Formation of C7-species pyrolysis products from ethylene-propylene heterosequences of poly(ethylene-co-propylene)

Properties of ethylene-propylene copolymer (EPM) are determined by ethylene/propylene ratio and degree of block and random sequences. EPM was pyrolyzed and the pyrolysis products were analyzed using gas chromatography/mass spectrometry (GC/MS) to examine pyrolysis products formed from the ethylene-propylene heterosequences. Pyrolysis products formed from EPM were compared with those formed from polyethylene (PE) and polypropylene (PP) to determine the pyrolysis products formed from ethylene-propylene heterosequences of EPM. Principal pyrolysis products formed from ethylene-propylene heterosequences were 3-methyl-1-hexene, 4-methyl-1-hexene, 2-methyl-1-hexene, and 2-heptene. Order of the relative intensity of the pyrolysis products was 2-methyl-1-hexene > 4-methyl-1-hexene > 3-methyl-1-hexene > 2-heptene. The relative abundances of the pyrolysis products decreased as the pyrolysis temperature increased. Relative abundances of the specific pyrolysis products formed from ethylene-propylene heterosequences may be used for determination of the relative degree of random sequences of EPM as well as ethylene-propylene-diene terpolymer (EPDM).     

Segmentation of Heteropolymer Sequences Specifying Subsequences with Different Composition and Statistical Properties

We have studied the segmentation of two‐letter AB heterosequences composed of subsequences with different composition and distribution of A and B monomer units along the chain. Our approach is based on the segmentation function S(k) introduced in the present work and on the Jensen–Shannon divergence measure determined with respect to the probabilities of the lengths of uniform blocks of A and B monomer units. It is shown that the function S(k) is extremely sensitive to the sequence statistics. Even visual analysis of S(k) allows judgment on some features of sequence statistics. In particular, function S(k) is constant for random copolymers, it is an oscillating function for random block copolymers and shows monotonic growth up to some constant value for proteinlike copolymers. However, due to significant fluctuations observed for short sequences, the function S(k) can be effectively used only for segmentation of a heterosequence composed of very long subsequences. On the other hand, we find that the Jensen–Shannon divergence measure does not allow one to judge the type of statistics, but is extremely efficient for segmentation of a heterosequence. Therefore, the two introduced functions, being mutually complementary, provide an effective approach for recognizing and segmentation of heterosequences. As an example, the methods developed are applied for concatenating sequences of different proteins.

Segmentation function S(k, l, x) as a function of parameter k and starting number x of “window” for a sequence composed of elastin and ribonuclease sequences.     

乳液共聚反应过程与聚合物结构关系及~（13）C－NMR对聚合物结构的表征

用间歇法和半连续法进行了丙烯酸丁酯（ＢｕＡ）与醋酸乙烯酯（ＶＡｃ）乳液共聚合．１３Ｃ－ＮＭＲ对共聚产物分子结构测试表明，在间歇法共聚合中随着反应进行其组成及结构发生很大变化，而半连续法确能制得成份及结构均匀一致的Ｐ（ＢｕＡ－ＶＡｃ）共聚物．由于ＢｕＡ水溶性小于ＶＡｃ，而其竟聚率远大于ＶＡｃ，间歇法共聚合反应初期只有少量ＶＡｃ参加共聚合．通过对间歇法共聚合中不同反应时间聚合物的１３Ｃ－ＮＭＲ测试，表明反应初期聚合的ＶＡｃ以单链节或二元序列形式存在于主要由ＢｕＡ单元构成的分子链中，而并未形成较长ＶＡｃ链段．对上述试样玻璃化转变温度的测试结果与１３Ｃ－ＮＭＲ实验结果颇为一致．     

Analysis of pyrolysis products formed from ethylene-tetrafluoroethylene heterosequences of poly(ethylene-co-tetrafluoroethylene)

Poly(ethylene-co-tetrafluoroethylene) (PETFE) was pyrolyzed and the pyrolysis products formed from the ethylene-tetrafluoroethylene heterosequences were analyzed using gas chromatography/mass spectrometry (GC/MS). Major pyrolysis products were 3,3-difluoropropene (DFP), 3,3,4,4-tetrafluoro-1-butene (TFB), 1,1,2,2,3,3-hexafluorocyclopentane (HFCP), 1,1,2,2,3,3-hexafluorocyclohexane (HFCH), 1,1,2,2,3,3,4,4-octafluorocyclohexane (OFCH), and 3-trifluoromethyl-3,4,4,5,5-pentafluorocyclohexene (FMPFCH). Their formation mechanisms were proposed. Peak intensity ratios of HFCP, HFCH, and FMPFCH compared to OFCH increased as the pyrolysis temperature increased, while those of DFP, TFB, HFCP, and HFCH compared to tetrafluoroethylene decreased. Order of the relative abundances of the major pyrolysis products formed from PETFE was OFCH > HFCP > HFCH > TFB > DFP. The order may be due to the difference in bond energies of CH₂-CH₂, CF₂-CH₂, and CF₂-CF₂. Formation of the pyrolysis product through the CH₂-CH₂ bond cleavage was more favorable than those through the CF₂-CH₂ and CF₂-CF₂ ones.     

Manipulation of globular DNA molecules for sizing and separation

Handling large DNA molecules, such as chromosomal DNA, has become necessary due to recent developments in genome science. However, large DNA molecules are fragile and easily broken by shear stress accompanying flow in solution. This fragility causes difficulties in the preparation and handling of large DNA molecules. This study demonstrates the transition of DNA from a coiled to a globular form, which is highly condensed. This state suppresses DNA fragmentation due to shear stress in solution. The transition enables large DNA molecules to undergo mechanical manipulation. We confirmed that the fluorescence intensity of stained globular DNA increases with increasing length, suggesting that the resistance of globular DNA to shear stress is the factor that allows analysis of large DNA by flow cytometry.     

酸性条件下的DNA构象变化加速DNA变性解链

调控DNA的变性解链过程是DNA扩增与检测的关键步骤。对于传统的热循环DNA扩增策略,由于变温过程中热量分布不均一以及变温速度慢等不利因素,会直接影响DNA变性解链过程,从而降低DNA检测放大的效果、延长检测的时长。因此,探索快速、高效的调控DNA变性解链的方法具有重要的研究意义。本文发展了以胞嘧啶在酸性条件下的质子化反应为基础,通过改变溶液的pH值,来诱导DNA构象在Watson-Crick（WC）碱基对与Hoogsteen（HG）碱基对之间的分子构象转换,从而实现精准、快速、高效的DNA变性解链调控目标。结果表明,相较于传统的温控方法,pH调控方法能显著提高DNA变性的速率约6倍以上。本文发现pH调控方法通过降低双链DNA的反应焓约160 kJ/mol,从而提高双链DNA变性速率和效率。该方法具有用于DNA信号放大与检测等相关应用的潜力。     

THE PHOTOCHEMICAL INTERACTION OF DEOXYRIBONUCLEIC ACID AND PROTEIN IN VIVO AND ITS BIOLOGICAL IMPORTANCE*,†

Summary When bacteria are irradiated with u.v. light there is a dose dependent decrease in the amount of DNA that can subsequently be extracted free of protein with detergent. This appears to be due to the crosslinking of the DNA with protein and the precipitation of the linked DNA when the denatured proteins are precipitated in the procedure used for the isolation of the DNA. The type of linkage between the DNA and the protein is unknown except that it resists the sequential attack of 2% sodium lauryl sulfate and 0.5 M KCI or 55% CsCI. The main evidence that the loss of DNA in vivo is due to the crosslinking of DNA and protein is that the crosslinking of DNA and protein can be demonstrated in vitro . X-rays do not crosslink DNA and protein in vivo , but acridine orange and visible light cause the crosslinking of DNA and protein both in vivo and in vitro .
By pulse labeling the DNA of bacteria with tritated thymine it can be shown that newly synthesized DNA is most sensitive to crosslinking and that this sensitivity shows a cyclic response keyed to the generation time of the bacteria. Under conditions of thymine starvation where the intrinsic sensitivity of the cells to killing by u.v. is markedly increased, there is a parallel increase in the sensitivity of the DNA of these cells to be crosslinked to protein. The similarity in the time sequence of these two events strongly suggests that the crosslinking may play an important role in the loss of viability following u.v. irradiation.     

Global DNA Methylation Level Monitoring by methyl-CpG Binding Domain-Fused Luciferase

DNA methylation is an epigenetic modification that represses gene expression. In cancer cells, alterations of the DNA methylation state in promoter regions and repetitive DNA sequences are observed; therefore, DNA methyltransferase inhibitors have been the focus of interest as potential anticancer drugs. We previously reported a simple global DNA methylation level-sensing assay using methyl-CpG binding domain (MBD) fused to luciferase (MBD-luciferase). In the assay, the MBD-luciferase binds to methyl-CpG sites on genomic DNA. Subsequently, bioluminescence resonance energy transfer (BRET) between the luciferase and a fluorescent DNA intercalating dye generates a signal that is dependent on DNA methylation level. In this study, we investigated whether global DNA hypomethylation induced by a DNA methyltransferase inhibitor or nutrient can be monitored by the BRET assay. 5-Aza-2′-deoxycytidine and folic acid were utilized as the DNA-methyltransferase inhibitor and nutrient that affect DNA methylation in cells. The HeLa cells were cultured with the inhibitor or in folic acid-deficient medium and their global DNA methylation levels measured. Both time- and concentration-dependent hypomethylation were detected by the BRET assay. These results demonstrate that global DNA hypomethylation can be monitored by the BRET assay, indicating that the assay is applicable to cell-based screening of DNA-methyltransferase inhibitors.     

Direct visualization of a DNA glycosylase searching for damage

DNA glycosylases preserve the integrity of genetic information by recognizing damaged bases in the genome and catalyzing their excision. It is unknown how DNA glycosylases locate covalently modified bases hidden in the DNA helix amongst vast numbers of normal bases. Here we employ atomic-force microscopy (AFM) with carbon nanotube probes to image search intermediates of human 8-oxoguanine DNA glycosylase (hOGG1) scanning DNA. We show that hOGG1 interrogates DNA at undamaged sites by inducing drastic kinks. The sharp DNA bending angle of these non-lesion-specific search intermediates closely matches that observed in the specific complex of 8-oxoguanine-containing DNA bound to hOGG1. These findings indicate that hOGG1 actively distorts DNA while searching for damaged bases.     

Effects of photo-activated bleomycin on deoxyribonuclease I, exonuclease III and deoxyribonucleic acid polymerase I reactions

The activity of bleomycin to break the strand of deoxyribonucleic acid (DNA) in the presence of 2-hydroxy-1-ethanethiol (2-mercaptoethanol) was enhanced by ultraviolet (UV) irradiation. Photo-activated bleomycin stimulated the action of deoxyribonuclease I (DNase I) to degrade DNA and the DNA synthesis by DNA polymerase I with DNase I. On the other hand, although UV-irradiated bleomycin scarcely broke the DNA strand in the presence of 1,2-benzenediol (catechol), it stimulated the action of DNase I to degrade DNA in the presence of catechol. In accordance with the inhibition by catechol, when DNA treated with UV-irradiated bleomycin in the presence of catechol was employed as a primer for the DNA synthesis, the incorporation of precursor into the acid-insoluble fraction by DNA polymerase I with exonuclease III was reduced to about one-half of the incorporation into DNA treated with unirradiated bleomycin. These findings suggest that the ability of bleomycin to bind to double-helical DNA forming regions sensitive to DNase I was increased by an appropriate dose of UV irradiation and that catechol inhibited the activity of the UV-irradiated bleomycin to break the DNA strand rather than to bind to DNA.     

Hybridization of oligonucleotide by using DNA self-assembled monolayer

The interaction between DNA immobilized on surface and oligonucleotides at the interface is important in detection and diagnostic processes. However, it is difficult to immobilize DNA with maintaining its activity and to realize an efficient hybridization in previous methods. Here, to establish a novel DNA-functionalized surface, the DNA self-assembled monolayer (SAM) was constructed on a gold substrate using thiolated DNA composed of double-stranded (ds) and single-stranded (ss) portion. The DNA SAM was characterized by surface plasmon resonance (SPR), XPS. The hybridization of ss portion of DNA was attempted using the SAM, and in situ monitored by SPR. XPS measurement indicated that the thiolated DNA could form a stable monolayer on a gold substrate through sulfur–gold interaction. SPR measurement implied that the long axis of the DNA standing on the substrate. These results indicated formation of the DNA SAM on the substrate. Hybridization of target DNA containing a complementary sequence for the probe portion was observed by SPR. Moreover, one mismatch of oligonucleotide could be distinguished using the DNA SAM. The SPR result indicates that hybridization of target DNA and probe DNA on the DNA SAM occurs on the DNA SAM.     

High-density DNA alignment on an Au(111) surface starting from folded DNA

High-density uniform DNA alignment on a metal substrate is essential for creating sensitive DNA devices. We develop a self-sensing DNA alignment process starting from folded DNA to achieve high-density, uniform DNA alignment on an Au(111) surface. We demonstrate that folded DNA plays a critical role in avoiding DNA aggregation and distributing the DNA uniformly on an Au(111) surface at the greatest density and quality ever attained. We also verify that the distributed, folded DNA can be stimulated to align only when the appropriate buffer flow is applied. This selective self-sensing DNA alignment on an Au surface will be a key technology for creating dynamic DNA sensors and switches.     

Critical behavior of megabase-size DNA toward the transition into a compact state

We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.     

A microfluidic study of mechanisms in the electrophoresis of supercoiled DNA

In this work, microfluidic chips were used to study the electrophoresis of supercoiled DNA (SC DNA) in agarose. This system allowed us to study the electrophoretic and trapping behaviours of SC DNA of various lengths, at various fields and separation distances. Near a critical electric field the DNA is trapped such that the concentration falls exponentially with distance. The trapping of such circular DNA has been explained in terms of the 'lobster trap' or 'impalement' model where shorter fibres become trapping sites at higher fields, leading to an ongoing (and gradual) increase in trapping with increasing field. By contrast, the present study suggests that under some circumstances the traps have a barrier such that only when the DNA has sufficient energy (at high enough fields) can it become trapped, leading to a sudden transition in behaviours at the critical field. We propose an 'activated impalement' mechanism of trapping in which only at sufficiently high fields is the SC DNA impaled and trapped for long times. The critical electric field appears to be inversely proportional to the length of the DNA molecule, suggesting that the force required to impale the SC DNA is constant.     

Long-range oxidative damage to DNA: protection of guanines by a nonspecifically bound disulfide

One-electron oxidation of DNA generates a base radical cation ("hole") that migrates through the duplex and causes damage at guanines. Unrepaired damage may lead to mutations. It has been suggested that "sacrificial guanines" in intron regions of DNA might serve to protect genes from damage. We have investigated the ability of a noncovalently bound sacrificial reagent to protect DNA from damage. Irradiation of an anthraquinone (AQ)-linked DNA duplex injects a radical cation into the DNA that causes reactions at GG steps close to and farther from the AQ. Bis[2-(3-(aminopropyl)amino)ethyl]disulfide, an analogue of spermine, binds to duplex DNA. Irradiation of the AQ-linked DNA in the presence of this disulfide suppresses the reaction at both GG steps and protects the DNA from damage. It is suggested that evolutionary pressure for the preservation of genomic integrity would yield disulfide-containing compounds optimized to bind to DNA and neutralize base radical cations.     

脱氧核糖核酸变性和损伤的原子力显微镜液相观察

脱氧核糖核酸（DNA）的变性和损伤很大程度地阻碍DNA的复制和转录,所以研究DNA在生理环境下损伤和变性的机理能更好地研究其理化性质,并对基因治疗具有重要意义. 首先使用原子力显微镜（AFM）对气相和液相环境下DNA进行对比,发现液相环境中获得的DNA图像比在气相环境中的更清晰,并且液相中的DNA更柔韧、松弛. 其次研究在液相环境下二甲基亚砜（DMSO）、过氧亚硝酸盐（PN）对DNA形态的影响. 研究发现,随着DMSO浓度增加,DNA的变性程度增强,环状DNA分子由没有缠绕的结构扭转为重叠螺旋的结构. 同时随着PN浓度的增加,线状DNA从自然拉伸变为更加弯曲的状态,而且会断裂成较短的DNA片段. 最后使用模型图加以解释,DMSO和PN使DNA的结构发生变化,变得不稳定后发生损伤和变性.     

Influence of branch length asymmetry on the electrophoretic mobility of rigid rod-like DNA

The electrophoretic mobility of three-arm asymmetric star DNA molecules, produced by incorporating a short DNA branch at the midpoint of rigid-rod linear DNA fragments, is investigated in polyacrylamide gels. We determine how long the added branch must be to separate asymmetric star DNA from linear DNA with the same total molecular weight. This work focuses on two different geometric progressions of small DNA molecules. First, branches of increasing length were introduced at the center of a linear DNA fragment of constant length. At a given gel concentration, we find that relatively small branch lengths are enough to cause a detectable reduction in electrophoretic mobility. The second geometric progression starts with a small branch on a linear DNA fragment. As the length of this branch is increased, the DNA backbone length is decreased such that the total molar mass of the molecule remains constant. The branch length was then increased until the asymmetric branched molecule becomes a symmetric three-arm star polymer, allowing the effect of molecular topology on mobility to be studied independent of size effects. DNA molecules with very short branches have a mobility smaller than linear DNA of identical molar mass. The reason for this change in mobility when branching is introduced is not known, however, we explore two possible explanations in this article. (i) The branched DNA could have a greater interaction with the gel than linear DNA, causing it to move slower; (ii) the linear DNA could have modes of motion or access to pores that are unavailable to the branched DNA.     

Influence of mobile DNA-protein-DNA bridges on DNA configurations: coarse-grained Monte-Carlo simulations

A large literature exists on modeling the influence of sequence-specific DNA-binding proteins on the shape of the DNA double helix in terms of one or a few fixed constraints. This approach is inadequate for the many proteins that bind DNA sequence independently, and that are present in very large quantities rather than as a few copies, such as the nucleoid proteins in bacterial cells. The influence of such proteins on DNA configurations is better modeled in terms of a great number of mobile constraints on the DNA. Types of constraints that mimic the influence of various known non-specifically DNA binding proteins include DNA bending, wrapping, and bridging. Using Monte-Carlo simulations, we here investigate the influence of (non-interacting) mobile DNA-protein-DNA bridges on the configurations of a 1000 bp piece of linear DNA, for both homogeneous DNA and DNA with an intrinsic planar bend. Results are compared to experimental data on the bacterial nucleoid protein H-NS that forms DNA-protein-DNA bridges. In agreement with data on H-NS, we find very strong positioning of DNA-protein-DNA bridges in the vicinity of planar bends. H-NS binds to DNA very cooperatively, but for non-interacting bridges we only find a moderate DNA-induced clustering. Finally, it has been suggested that H-NS is an important contributor to the extreme condensation of bacterial DNA into a nucleoid structure, but we find only a moderate compaction of DNA coils with increasing numbers of non-interacting bridges. Our results illustrate the importance of quantifying the various effects on DNA configurations that have been proposed for proteins that bind DNA sequence independently.     

A new quantitative method for circulating DNA level in human serum by capillary zone electrophoresis with laser-induced fluorescence detection

We present a method for the quantification of circulating DNA in serum by capillary zone electrophoresis (CZE) with laser-induced fluorescence detection (LIF). The serum was digested by proteinase to release free DNA. SYBR Gold was utilized as DNA intercalating dye, fluorescein as internal standard (ISTD). CZE-LIF was applied for the separation and quantification of total circulating DNA. Good linearity (R = 0.9992) in the low range of DNA concentrations (0.5-40 ng/mL) and a detection limit of 0.5 ng/mL for DNA (S/N = 3) were obtained. Our data demonstrated that CZE-LIF system has a good linearity with excellent sensitivity and satisfactory reproducibility in the quantification of circulating DNA in serum. This method was successfully used for the quantification of circulating DNA levels in serum. We observed that the circulating DNA levels in certain cancer patients were significantly higher than that in healthy individuals. Compared to current methods, our protocol does not need the extraction of DNA from serum. Our preliminary results have illustrated that CZE-LIF system is simple, rapid, and sensitive, and it is well suitable for large-scale quantification of circulating DNA levels in clinical diagnosis.