Interaction of dipropyltin(IV) with amino acids,peptides, dicarboxylic acids and DNA constituents

Interaction of dipropyltin(IV) with selected amino acids, peptides, dicarboxylic acids or DNA constituents was investigated using potentiometric techniques. Amino acids form 1?:?1 and 1?:?2 complexes and, in some cases, protonated complexes. The amino acid is bound to dipropyltin(IV) by the amino and carboxylate groups. Serine is complexed to dipropyltin(IV) with ionization of the alcoholic group. A relationship exists between the acid dissociation constant of the amino acids and the formation constants of the corresponding complexes. Dicarboxylic acids form both 1?:?1 and 1?:?2 complexes. Diacids forming five- and six-membered chelate rings are the most stable. Peptides form complexes with stoichiometric coefficients 111(MLH), 110(ML) and 11-1(MLH_?1)(tin: peptide: H⁺). The mode of coordination is discussed based on existing data and previous investigations. DNA constituents inosine, adenosine, uracil, uridine, and thymine form 1?:?1 and 1?:?2 complexes and the binding sites are assigned. Inosine 5′-monophosphate, guanosine 5′-monophosphate, adenosine 5′-monophosphate and adenine form protonated species in addition to 1?:?1 and 1?:?2 complexes. The protonation sites and tin-binding sites were elucidated. Cytosine and cytidine do not form complexes with dipropyltin(IV) due to low basicity of the donor sites. The stepwise formation constants of the complexes formed in solution were calculated using the non-linear least-square program MINIQUAD-75. The concentration distribution of the various complex species was evaluated as a function of pH.     

Interaction of Cationic Manganese Porphyrins with DNA. A Binding Model

The DNA cleavage properties of two cationic manganese porphyrins possessing different peripheral substituents were compared. The identical nature of the strand scission patterns of the porphyrins on a 139 base pair restriction fragment of pBR-322 DNA, along with other evidence, suggests that the porphyrin is end-on bound via the minor groove in a melted or partially melted region of DNA. This unusual binding mode underscores the potential of outisde binding cationic metalloporphyrins as probes for low melting regions of DNA     

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S⁻)=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G^.+-P(S⁻)=S. The ionization potential of G-P(S⁻)=S was calculated to be slightly lower than that of guanine in 5′-dGMP. Subsequent thermally activated hole transfer from G^.+ to P(S⁻)=S led to dithiyl radical (P-2S^.) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S^. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S⁻)=S concentrations showed a bimolecular conversion of P-2S^. to the σ²-σ*¹-bonded dimer anion radical [-P-2S 2S-P-]⁻ [ΔG (150 K, DFT)=−7.2 kcal mol⁻¹]. However, [-P-2S 2S-P-]⁻ formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=−1.4 kcal mol⁻¹]. Neither P-2S^. nor [-P-2S 2S-P-]⁻ oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.     

字符串匹配算法在DNA序列比对中的应用

高通量测序技术的飞速发展让生物信息领域迎来了大数据时代。新技术在提供海量生物遗传信息的同时,也给分析这些数据带来了新的挑战。DNA序列比对是信息分析流程中的关键步骤,为后续的变异检测提供序列比对信息。2015“深圳杯”数学建模夏令营B题以DNA序列比对为研究课题,希望参赛学生给出序列快速比对的最佳方案。本文简要点评了各参赛队伍的解答情况,然后介绍了现有DNA序列比对软件中用到的算法和数据结构。     

Small Targeted Cytotoxics: Current State and Promises from DNA‐Encoded Chemical Libraries

The targeted delivery of potent cytotoxic agents has emerged as a promising strategy for the treatment of cancer and other serious conditions. Traditionally, antibodies against markers of disease have been used as drug‐delivery vehicles. More recently, lower molecular weight ligands have been proposed for the generation of a novel class of targeted cytotoxics with improved properties. Advances in this field crucially rely on efficient methods for the identification and optimization of organic molecules capable of high‐affinity binding and selective recognition of target proteins. The advent of DNA‐encoded chemical libraries allows the construction and screening of compound collections of unprecedented size. In this Review, we survey developments in the field of small ligand‐based targeted cytotoxics and show how innovative library technologies will help develop the drugs of the future.     

Use of Mercury Film Glassy Carbon Electrode Modified with Multiwalled Carbon Nanotubes in Electrochemical Analysis of DNA

Mercury film plated on a glassy carbon electrode modified with multiwalled carbon nanotubes (MF/MWNTs/GCE) was used for the analysis of single (ss) and double stranded (ds) DNA, as well as for Jurkat genomic DNAs methylated to different degrees. The results indicated that the DNA molecules adsorbed quite strongly on the MF/MWNTs/GCE surface allowing ex situ adsorption and produce well developed peaks (due to cytosine and adenine) by using adsorptive stripping (Ads, ex situ) square wave voltammetry (SWV). Also, SWV of Jurkat DNA mixtures methylated to different degrees revealed a linear decrease of the peak height with increasing methylation indicating an increase of structural rigidity.     

Error analysis of idealized nanopore sequencing

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single‐stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K‐12) at least 140 times to achieve 99.99% accuracy (Q40). By exploiting the ability to reread each strand at each pore in an array, arbitrary positioning on an error rate versus throughput tradeoff curve is possible if systematic errors are absent, with throughput governed by the number of pores in the array and the enzyme turnover rate.     

Synthesis and Properties of Isobicyclo‐DNA

We present the synthesis of the isobicyclo‐DNA building blocks with the nucleobases A, C, G and T, as well as biophysical and biological properties of oligonucleotides derived thereof. The synthesis of the sugar part was achieved in 5 steps starting from a known intermediate of the tricyclo‐DNA synthesis. Dodecamers containing single isobicyclo‐thymidine incorporations, fully modified A‐ and T‐containing sequences, and fully modified oligonucleotides containing all four bases were synthesized and characterized. Isobicyclo‐DNA forms stable duplexes with natural nucleic acids with a pronounced preference for DNA over RNA as complements. The most stable duplexes, however, arise by self‐pairing. Isobicyclo‐DNA forms preferentially B‐DNA‐like duplexes with DNA and A‐like duplexes with complementary RNA as determined by circular dichroism (CD) spectroscopy. Self‐paired duplexes show a yet unknown structure, as judged from CD spectroscopy. Biochemical tests revealed that isobicyclo‐DNA is stable in fetal bovine serum and does not elicit RNaseH activity.