to the four natural bases with a range as narrow as 1.4°. When compared to pyrene, naphthalimide with the same linker‐length gave significantly higher thermal meltings when hybridized to DNA.     

A High-Sensitivity Assay of Nucleic Acids with Tetraphenyl Porphyrin Cobalt Chlorine by Resonance Light Scattering Technique

Abstract

A novel probe, tetraphenyl porphyrin cobalt chlorine (CoTPPCl), is first applied to determine nucleic acids at the nanogram level based on the measurement of resonance light scattering (RLS) signals, which result from the interaction of CoTPPCl with nucleic acids. Under pH 6.37 conditions, the reaction between CoTPPCl and nucleic acid enhances the weak resonance light scattering (RLS) signal of CoTPPCl, and the enhanced light scattering intensity is proportional to the concentration of nucleic acid. The method is sensitive (3.45 ng/mL for ctDNA), simple (one step and a common fluorimeter), and tolerant of the metal ions and other coexistent substances. The mode of the combination between CoTPPCl and nucleic acids and the reasons for RLS enhancement are clearly clarified. Synthetic samples were determined with satisfactory results.     

MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures

One major challenge in nucleic acids analysis by hybridization probes is a compromise between the probe's tight binding and sequence‐selective recognition of nucleic acid targets folded into stable secondary structures. We have been developing a four‐way junction (4WJ)‐based sensor that consists of a universal stem‐loop (USL) probe immobilized on an electrode surface and two adaptor strands (M and F). The sensor was shown to be highly selective towards single base mismatches at room temperature, able to detect multiple targets using the same USL probe, and have improved ability to detect folded nucleic acids. However, some nucleic acid targets, including natural RNA, are folded into very stable secondary and tertiary structures, which may represent a challenge even for the 4WJ sensors. This work describes a new sensor, named MVF since it uses three probe stands M, V and F, which further improves the performance of 4WJ sensors with folded targets. The MVF sensor interrogating a 16S rRNA NASBA amplicon with calculated folding energy of ?32.82 kcal/mol has demonstrated 2.5‐fold improvement in a signal‐to‐background ratio in comparison with a 4WJ sensor lacking strand V. The proposed design can be used as a general strategy in the analysis of folded nucleic acids including natural RNA.     

Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology

Azobenzene has been widely used as a photoregulator due to its reversible photoisomerization, large structural change between E and Z isomers, high photoisomerization yield, and high chemical stability. On the other hand, some azobenzene derivatives can be used as universal quenchers for many fluorophores. Nucleic acid is a good candidate to be modified because it is not only the template of gene expression but also widely used for building well‐organized nanostructures and nanodevices. Because the size and polarity distribution of the azobenzene molecule is similar to a nucleobase pair, the introduction of azobenzene into nucleic acids has been shown to be an ingenious molecular design for constructing light‐switching biosystems or light‐driven nanomachines. Here we review recent advances in azobenzene‐modified nucleic acids and their applications for artificial regulation of gene expression and enzymatic reactions, construction of photoresponsive nanostructures and nanodevices, molecular beacons, as well as obtaining structural information using the introduced azobenzene as an internal probe. In particular, nucleic acids bearing multiple azobenzenes can be used as a novel artificial nanomaterial with merits of high sequence specificity, regular duplex structure, and high photoregulation efficiency. The combination of functional groups with biomolecules may further advance the development of chemical biotechnology and biomolecular engineering.     

Glycerol-salt Mediated Stacking of Nucleic Acids in CZE

Nucleic acid samples with high concentrations of salt could be stacked and well separated during capillary zone electrophoresis (CZE) by adding glycerol into the samples and using a Tris-Borate-EDTA (TBE) buffer (pH 8.3) as the separation medium. The so-called glycerol-salt mediated stacking was found applicable to different types of nucleic acids. Three nucleic acids: a 16s rRNA (1,542 nt), a double stranded DNA (1.6 k bp), and a single stranded DNA (30 nt), were tested as demos in the experiments. When the sample matrix contained 50 mM KCl and 50% (w/v) glycerol, the 16s rRNA sample could be stacked as high as 30 times compared with the sample without KCl. All the nucleic acids could be stacked effectively when high concentrations of glycerol (>50%) and salt (more than 50 mM) were present in the sample matrix, while the dsDNA could be stacked with high concentrations of glycerol (>50%) alone. Cen Qi and Hongping Wei contributed equally to this work.     

From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives

Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using ¹³C, ¹⁵N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.     

Microfluidic Isolation of Nucleic Acids

The detection of nucleic acids (NAs) within micro total analysis systems (μTASs) for point‐of‐care use is a rapidly developing research area. The efficient isolation of NAs from a raw sample is crucial for these systems to be maximally effective. The use of microfluidics assists in reducing sample sizes and reagent consumption, increases speed, avoids contamination, and enables automation. Through miniaturization into microchips, new techniques have been realized that would be unfavorable and inconvenient to use on a macroscopic scale, but provide an excellent platform for the purification of NAs on a microscopic scale. This Review considers the complexities of NA isolation with miniaturized and microfluidic devices, as well as the considerations when choosing a technique for microfluidic NA isolation, along with their advantages, disadvantages, and potential applications. The techniques presented include using silica‐based surfaces, functionalized paramagnetic beads, oligonucleotide‐modified polymer surfaces, pH‐dependent charged surfaces, Al₂O₃ membranes, and liquid‐phase isolation. This Review provides a basis to develop the chemistry to improve NA isolation and move it toward achieving 100 % efficiencies.     

From Alkanes to Carboxylic Acids: Terminal Oxygenation by a Fungal Peroxygenase

A new heme–thiolate peroxidase catalyzes the hydroxylation of n‐alkanes at the terminal position—a challenging reaction in organic chemistry—with H₂O₂ as the only cosubstrate. Besides the primary product, 1‐dodecanol, the conversion of dodecane yielded dodecanoic, 12‐hydroxydodecanoic, and 1,12‐dodecanedioic acids, as identified by GC–MS. Dodecanal could be detected only in trace amounts, and 1,12‐dodecanediol was not observed, thus suggesting that dodecanoic acid is the branch point between mono‐ and diterminal hydroxylation. Simultaneously, oxygenation was observed at other hydrocarbon chain positions (preferentially C2 and C11). Similar results were observed in reactions of tetradecane. The pattern of products formed, together with data on the incorporation of ¹⁸O from the cosubstrate H₂¹⁸O₂, demonstrate that the enzyme acts as a peroxygenase that is able to catalyze a cascade of mono‐ and diterminal oxidation reactions of long‐chain n‐alkanes to give carboxylic acids.     

核酸对氯化银胶体溶液共振光散射的猝灭作用及其应用

报道了一种测定水溶液中核酸的方法,该法基于核酸对氯化银溶胶共振射光的猝灭作用。在理想测定条件下,散射光的猝灭程度正比于核酸的浓度,三种核酸（ｃａｌｆ ｔｈｙｍｕｓ ＤＮＡ,ｈｅｒｒｉｎｇ ＤＮＡ ａｎｄ ＹｅａｓｔＲＮＡ）的线性范围分别为０－２０μｇ／Ｌ,０－６０μｇ／Ｌ和０－８０μｇ／Ｌ,检测限分别为０．６５μｇ／Ｌ,１．１μｇ／Ｌ和１．９μｇ／Ｌ。６种合成样品的测定结果令人满意,机理研究结果表明,核酸中的碱基（尤其是嘌呤碱）同银离子具有很强的结合能力,这种结合影响了氯化银的沉淀平衡,导致了氯化银溶胶共振散射光的猝灭。