遗传密码扩充技术

遗传密码的扩充打破了天然生命体基因只能编码天然氨基酸的限制.遗传密码扩充技术使人们可以将具有特殊性质的非天然氨基酸通过基因表达到生物活体的蛋白质中.该文对遗传密码扩充的原理、方法及意义进行简述.     

Coding Rules for Amino Acids in the Genetic Code: The Genetic Code is a Minimal Code of Mutational Deterioration

Coding rules for amino acids in the genetic code are discussed from the point that the genetic code is a minimal code ofmutational deterioration. The global mutational deterioration(GMD) function is defined through several parameters describingsingle base mutations and amino acid distances. The problem ofsearching for the global minimum of the GMD function is discussedin some detail. From GMD minimization under initial constraintswe have succeeded in deducing the standard genetic code.     

Genetic Code Variations in Mitochondria: tRNA as a Major Determinant of Genetic Code Plasticity

Characteristic features of tRNA such as the anticodon sequence and modified nucleotides in the anticodon loop are thought to be crucial effectors for promoting or restricting codon reassignment. Our recent findings on basepairing rules between anticodon and codon in various metazoan mitochondria suggest that the complete loss of a codon is not necessarily essential for codon reassignment to take place. We postulate that a possible competition between two tRNAs with cognate anticodon sequences towards the relevant codon to be varied has a potential role in codon reassignment. Our proposition can be viewed as an expanded version of the codon capture theory proposed by Osawa and Jukes (J Mol Evol 28: 271–278, 1989). Received: 28 December 2000 / Accepted: 12 March 2001     

Regional Context in the Alignment of Biological Sequence Pairs

Sequence divergence derives from either point substitution or indel (insertion or deletion) processes. We investigated the rates of these two processes both in protein and non-protein coding DNA. We aligned sequence pairs using two pair-hidden Markov models (PHMMs) conjoined by one silent state. The two PHMMs had their own set of parameters to model rates in their respective regions. The aim was to test the hypothesis that the indel mutation rate mimics the point mutation rate. That is, indels are found less often in conserved regions (slow point substitution rate) and more often in non-conserved regions (fast point substitution rate). Both polypeptides and rRNA molecules in our data exhibited a clear distinction between slow and fast rates of the two processes. These two rates served as surrogates to conserved and non-conserved secondary structure components, respectively. With polypeptides we found both the fast indel rate and the fast replacement rate were co-located with hydrophilic residues. We also found that the average concordance, of our alignments with corresponding curated alignments, improves markedly when the model allows either of the two fast rates to colocate with hydrophilic residues. With rRNA molecules, our model did not detect colocation between the fast indel rate and the fast substitution rate. Nevertheless, coupling the indel rates with the point substitution rates across the two regions markedly increased model fit. This result suggests that rRNA pairwise alignments should be modeled after allowing for the two processes to vary simultaneously and independently in the two regions.     

Structures of Non-canonical Tandem Base Pairs in RNA Helices: Review

Abstract

The structures of tandem non-canonical base pairs, a frequently recurring motif in RNA molecules, are reviewed and analysed. The tandem non-canonical base pair motifs can be roughly divided in three groups, containing seven subgroups based on their base pairing patterns and local geometries. Structural details and helical parameters that can be used to numerically distinguish between the subgroups are tabulated. Remarkably, while the individual helical twists of the tandem and adjacent base pair steps can be substantially smaller or larger than the typical A-form value of 32.7°, the average value is close to A-form. This and other striking regularities resulting from compensating geometrical adjustments, important for understanding and predicting the configurations of non-canonical base pairs geometries are discussed.     

New Unnatural L-Nucleoside Enantiomers:From Their Stereospecific Synthesis to Their Biological Activities

Abstract

Several purine and pyrimidine β-L-dideoxynucleosides were stereospecifically synthesized and their antiviral properties examined. Two of them, namely β-L-2′,3′-dideoxyadenosine (β-L-ddA) and its 2′,3′-didehydro derivative (β-L-d4A) were found to have significant anti-human immunodeficiency virus (HIV) and anti-hepatitis B virus (HBV) activities in cell culture.     

Molecular Informatics: Quantifying Information Patterns in the Genetic Code

The Genetic Code appears to be a non-random triplet code in which both the position of a nucleotide within a codon, as well as its physicochemical nature, contribute to the identity of the expressed amino acid. The non-randomness of the code is manifested in apparent patterns in the mapping from codon to amino acid; some of the patterns seem quite clear, while other more subtle patterns are less obvious or certain. Discussion in the literature has been largely qualitative in nature. In this study, we employ evolution similarity data, widely employed in the field of bioinformatics, to explore the patterns relating nucleotide features to amino acids. The results support a hierarchical order based on position and physicochemical features proposed by Jimenez-Montaño et al., [“The Hypercube Structure of the Genetic Code Explains Conservative and Non-Conservative Amino Acid Substitutions in vivo and in vitro” Biosystems (1996) 39, pp. 117–125]. The method also provides a quantitative approach to testing the importance of other putative patterns.     

Error-reducing Structure of the Genetic Code Indicates Code Origin in Non-thermophile Organisms

During the RNA World, organisms experienced high rates of genetic errors, which implies that there was strong evolutionary pressure to reduce the errors’ phenotypical impact by suitably structuring the still-evolving genetic code. Therefore, the relative rates of the various types of genetic errors should have left characteristic imprints in the structure of the genetic code. Here, we show that, therefore, it is possible to some extent to reconstruct those error rates, as well as the nucleotide frequencies, for the time when the code was fixed. We find evidence indicating that the frequencies of G and C in the genome were not elevated. Since, for thermodynamic reasons, RNA in thermophiles tends to possess elevated G+C content, this result indicates that the fixation of the genetic code occurred in organisms which were either not thermophiles or that the code’s fixation occurred after the rise of DNA. Supplementary Materials Original data and programs are available at the author’s web site: .     

Variable Temperature Infrared Spectroscopy of Cytosine-Guanine Base Pairs: Tautomerism Versus Polarization

Abstract

This report describes an infrared (IR) spectroscopic study of a model cytosine - guanine base pair. This base pair is part of a self-consistent experimental system based on lipophilic ribose derivatives of cytidine (C), guanosine (G) and O⁶-methylguanosine (O⁶MeG) that are soluble in non-aqueous, low dielectric solvents at appreciable concentrations. Previous experiments on this system have revealed different rotation dynamics for the amino bonds within the CG base pair, an observation that could be explained by the presence of rare tautomers (P.O. Lowdin, Reviews of Modern Physics 35, 724 (1963)), or by mutual polarization of the base pairs (L.D. Williams, N.G. Williams and B.R. Shaw, J. Am. Chem. Soc. 112, 829 (1990)). The IR spectra in the OH and NH stretching region indicate formation of hydrogen-bonded CG base pairs and self associates in 1,2-dichlorobenzene over a temperature range from 10 to 290K. Changes in the lineshapes and intensities of the IR bands with temperature correlate with phase transitions of the solvent but no evidence is seen for an OH stretching band that would indicate the formation of hydroxyl tautomers within base pairs. Similarly, the relative intensities of the C=O stretching bands of CG in cyclohexane solution remain constant over this same temperature range, confirming that within the base pair, the tautomeric states of the bases remain essentially unperturbed in the 2-amino/6-keto form of G and the 2-keto/4-amino form of C. The spectra of O⁶-MeG aid in the band assignments, since this molecule is frozen in an equivalent of the 2-amino/6-hydroxyl tautomer, but without the OH group and its associated stretching band. We conclude that the probability of tautomerism does not appear to be sufficient to explain the different rotation dynamics for the two amino bonds of the CG base pair. Rather it is argued that mutual polarization within the base pair, which would increase the bond order of the amino bond of C within the base pair, can explain the results without the formation of unconventional tautomers.     

New Punctuation for the Genetic Code: Luteovirus Gene Expression

The luteovirus genome consists of a single RNA from which genes are expressed via subgenomic mRNAs and a variety of noncanonical translation events. We propose mechanisms of subgenomic RNA synthesis that accommodate the frequent recombination that has occurred at the termini of genomic and subgenomic RNAs. Luteoviral genes are translated by cap-independent translation, leaky scanning, ribosomal frameshifting, and stop-codon readthrough. Using the PAV barley yellow dwarf luteovirus as a model, we find that most of these translation events are controlled by sequences located hundreds to thousands of bases downstream in the viral genome. These signals are unprecedented in nature. A model is proposed in which a 3′ translational enhancer regulates viral RNA translation throughout the infection cycle.     

Out of the Randomness: Correlating Noise in Biological Systems

The study of the dynamics of biological systems requires one to follow relaxation processes in time with micron-size spatial resolution. This need has led to the development of different fluorescence correlation techniques with high spatial resolution and a tremendous (from nanoseconds to seconds) temporal dynamic range. Spatiotemporal information can be obtained even on complex dynamic processes whose time evolution is not forecast by simple Brownian diffusion. Our discussion of the most recent applications of image correlation spectroscopy to the study of anomalous sub- or superdiffusion suggests that this field still requires the development of multidimensional image analyses based on analytical models or numerical simulations. We focus in particular on the framework of spatiotemporal image correlation spectroscopy and examine the critical steps in getting information on anomalous diffusive processes from the correlation maps. We point out how a dual space-time correlative analysis, in both the direct and the Fourier space, can provide quantitative information on superdiffusional processes when these are analyzed through an empirical model based on intermittent active dynamics. We believe that this dual space-time analysis, potentially amenable to mathematical treatment and to the exact fit of experimental data, could be extended to include the rich phenomenology of subdiffusive processes, thereby quantifying relevant parameters for the various motivating biological problems of interest.