Informational symmetry breaking between proteins and nucleic acids.

Anti-symmetry of the information-processing mechanisms between proteins and nucleic acids is generalized to informational symmetry breaking between a genetic polymer and an anti-genetic polymer so as not to depend on particular chemical species. In a genetic polymer, e.g. nucleic acids, any sequence can form a closed double-stranded structure with a specific partner sequence. On the other hand, in an anti-genetic polymer, e.g. proteins, a chain could fold to an open multi-stranded structure and reinterpretation of the genetic information through slides or shifts between stacked strands could be induced by external perturbations. The possibility of the informational symmetry breaking by hierarchical organization of a single chemical species, i.e. polypeptides as a genetic polymer and nucleic acids as an anti-genetic polymer, is examined. The informational functions of genetic polymers and anti-genetic polymers in a complex mixture of macromolecules are characterized.     

A new reaction useful for chemical cross-linking between nucleic acids and proteins

Cytosine in nucleic acids can be converted into N4-aminocytosine by treatment with a mixture of hydrazine and bisulfite. The hydrazino group thus formed at position 4 of the pyrimidine ring can be linked to a sulhydryl group in proteins by the use of bromopyruvate as a linker. Successful use of this scheme of chemical cross-linking between nucleic acid and protein was demonstrated in the linking of poly(C) with glutathione, and of RNA with protein in the E. coli 30 S ribosomal subunit.     

Electric chips for rapid detection and quantification of nucleic acids

A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the bio-recognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and with a detection probe in the reaction solution, followed by enzyme labeling of the detection probe, enzymatic reaction, and finally, potentiometric measurement of the enzyme product at the chip surface. Anti-DIG-alkaline phosphatase conjugate was used for the enzyme labeling of the DIG-labeled detection probe. p-Aminophenol phosphate (pAPP) was used as a substrate. The enzyme reaction product, p-aminophenol (pAP), is oxidized at the anode of the chip to quinoneimine that is reduced back to pAP at the cathode. The cycling oxidation and reduction of these compounds result in a current producing a characteristic signal that can be related to the concentration of the analyte. The performance of the different steps in the assay was characterized using in vitro synthesized RNA oligonucleotides and then the instrument was used for analysis of 16S rRNA in Escherichia coli extract. The assay time depends on the sensitivity required. Artificial RNA target and 16S rRNA, in amounts ranging from 10(11) to 10(10) molecules, were assayed within 25 min and 4 h, respectively.     

Self-assembly of proteins and their nucleic acids

We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system. We have shown that functional proteins or protein domains can be produced in vitro and physically linked to their DNA in a single enzymatic reaction. Such self-assembled protein-DNA complexes can be used for protein cloning, the cloning of protein affinity reagents or for the production of proteins which self-assemble on a variety of solid supports. Self-assembly can be utilised for making libraries of protein-DNA complexes or for labelling the protein part of such a complex to a high specific activity by labelling the nucleic acid associated with the protein. In summary, self-assembly offers an opportunity to quickly generate cheap protein affinity reagents, which can also be efficiently labelled, for use in traditional affinity assays or for protein arrays instead of conventional antibodies.     

Recent advances in studies of evolutionary relationships between proteins and nucleic acids

Evolution depends upon the occurrence of occasional changes, large or small, in hereditary characteristics. Molecular genetics gave rise to the new field of molecular evolution, which is currently exploring the changes that take place in proteins and nucleic acids over long periods of time. The following are some of the fundamental assumptions:

1. The phenotypic characteristics of organisms depend directly on proteins.
2. Proteins are synthesized in accordance with information carried in molecules of DNA as sequences of the four bases, adenine, guanine, cytosine, and thymine. The information is transcribed into molecules of messenger RNA and is translated into proteins by the intervention of the genetic code.
3. Changes in the composition of the base sequences in DNA can take place in living organisms, and these changes can affect the phenotypic characteristics of the next generation.
4. The process of natural selection favors the perpetuation of organisms which compete successfully in the struggle for existence. This process leads to the elimination of all but a small fraction of the astronomical number of possible protein molecules that could result from genetic translation of the possible variants of DNA. Furthermore, the number of protein molecules was originally much smaller than it is to-day, and it has increased by hereditary processes rather than by the chance appearance of entirely new proteins.
5. The DNA present in any single cell contains the complete information for all the hereditary characteristics of the organism. The amount of DNA per cell may increase during evolution and this increase has produced modern organisms that are ‘higher’, more specialized, and more complex, from carlicr and simpler forms.
6. Protein molecules are slowly and steadily differentiated during evolution if their genes are physically separated from each other, by allopatric speciation or even by duplication and translocation, whether or not the function of the proteins are changed.
7. Mutations, together with recombination, contribute to changes in the genetic pool which provide the variability within populations that is necessary for evolution of species.

The field of molecular evolution should include a theory of the chemical events leading to the formation of the first living organism from molecules of non-living origin. The gentic code may have evolved through multiplication of transfer RNA molecules by gene duplication followed by differentiation. This proposal is supported by the similarities between all tRNA molecules of known structures. The DNA of higher organisms contains families of repetitive sequences. The families may contain thousands or hundreds of thousands of individual members. The ‘family resemblance’ within each group grows less with the passage of time because this leads to differentiation resulting from the accumulation of point mutations.     

Improved method for simultaneous isolation of proteins and nucleic acids

Here we combine the use of fluorescence-enhancing silicon substrates coated by copoly(DMA–NAS–MAPS), a ter-copolymer based on N,N-dimethylacrylamide (DMA), N-acryloyloxysuccinimide (NAS), and 3-(trimethoxysilyl)propyl-methacrylate (MAPS), with an efficient dynamic incubation to overcome mass transport limitations and obtain femtomolar limits of detection. The high sensitivity was obtained with a conventional microarray scanner without the use of any sophisticated detection strategy or protocol. When the method was applied, an improvement of the analytical sensitivity of approximately three orders of magnitude was achieved for antibody detection when compared with the same assay performed on regular glass slides and static conditions. Moreover, limits of detection of 45 and 54 pg/ml were obtained for hepatitis B superficial antigen and HIV p24 antigen, respectively.     

Plasmodesmal cell-to-cell transport of proteins and nucleic acids

The complexity associated with post-translational processing, in terms of protein sorting and delivery is now well understood. Although such studies have been focused almost exclusively on the fate of proteins within the cell in which they are synthesized, recent studies indicate that it is time to broaden this focus to incorporate the concept of intercellular targeting of proteins. Direct evidence is now available that viral and endogenous proteins can be synthesized in a particular cell and subsequently transported into neighboring (or more distant) cells. Plasmodesmata, plasma membrane-lined cytoplasmic pores, are thought to establish the intercellular pathway responsible for this cell-to-cell trafficking of macromolecules (proteins and nucleic acids). These recent findings establish a new paradigm for understanding the manner in which higher plants exert control over developmental processes. We discuss the concept that programming of plant development involves supracellular control achieved by plasmodesmal trafficking of informational molecules, herein defined as supracellular control proteins (SCPs). This novel concept may explain why, in plants, cell fate is determined by position rather than cell lineage. Finally, the circulation of long-distance SCPs, within the phloem, may provide the mechansm by which the plant signals to the shoot apical meristem that it is time to switch to the reproductive phase of its development.     

连锁基因自交后代中各种基因型、表现型概率的简捷计算

对连锁基因自交后代中各种基因型、表现型概率的计算进行了研究,提出了从规则Ⅰ到规则Ⅵ的简捷快速计算方法,这些方法的运用有利于学生对连锁互换规律的进一步理解,同时也能指导老师在对学生及生物学奥林匹克竞赛等各种类型的考试中设计出新类型的遗传学试题。     

A rapid and efficient method to remove labelled molecular probes from nucleic acids immobilized on solid supports

A rapid and efficient method is described for the removal of radio-active molecular probes from nucleic acids immobilized on nylon membranes. This method involves boiling in distilled water in a microwave oven. This procedure can be completed within ten minutes, does not require the use of any buffers or reagents, and produces results comparable with conventional buffer-wash procedures recommended by the suppliers of the transfer membranes.