Spectroscopic and Binding Properties of Berberine to DNA and Its Application to DNA Detection

Berberine(BER) binds to the double helical DNA with a high affinity There is only a much smaller hypochromism and no shifts in the absorption spectra when BER binds to calf thymus DNA(CT DNA) The fluorescence yields increase dramatically when BER binds to DNA, with no shifts in the emission maximum. These spectral changes are in contrast to the behavior observed with many fluorescent intercalates Groove binding rather than intercalation was suggested to be the cause of these spectral changes. Consistent with groove binding, for polyamide anion quenching studies showed that the magnitude of K_sv of the bound BER was higher than that of the free BER. The addition of salt to the solution releases the DNA-bound drug action from the groove and causes a decrease in the fluorescence yield. The results of all above studies proved the groove binding of BER to DNA. The large fluorescence enhancements observed when BER binds to DNA and the poor fluorescence yield of BER in the absence of DNA can be used for sensitive detection of DNA The linear concentration range was 0–20μg/ml The limit of detection for CT DNA was 12 ng/ml     

Markov chain order estimation with conditional mutual information

We introduce the Conditional Mutual Information (CMI) for the estimation of the Markov chain order. For a Markov chain of K$K$ symbols, we define CMI of order m$m$, _Ic(m)$I_c\left(m\right)$, as the mutual information of two variables in the chain being m$m$ time steps apart, conditioning on the intermediate variables of the chain. We find approximate analytic significance limits based on the estimation bias of CMI and develop a randomization significance test of _Ic(m)$I_c\left(m\right)$, where the randomized symbol sequences are formed by random permutation of the components of the original symbol sequence. The significance test is applied for increasing m$m$ and the Markov chain order is estimated by the last order for which the null hypothesis is rejected. We present the appropriateness of CMI-testing on Monte Carlo simulations and compare it to the Akaike and Bayesian information criteria, the maximal fluctuation method (Peres–Shields estimator) and a likelihood ratio test for increasing orders using ?$?$-divergence. The order criterion of CMI-testing turns out to be superior for orders larger than one, but its effectiveness for large orders depends on data availability. In view of the results from the simulations, we interpret the estimated orders by the CMI-testing and the other criteria on genes and intergenic regions of DNA chains.     

A new graphical coding of DNA sequence and its similarity calculation

The DNA primary sequence is translated into “structure graph” based on classification of its four bases. Then the invariants, such as topological indices, are extracted from those graphic representations of DNA primary sequences, and used to calculate the similarities among the eleven species. From these similarities/dissimilarities the homologies can be revealed that they are in agreement with evolutionary relation satisfactorily.     

Single‐Cell Investigations of Silver Nanoparticle–Bacteria Interactions

Interaction of bacteria with citrate‐reduced silver nanoparticles (AgNPs) of size 25 nm ± 8.5 nm is studied using Raman spectroscopy in conjunction with plasmon resonance imaging of single bacterial cells. Distribution of isolated nanoparticles (NPs) inside Escherichia coli (ATCC 25922; E. coli) is observed by hyperspectral imaging (HSI) as a function of incubation time. Time‐dependent degradation of bacterial DNA upon incubation of AgNPs with E. coli is proven by Raman spectroscopic studies. While attachment of NPs is evident in HSI, molecular changes are evident from the surface‐enhanced Raman spectra of adsorbed DNA and its fragments. Distinct enhancement of DNA features is observed upon interaction of AgNPs and the number of such distinct features increases with incubation time, reaches a maximum, and decreases afterwards. This systematic interaction of DNA with the NPs system and its gradual chemical evolution is proven by investigating isolated plasmid DNA. A comparative Raman study with silver ions has shown that DNA features are observable only when bacteria are incubated with AgNPs. Energetics of interaction examined with microcalorimetry suggests the exothermicity of ?1.547 × 10¹⁰ cal mol^?1 for the NP–bacteria system. Specific interaction of AgNPs with exocyclic nitrogen present in the bases, adenine, guanine, and cytosine, leads to the changes in DNA.     

DNA分子电输运特性的相干隧穿研究

把DNA分子的碱基堆积相互作用视为多个单势垒的组合,电荷逐级隧穿随电压变化的势垒,利用相干隧穿理论计算了8 bp和30 bp的均匀序列DNA分子两端在硫化和非硫化情况下的伏安特性曲线,得到了与实验一致的结论.     

Complexation of heterocyclic ligands with DNA in aqueous solution

We have used spectrophotometry to study self-association and complexation with DNA by organic heterocyclic compounds in the acridine and phenothiazine series: proflavin, thionine, and methylene blue. Based on the experimental concentration dependences of the molar absorption coefficient of the molecules in an aqueous buffer solution (0.01 M NaCl, 0.01 M Na₂EDTA, 0.01 M Tris, pH 7.4, T = 298 K), we have determined the equilibrium dimerization constants for the dyes and the DNA complexation parameters using the Scatchard and McGhee-von Hippel models. The observed increase in the cooperativity parameters as the dimerization constants of the ligands increase allowed us to hypothesize that the same interactions occur between dye molecules adsorbed on DNA as in their self-association. The equilibrium DNA-binding constants for the ligands, obtained using the McGhee-von Hippel cooperative model, are (20.9 ± 2.7)·10³ M⁻¹ for proflavin and (33.8 ± 4.1)·10³ M⁻¹ for thionine. Using the Scatchard model, taking into account intercalation and “external” binding of ligands with DNA, we determined the DNA complexation constants for methylene blue: (26.4 ± 4.6)·10³ and (96 ± 17)·10³ M⁻¹ respectively. Based on analysis of the data obtained, we hypothesized that the predominant type of binding with DNA is intercalation binding in the case of proflavin and thionine, and “external” binding with the DNA surface in the case of methylene blue. __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 2, pp. 242–249, March–April, 2008.     

Dynamics of DNA: Experimental controversies and theoretical insights

Recent experimental advances using fluorescence correlation spectroscopy (FCS) have given unprecedented information about the small-scale kinetics of large biopolymers in solution. However some of the first studies in this direction yielded conflicting results for the mean squared displacement of the tagged end-point of a DNA chain, deviating from traditional theories of polymer dynamics. Spurred by this controversy, we have developed a hydrodynamic mean-field theory for single semiflexible polymers which points to a resolution of the differing experimental observations. The theory precisely captures, without fitting parameters, one set of recent FCS results, reproducing the experimental dynamics over five decades in time and three decades of chain lengths. The success of the theory makes it an excellent candidate for a variety of biophysical contexts where the internal fluctuations of semiflexible polymers play a role.     

Recent advances in rice genome and chromosome structure research by fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) is an effective method for the physical mapping of genes and repetitive DNA sequences on chromosomes. Physical mapping of unique nucleotide sequences on specific rice chromosome regions was performed using a combination of chromosome identification and highly sensitive FISH. Increases in the detection sensitivity of smaller DNA sequences and improvements in spatial resolution have ushered in a new phase in FISH technology. Thus, it is now possible to perform in situ hybridization on somatic chromosomes, pachytene chromosomes, and even on extended DNA fibers (EDFs). Pachytene-FISH allows the integration of genetic linkage maps and quantitative chromosome maps. Visualization methods using FISH can reveal the spatial organization of the centromere, heterochromatin/euchromatin, and the terminal structures of rice chromosomes. Furthermore, EDF-FISH and the DNA combing technique can resolve a spatial distance of 1 kb between adjacent DNA sequences, and the detection of even a 300-bp target is now feasible. The copy numbers of various repetitive sequences and the sizes of various DNA molecules were quantitatively measured using the molecular combing technique. This review describes the significance of these advances in molecular cytology in rice and discusses future applications in plant studies using visualization techniques.     

Passivation of aluminum with alkyl phosphonic acids for biochip applications

Self-assembly of decylphosphonic acid (DPA) and octadecylphosphonic acid (ODPA) was studied on aluminum films using XPS, ToF-SIMS and surface wettability. Modified aluminum films were tested for passivation against silanization and subsequent oligonucleotide attachment. Passivation ratios of at least 450:1 compared to unprotected aluminum were obtained, as quantified by attachment of radio-labeled oligos.     

Revised Assignment of the Raman Active Fundamental Vibrations of Tetracyanoethylene

We present a revised assignment of the Raman active fundamental vibrations of TCNE which utilizes new information obtained from Raman studies of electron donor/acceptor complexes of TCNE. This new assignment is consistent with and supported by all available evidence from previous studies.