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.     

Genome size,self‐organization and DNA's dark matter

Chromosomes exhibit several features indicating that its spatiotemporal dynamics is self‐organized. It has been recently suggested that a negative correlation between genome size and mean chromosome number would also be a fingerprint of selforganization, related to how human language is organized at the level of words and syllables. However, the vast dominance of non‐coding DNA in eukaryotic genomes should prevent an interpretation of genome/chromosome size based on functional trade‐offs related to information storage and transmission. Moreover, the reported negative correlation is shown to be an inevitable consequence of the definitions of chromosome and genome length and it is thus unrelated to any type of special generative process. © 2010 Wiley Periodicals, Inc. Complexity 16: 20–23, 2010     

甲硝唑与钴（Ⅱ）、镍（Ⅱ）配合物的合成及与DNA作用

甲硝唑与过渡金属钴（Ⅱ）、镍（Ⅱ）的卤盐反应得到配合物[Co（C6H9O3N3）2Br2]（1）和[Ni（C6H9O3N3）2Cl2]·2H2O（2）,通过元素分析、红外光谱分析及热重分析对配合物可能的组成进行了表征.并进一步对两种配合物与DNA的相互作用进行研究,光谱分析及黏度分析表明两者均以部分插入的方式与DNA的相互作用.     

Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR,NBO and AIM analyses

Protonation increases the total binding energy of the 8-oxoguanine-cytosine (8OG:C) base pair by 60–70% at the B3LYP/6-311++G(d,?p) level of theory. It changes the individual H-bond energies, estimated from electron charge densities at bond critical points, by 1.16 to ?16.41?kcal?mol^?1. The individual H-bond energies and the two bond X–Y spin–spin coupling constants (^2hJ_X–Y) increase with protonation where 8OG behaves as an H-bond donor; the reverse is true for the H-bonds in which the 8OG unit acts as an H-bond acceptor. Similar to ^2hJ_X–Y, the value of ^1hJ_O–H (a one-bond H?···?Y spin–spin coupling constant) is distance dependent and in linear correlation with the O?···?H distance, but the ^1hJ_N–H values are independent of the N–H distance and the PSO term is the predominant portion in it. The ¹J_X–H spin–spin coupling constant is dominated by the negative FC term for all hydrogen bonds, although the PSO term is the best to investigate the behaviour of ¹J_X–H across the X–H?·?Y H-bond.     

Responsive DNA‐Based Hydrogels and Their Applications

The term hydrogel describes a type of soft and wet material formed by cross‐linked hydrophilic polymers. The distinct feature of hydrogels is their ability to absorb a large amount of water and swell. The properties of a hydrogel are usually determined by the chemical properties of their constituent polymer(s). However, a group of hydrogels, called “smart hydrogels,” changes properties in response to environmental changes or external stimuli. Recently, DNA or DNA‐inspired responsive hydrogels have attracted considerable attention in construction of smart hydrogels because of the intrinsic advantages of DNA. As a biological polymer, DNA is hydrophilic, biocompatible, and highly programmable by Watson‐Crick base pairing. DNA can form a hydrogel by itself under certain conditions, and it can also be incorporated into synthetic polymers to form DNA‐hybrid hydrogels. Functional DNAs, such as aptamers and DNAzymes, provide additional molecular recognition capabilities and versatility. In this Review, DNA‐based hydrogels are discussed in terms of their stimulus response, as well as their applications.

     

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.     

An Efficient Chosen-Plaintext Attack on an Image Fusion Encryption Algorithm Based on DNA Operation and Hyperchaos

This paper proposes a more efficient attack method on an image fusion encryption algorithm based on DNA operation and hyperchaos. Although several references have reported some methods to crack the image encryption algorithm, they are not the most efficient. The proposed chosen-plaintext attack method can break the encryption scheme with (4×N/M+1) or (M/(4×N)+1) chosen-plaintext images, which is much less than the number of chosen-plaintext images used in the previous cracking algorithms, where M and N represent the height and width of the target ciphertext image, respectively. The effectiveness of the proposed chosen-plaintext attack is supported by theoretical analysis, and verified by experimental results.     

Modifications Induced by UV-Vis Irradiation on DNA Extract of Kiwifruit Investigated by Spectroscopic and Statistic Methods

ABSTRACT

Revealing molecular alterations induced on kiwifruit under UV-Vis irradiation requires a discussion of biochemical-cell infrared (IR) fingerprint (900 cm^?1–1800 cm^?1) bands characteristic of nucleic acids. FTIR-ATR spectroscopy and statistics and nondestructive methods for screening exposure effects induced by irradiation were used. There the irradiation influence on the main molecular bonds (i.e., ν(C-C), ν_s(PO₂?) and ν_as(PO₂?)) can be observed. Regression methods were used for statistical investigations. Two categories of variables were used: the absorbance measured at fixed wavenumber variables and the exposure dose. The bivariate correlations, partial correlations, and polynomial regression methods from SPSS were used for statistical investigations. The obtained results show that FTIR-ATR, in correlation with statistics techniques, might be useful to assess immediate radiation and oxidative-induced damage to nucleic acids. In this case IR spectroscopy can be used successfully to study conformational changes during DNA reversible denaturation especially on the sugar-phosphate vibrations domain.