Evolution of the genetic code. Emergence of DNA
Denis A. Semenov
这一假说可以提供一个机会，逻辑上追溯的过程中出现的DNA双螺旋。AT-富集是RNA双螺旋进化为DNA双螺旋的主要因素。
This hypothesis can provide an opportunity to trace logically the process of the emergence of the DNA double helix. AT-enrichment in this hypothesis is main factor of evolution of DNA double helix from RNA double helix.
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Evolution of the genetic code. From the CG- to the CGUA-alphabet, from RNA double helix to DNA
提出了遗传密码进化的假说，其主要机制是核苷酸自发损伤导致基因组AT富集。该假说解释了遗传密码对点突变的稳定性、密码方言的存在、终止密码子的出现、DNA双螺旋的出现以及遗传密码表的对称性。遗传密码最初的三联体结构的假设已经得到证实。已经提出了关于第一个基因和第一个蛋白质的一级结构的假说。
Evolution of the genetic code. Emergence of stop codons
在遗传密码的进化过程中，是什么导致了非编码密码子的出现？终止密码子的存在是由于遗传密码从GC进化到AGUC字母表的假说。
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations to show that sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulated overextension on four different sequences of DNA ((AA)12, (AT)12, (GG)12 and (GC)12) with supercoiling densities w…
Zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) comprise a powerful class of tools that are redefining the boundaries of biological research. Although these technologies have begun to enable targeted genome modifications, there remains a need for new technologies that are affordable, scalable, and easy to engineer. In this paper, we propose a new tool for genetic engineering, the pseudocomplementary peptide nucleic acid nucleases (pcPNANs), which are composed of a pseudocomplementary PNA (pcPNA) specific for a DNA target sequence, a FokI nuclease cleav…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing, given the inherent difficulties in the simultaneous and localized prebiotic synthesis of all four monomers of progenitors of DNA from common precursors on early Earth. Excluding the scenario where a two-letter alphabet genome eventually expanded to include two more letters to code for more amino acids on teleological grounds, we show here that a heteropolymer …
Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome are poorly understood. The scale by which homology recognition takes place is of a few tens of base pairs, after which the quest for homology is over. To study the mechanism of homology recognition, RecA-promoted homologous recombination between short DNA oligomers with different degrees of heterology was studied in vitro, using fluorescence resonant energy …
Modular Golden Gate Assembly of Linear DNA Templates for Cell-free Prototyping
本文提出一种基于 Golden Gate 组装的无细胞原型工作流程，通过体外一锅法组装和 PCR 扩增快速生成线性 DNA 模板，消除了细胞内克隆步骤，可在一天内为大量新构建体生成数据，显著加速合成生物学设计-构建-测试周期。
Liapunov exponent distributions and maps for multiple parameter logistic equation. Application to DNA and RNA sequences
本文将多参数逻辑斯蒂方程推广到DNA和RNA序列分析，通过Liapunov指数分布及基于嘌呤/嘧啶分类的二值映射，揭示核苷酸排列的稳定性与动态行为，为理解遗传复制和蛋白质合成提供新框架。
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments I show here that direct recognition between homologous dsDNA is possible through formation of short quadruplexes due to direct complementary hydrogen bonding of major groove surfaces in parallel alignment. The cons…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles wit…
DNA energy constraints shape biological evolutionary trajectories
本研究表明dsDNA序列的对称性和模式源于分子物理特性与最大熵原理而非进化压力，双螺旋能量约束是DNA架构的硬驱动因素，生物选择仅为软驱动因素。
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the breathing of DNA, are generally localized and, microscopically, are due to the breaking of the hydrogen bonds linking the base pairs (\emph{bps}). I apply imaginary time path integral techniques to a mesoscopic Hamiltonian which accounts for the helicoidal geometry of a short circular DNA molecule. The \emph{bps} displacements with respect to the ground state …
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