短DNA片段缩合结构的比较研究

本文利用透射式电镜对四种短DNA片段(500、1100、1500、2700 bP)的缩合结构进行了比较研究得出很有意义的结果。定量研究证实短至500 bP的DNA分子仍可形成复曲面,且分子量相差5倍多的DNA片段缩合形成的复曲面尺度大小一致。复曲面外径为400A左右。从而进一步证实作者与Arscott及Bloomfield关于复曲面尺度独立于DNA分子量,及短DNA片段的缩合是多分子缩合的结论。此外,观测到缩合中间结构的尺度依DNA分子量大小不同而变化,同时分子量愈小的DNA片段产生另一种缩合结构—棒体的几率愈大。     

短DNA片段缩合结构的比较研究

本文利用透射式电镜对四种短DNA片段(500、1100、1500、2700 bP)的缩合结构进行了比较研究得出很有意义的结果。定量研究证实短至500 bP的DNA分子仍可形成复曲面,且分子量相差5倍多的DNA片段缩合形成的复曲面尺度大小一致。复曲面外径为400A左右。从而进一步证实作者与Arscott及Bloomfield关于复曲面尺度独立于DNA分子量,及短DNA片段的缩合是多分子缩合的结论。此外,观测到缩合中间结构的尺度依DNA分子量大小不同而变化,同时分子量愈小的DNA片段产生另一种缩合结构—棒体的几率愈大。     

DNA多分子缩合理论模型

在多分子缩合的实验研究基础上,本文以Tanford的递次结合模型为基础,建立了DNA多分子缩合的理论模型.此模型描述了缩合粒子的多分子结合特性,并预测缩合粒子的聚合数分布.模型的理论分布与作者用电镜获得的统计实验分布符合一致.同时,由于一组参量可同时拟合两种不同DNA长度的复曲面分布曲线,因而从理论上阐明缩合粒子的尺度独立于DNA的分子量.此外,还以高斯分布对复曲面的聚合数分布进行了模拟与比较.     

转基因鱼品系的纯化

外源基因(双链DNA)作为外显子可能整合在一条染色体上的不同DNA链上,转基因鱼的第1代为嵌合体。三杂交纯化过程方可获得转基因鱼纯合体:嵌合体与纯系个体2次回交,获得杂合子单一的杂合体;第2代杂合体自交可以获得纯合体。     

盐效应对DNA大分子构象的影响

用CD光谱监测了Micrococcus luteus DNA在不同MgCl_2浓度下[θ]值的变化,发现随着MgCl_2浓度的增加,在275nm处其[θ]值减少;而在220—250nm处,其负[θ]值加大.这个结果表明DNA大分子在空间上趋于缩拢.在同样条件下也用紫外光谱进行了监测,发现随着MgCl_2浓度的增加,在260nm处有明显的减色效应出现,这便又进一步印证了上述结果.而又用Batch-2107微量热计进行了热力学上的研究,结果表明在上述条件下,随着DNA大分子在空间上缩拢程度的加大,则伴有较高的释热值.这便从热力学的角度进一步佐证了这样的结果:随着MgCl_2浓度的增加,使溶液中的DNA大分子在空间上产生明显的缩拢现象.同时,所有上述测定结果都一致表明:这种DNA大分子构象变化过程是时间依赖的,约持续10分钟.     

用改良三酯法合成富集d-A的脱氧十一核苷酸d-AAACCACCATA

本文报道用改良三酯法合成富集d-A的脱氧十一核苷酸片段d-AAACCACCATA。以TPSCl+Te(1:4)为缩合剂进行片段缩合,反应在1～2小时内即可达到完全。Dmt基的脱除采用ZnBr_2/硝基甲烷溶液,几乎没有发现脱嘌呤副反应。最终的合成产物经核苷酸顺序分析证明具有正确的排列顺序。     

阳离子脂质体运载基因的跨膜机制

阳离子脂质体等非病毒载体以其制备简单、低毒性、低免疫原性、可生物降解等优点,成为近年来基因转运中的常用载体。理解阳离子脂质体运载基因的机制对阳离子脂质体的研究具有重要意义。从跨膜机制和信号调控的角度,介绍了脂质体/DNA复合体以特定构象避免细胞外基质中核酸酶的降解,跨越细胞膜进入细胞的过程;阐明了DNA在信号调控的作用下,逃离溶酶体并安全释放的机制;讨论了基因穿过核被膜进入到细胞核的方式,为进一步阐明阳离子脂质体运载基因的分子机制奠定基础。     

表面电荷对阳离子基因载体的影响

阳离子基因载体表面带有大量正电荷,由于许多DNA和细胞膜表面带负电荷,因此阳离子基因载体表面电荷有利于提高结合DNA的效率,纳米粒子与细胞膜的吸附也受粒子表面电荷的影响。同时,其表面电荷也是产生细胞毒性的主要原因之一,因此揭示细胞毒性及其作用机制有利于开发出更安全高效的基因递送载体。本文综述了阳离子基因载体表面电荷对DNA结合能力、细胞摄入、转染效率以及细胞毒性及其作用机制的影响。     

多聚酶链反应——方法和仪器

<正>多聚酶链反应(PCR)类似体内DNA复制过程,在待扩增的“靶”或“模板”DNA双链分子的的两端各接一个引物,经一次循环后,可得到两个相同的双链靶DNA分子。DNA分子数随循环次数呈几何级数增长,30次循环后,靶DNA被放大2~(30)倍,其拷贝数可达10~9以上,在100ul PCB反应混合物中约产生2～3μ DNA。扩增的靶DNA分子长达10～18kb,但4kb抗更短的靶DNA最适宜PCR扩增,PCR能测出10~6基因组中的一个DNA拷贝。     

DNA计算的规律及其在解题中的应用

归纳了DNA计算题的解题规律．如DNA分子中碱基数目的计算规律、DNA复制所消耗的脱氧核苷酸数的计算规律、基因指导蛋白质合成的计算规律、脱氧核苷酸脱水缩合的规律、碱基排列顺序数的计算规律和DNA分子中氢键数的计算规律等及其在解题中的应用。     

DNA condensation by multivalent cations

In the presence of multivalent cations, high molecular weight DNA undergoes a dramatic condensation to a compact, usually highly ordered toroidal structure. This review begins with an overview of DNA condensation : condensing agents, morphology, kinetics, and reversibility, and the minimum size required to form orderly condensates. It then summarizes the statistical mechanics of the collapse of stiff polymers, which shows why DNA condensation is abrupt and why toroids are favored structures. Various ways to estimate or measure intermolecular forces in DNA condensation are discussed, all of them agreeing that the free energy change per base pair is very small, on the order of 1% of thermal energy. Experimental evidence is surveyed showing that DNA condensation occurs when about 90% of its charge is neutralized by counterions. The various intermolecular forces whose interplay gives rise to DNA condensation are then reviewed. The entropy loss upon collapse of the expanded wormlike coil costs free energy, and stiffness sets limits on tight curvature. However, the dominant contributions seem to come from ions and water. Electrostatic repulsions must be overcome by high salt concentrations or by the correlated fluctuations of territorially bound multivalent cations. Hydration must be adjusted to allow a cooperative accommodation of the water structure surrounding surface groups on the DNA helices as they approach. Undulations of the DNA in its confined surroundings extend the range of the electrostatic forces. The condensing ions may also subtly modify the local structure of the double helix. © 1998 John Wiley & Sons, Inc. Biopoly 44: 269–282, 1997     

Structural effects of cobalt-amine compounds on DNA condensation.

Light scattering and electron microscopy have been used to investigate the structural effects of the trivalent complexes hexaammine cobalt (III) chloride (Cohex), tris(ethylenediamine) cobalt(III) chloride (Coen), and cobalt(III) sepulchrate chloride (Cosep) on DNA condensation. These cobalt-amine compounds have similar ligand coordination geometries but differ slightly in size. Their hydrophobicity is in the order Cosep > Coen > Cohex, according to the numbers of methylene groups in these ligands. All of these compounds effectively precipitate DNA at high concentrations; but despite a lower surface charge density, Cosep condenses DNA twice as effectively as Coen or Cohex. UV and CD measurements of the supernatants of cobalt-amine/DNA solutions reveal a preferential binding of Delta-Coen over Lambda-Coen to the precipitated DNA, but there is no chiral selectivity for Cosep. Competition experiments show that the binding strengths of these three cobalt-amine compounds to aggregated DNA are comparable. A charge neutralization of 88-90% is required for DNA condensation. Our data indicate that 1) electrostatic interaction is the main driving force for binding of multivalent cations to DNA; 2) DNA condensation is dependent on the structure of the condensing agent; and 3) the hydration pattern or polarization of water molecules on the surface of condensing agents plays an important role in DNA condensation and chiral recognition.     

Condensation of DNA by multivalent cations: considerations on mechanism.

DNA is generally found within viruses and cells in a tightly packaged state, typically occupying only 10(-4)-10(-6) of the volume of the uncondensed DNA wormlike coil. Condensation can be induced in vitro at low salt by the naturally occurring polyamines spermidine3+ and spermine4+, by hexammine cobalt(III), and even by Mg2+ in methanol-water mixtures. These condensates generally have an orderly, toroidal, or rodlike shape and size similar to that of DNA gently lysed from phage heads. It is also striking that the condensate size distribution is independent of DNA molecular length from 400 to 40,000 base pairs (bp), but that shorter DNA molecules (e.g., 150-bp mononucleosomal DNA) cannot condense in this fashion. We have constructed a successive association equilibrium theory to attempt to explain these results, using an equation devised by Tanford for micelle formation. Most of the obvious attractive and repulsive free energy contributions (mixing, bending, hydration, and other nearest-neighbor interactions) are linear in the amount of DNA incorporated, but the net attractive delta G0 grows nonlinearly because of the increasing average number of nearest neighbors of each duplex as the particle grows. In order that the size distribution have a maximum, a quadratic repulsive free energy is also required, arising from the electrostatic self-energy of the incompletely neutralized particles. The net attractive free energy per base pair interaction is tiny, on the order of 10(-3) kT. Despite the apparent generally correct order of magnitude of the various free energy terms, the calculated size distribution is smaller and narrower than observed experimentally. It appears that the size distribution of condensed particles is determined kinetically rather than thermodynamically. Very short DNA molecules cannot nucleate stable aggregates because they cannot develop adequate overlap, either internally or intermolecularly. A substantial fraction of rodlike condensates is observed in aqueous solutions only with a rather inefficient condensing agent, permethylated spermidine. This suggests that slow condensation kinetics may be required to overcome the high activation energy of highly distorted DNA bends or kinks at the turning points of rods. Evidence is reviewed that condensation may be associated with localized helix structure distortion provoked by condensing agents.     

The effect of salt on oligocation-induced chromatin condensation

Condensation of model chromatin in the form of fully saturated 12-mer nucleosome arrays, induced by addition of cationic ligands (ε-oligolysines with charge varied from +4 to +11), was studied in a range of KCl concentrations (10-500mM) using light scattering and precipitation assay titrations. The dependence of EC(50) (ligand concentration at the midpoint of the array condensation) on C(KCl) displays two regimes, a salt-independent at low C(KCl) and a salt-dependent at higher salt concentrations. In the salt-dependent regime EC(50) rises sharply with increase of C(KCl). Increase of ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher salt. In the nucleosome array system, due to the partial neutralization of the DNA charge by histones, a lower oligocation concentration is needed to provoke condensation in the salt-independent regime compared to the related case of DNA condensation by the same cation. In the physiological range of salt concentrations (C(KCl)=50-300mM), K(+) ions assist array condensation by shifting EC(50) of the ε-oligolysines to lower values. At higher C(KCl), K(+) competes with the cationic ligands, which leads to increase of EC(50). Values of salt-dependent dissociation constant for the ε-oligolysine-nucleosome array interaction were obtained, by fitting to a general equation developed earlier for DNA, describing the dependence of EC(50) on dissociation constant, salt and polyelectrolyte concentrations.     

Atomic force microscopy reveals the assembly of potential DNA "nanocarriers" by poly-L-ornithine

Atomic force microscopy (AFM) has been used to visualize the process of condensation of plasmid DNA by poly-L-ornithine on mica surface. AFM images reveal that the transition of negatively charged DNA to condensed nanoparticles on addition of increasing amounts of positively charged poly-L-ornithine (charge ratio (Z+/Z-) varied between 0.1 and 1) at a wide range of DNA concentrations (3-20 ng/microl) occurs through formation of several distinct morphologies. The nature of the complexes is strongly dependent on both the charge ratio and the DNA concentration. Initiation of condensation when the concentration of DNA is low (approximately 3-7 ng/microl) occurs possibly through formation of monomolecular complexes which are thick rod-like in shape. On the contrary, when condensation is carried out at DNA concentrations of 13-20 ng/microl, multimolecular structures are also formed even at low charge ratios. This difference in pathway seems to result in differences in the extent of condensation as well as size and aggregation of the nanoparticles formed at the high charge ratios. To the best of our knowledge, this is the first direct single molecule elucidation of the mechanism of DNA condensation by poly-L-ornithine. Cationic poly-aminoacids like poly-L-ornithine are known to be efficient in delivery of plasmid DNA containing therapeutic genes in a variety of mammalian cell lines by forming condensed "nanocarriers" with DNA. Single molecule insight into the mechanism by which such nanocarriers are packaged during the condensation process could be helpful in predicting efficacy of intracellular delivery and release of DNA from them and also provide important inputs for design of new gene delivery vectors.     

Structure and dynamics of condensed DNA probed by 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-[[3- methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] tetraiodide fluorescence

Information on the structure and dynamics of condensed forms of DNA is important in understanding both natural situations such as DNA packaging and artificial systems such as gene delivery complexes. We have established the fluorescence of bisintercalator 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-[[3-methylbenz-1,3-oxazol-2-yl]methylidine]-1,4-dihydroquinolinium] tetraiodide (YOYO-1) as a novel probe for DNA condensation. When the level of DNA-bound YOYO-1 is sufficiently large, condensation by either polyethylenimine (PEI) or the cationic detergent cetyltrimethylammonium bromide (CTAB) leads to electronic interaction among YOYO-1 molecules bound on the same DNA molecule. This interaction results in an excitonic blue shift of the absorption spectra of YOYO-1 and dramatic decrease in the fluorescence quantum yield. These observations constitute a signature of the condensation of DNA. We further examined the comparative properties of DNA condensed by PEI, CTAB, or Co(NH(3))(6)(3+) through the steady-state and dynamic fluorescence of YOYO-1. Condensation by either PEI or CTAB was associated with a blue shift in the absorption spectra of YOYO-1, although the magnitude of the shift was larger in the case of PEI when compared to that of CTAB. In contrast, condensation by Co(NH(3))(6)(3+) was not associated with a measurable shift in the absorption spectra. These results were interpreted as signifying the varying level of compactness of the DNA condensates. Quenching of fluorescence by acrylamide showed that condensation by all three agents led to an increase in the level of solvent exposure of the base pairs. Observation of the decay of fluorescence intensity and anisotropy of DNA-bound YOYO-1 showed that while condensation by either PEI or CTAB froze the segmental mobility of the helix, condensation by Co(NH(3))(6)(3+) enhanced the flexibility of DNA. The relevance of our findings to functions such as efficiency of gene delivery is discussed.     

Surface charge density determines the efficiency of cationic gemini surfactant based lipofection

The efficiencies of the binary liposomes composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and cationic gemini surfactant, (2S,3R)-2,3-dimethoxy-1,4-bis(N-hexadecyl-N,N-dimethylammonium)butane dibromide as transfection vectors, were measured using the enhanced green fluorescent protein coding plasmid and COS-1 cells. Strong correlation between the transfection efficiency and lipid stoichiometry was observed. Accordingly, liposomes with X(SR-1) > or = 0.50 conveyed the enhanced green fluorescent protein coding plasmid effectively into cells. The condensation of DNA by liposomes with X(SR-1) > 0.50 was indicated by static light scattering and ethidium bromide intercalation assay, whereas differential scanning calorimetry and fluorescence anisotropy of diphenylhexatriene revealed stoichiometry dependent reorganization in the headgroup region of the liposome bilayer, in alignment with our previous Langmuir-balance study. Surface charge density and the organization of positive charges appear to determine the mode of interaction of DNA with (2S,3R)-2,3-dimethoxy-1,4-bis(N-hexadecyl-N,N-dimethylammonium)butane dibromide/1,2-dimyristoyl-sn-glycero-3-phosphocholine liposomes, only resulting in DNA condensation when X(SR-1) > 0.50. Condensation of DNA in turn seems to be required for efficient transfection.     

Novel cationic amphiphilic 1,4-dihydropyridine derivatives for DNA delivery

In order to find new efficient and safe agents for gene delivery, we have designed and synthesized nine novel single- and double-charged amphiphiles on the base of 1,4-dihydropyridine (1,4-DHP) ring. Some biophysical properties of the amphiphilic dihydropyridines and their complexes with DNA were examined. We investigated the transfer of beta-galactosidase gene into fibroblasts (CV1-P) and retinal pigment epithelial (D 4O7) cell lines in vitro. The structure-property relationships of the compounds were investigated in various ways. The net surface charges of 1,4-DHP liposomes were highly positive (25-49 mV). The double-charged compounds condensed DNA more efficiently than single-charged and the condensation increases with the increasing +/- charge ratio between the carrier and DNA. Double-charged compounds showed also buffering properties at endosomal pH and these compounds were more efficient in transfecting the cells, but transfection efficiency of amphiphiles was cell type-dependent. The length of alkyl chains in double-charged compounds affected the transfection efficacy. The most active amphiphile (compound VI) was double-charged and had two C(12) alkyl chains. At optimal charge ratio (+/- 4), it was 2.5 times more effective than PEI 25 and 10 times better than DOTAP, known efficient polymeric and liposomal transfection agents. Formulation of amphiphiles with DOPE did not change their activities. Our data demonstrate some important effects of amphiphile structure on biophysics and activity. The data also suggest that cationic amphiphilic 1,4-DHP derivatives may find use as DNA delivery system.     

Monitoring DNA/poly-L-lysine polyplex formation with time-resolved multiangle laser light scattering

Nonviral DNA complexes show promise as alternative and attractive gene delivery vectors for treating genetic diseases. Nonviral DNA complexes are typically formed by combining DNA with various condensing/complexing agents such as lipids, polyelectrolytes, polymers, polypeptides, and surfactants in solution. DNA/poly-L-lysine polyplex formation kinetics are probed by time-resolved multiangle laser light scattering (TR-MALLS), which yields the time evolution of the supramolecular complex mass and geometric size. Primary polyplexes whose geometric size is smaller than individual DNA molecules in solution are formed very rapidly upon mixing DNA and poly-L-lysine. Over time, these primary polyplexes aggregate into larger structures whose ultimate size is determined primarily by the relative concentrations of DNA and poly-L-lysine. This final polyplex size varies with the DNA/poly-L-lysine mass ratio in a non-monotonic fashion, with the maximum polyplex size occurring at a DNA/poly-L-lysine mass ratio of approximately two to three (charge ratio near unity). The utility of TR-MALLS for monitoring the temporal evolution of DNA loading and supramolecular complex size growth (mean square radius and molar mass) throughout the DNA/poly-L-lysine polyplex formation process is demonstrated. The polyplex DNA loading and size, both geometric and molar mass, are key to understanding the transfection process and for developing optimal gene therapy vectors.     

Site-directed modification of DNA duplexes by chemical ligation.

The efficiency of chemical ligation method have been demonstrated by assembling a number of DNA duplexes with modified sugar phosphate backbone. Condensation on a tetradecanucleotide template of hexa(penta)- and undecanucleotides differing only in the terminal nucleoside residue have been performed using water-soluble carbodiimide as a condensing agent. As was shown by comparing the efficiency of chemical ligation of single-strand breaks in those duplexes, the reaction rate rises 70 or 45 times if the 3'-OH group is substituted with an amino or phosphate group (the yield of products with a phosphoramidate or pyrophosphate bond is 96-100% in 6 d). Changes in the conformation of reacting groups caused by mismatched base pairs (A.A, A.C) as well as the hybrid rU.dA pair or an unpaired base make the template-directed condensation less effective. The thermal stability of DNA duplexes was assayed before and after the chemical ligation. Among all of the modified duplexes, only the duplex containing 3'-rU in the nick was found to be a substrate of T4 DNA ligase.