Akira Suyama

Diverse transcriptional initiation revealed by fine, large‐scale mapping of mRNA start sites

Determination of the mRNA start site is the first step in identifying the promoter region, which is of key importance for transcriptional regulation of gene expression. The ‘oligo‐capping’ method enabled us to introduce a sequence tag to the first base of an mRNA by replacing the cap structure of the mRNA. Using cDNA libraries made from oligo‐capped mRNAs, we could identify the transcriptional start site of an individual mRNA just by sequencing the 5′‐end of the cDNA. The fine mapping of transcriptional start sites was performed for 5880 mRNAs in 276 human genes. Contrary to our expectations, the majority of the genes showed a diverse distribution of transcriptional start sites. They were distributed over 61.7 bp with a standard deviation of 19.5. Our finding may reflect the dynamic nature of transcriptional initiation events of human genes in vivo.

Third letters in codons counterbalance the (G + C)-content of their first and second letters

The correlation among the frequencies of appearance of G and C bases at the first, second and third positions of codons is examined. It is found that the redundancy at the wobbling third base is utilized to counter‐balance the local (G + C)‐content variation due to the first and second bases of codons, so that a homogeneous (G + C)‐content is provided to each individual gene. We speculate that this levelling tendency of (G + C)‐content comes from the functional constraint to achieve a uniform double‐helix stability in a gene.

Joining and rotating data with molecules

DNA-based computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported in experiments. We suggest a data encoding in the form of (tag data tag)+, and report our experimental results of performing concatenation and rotation of DNA. Our results also show the possibility of join and other operations in a relational database with molecules.

Two types of linkage between codon usage and gene-expression levels

The relation between codon usage and gene‐expression levels is an intensively investigated and discussed topic in the field of molecular evolution. We statistically analyzed 25 Escherichia coli gene sequences by a new classification of synonymous codons and found that (i) there are two distinct types of linkage between codon usage and gene‐expression levels in E. coli, and (ii) one of the two kinds of codon preferences (the codon preference concerned with interaction of GC/AT choice at three codon positions) is observed significantly in weakly expressed genes.

Stabilization of DNA nanostructures by photo-cross-linking

Developing methods for stabilizing DNA nanostructures is a major challenge for next-generation nanofabrication, because stable DNA nanostructures are expected to work as building materials in the bottom-up assembly of functional biomolecules and nano-electronic components. Here we show the availability of cross-linking-type photoreaction with 3-cyanovinylcarbazole nucleosides (CNVKs) on DNA nanostructures. DNA double-crossover AB-staggered (DXAB) tiles including cross-linking molecules, CNVKs, self-assembled into two-dimensional (2D) periodic DNA arrays and were covalently connected by photo-cross-linking. The self-assembled DNA arrays before and after photo-cross-linking have been visualized by high-resolution, tapping mode atomic force microscopy (AFM) in buffer. The improvement of the heat tolerance of photo-cross-linked DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as a functional material in biotechnology and nanotechnology.

Statistical thermodynamic analysis and designof DNA-based computers

A principal research area in biomolecular computing is the development of analytical methods for evaluating computational fidelity and efficiency. In this work, the equilibrium theory of the DNA helix-coil transition is reviewed and expanded, as applied to the analysis and design of oligonucleotide-based computers. After a review of the equilibrium apparatus for modeling the helix-coil transition for single dsDNA species, application to complex hybridizing systems is discussed, via decomposition into component equilibria, which are presumed to proceed independently. The alternative approach, which involves estimation of a mean error probability per hybridized structure, or computational incoherence, ε is then presented, along with a discussion of a special-case exact solution (directed dimer formation), and an approximate general solution, applicable to conditions of uniform fractional-saturation. In order to clarify the opposing nature of the predictions of these two models, simulations are presented for the uniform saturation solution for ε, as applied to a small Tag–Antitag (TAT) system, along with the behavior expected via isolated melting curves. By a comparison with the predictions of a recent, TAT-specific solution for ε, the views provided by these generalized approximate models are shown to define the opposing limits of a more general error-response.

Correlation between thermal stability maps and genetic maps of double-stranded DNAs

The positional correlation of boundaries of cooperatively melting regions with boundaries of protein coding regions and mere open reading frames, and with cleavage sites of restriction enzymes and S1 nuclease are statistically examined for phi X174, G4, fd, SV40, BKV, and polyoma DNAs. A statistically significant correlation does exist in the case of boundaries of protein coding regions, but none is detected for boundaries of mere open reading frames or cleavage sites of restriction enzymes and S1 nuclease. The significant correlation disappears when the cooperativity of melting of the DNA double strand decreases to a nonphysiological condition. The result presents the first evidence showing that a physical property of DNAs correlates with their biological function.

Investigating a link between all-atom model simulation and the Ising-based theory on the helix–coil transition: Equilibrium statistical mechanics

To describe the polypeptide helix–coil transition, while the Ising-based theory has been playing the principal role for 40 years, we can now make use of computer simulation using the so-called “all-atom model” that is far more precise than the Ising-based model. In this study, by conducting molecular dynamics (MD) simulations of helix–coil transition exhibited by a short polyalanine chain, we investigated how the MD simulation results and the Ising-based theoretical values coincide with each other, placing a focus on their equilibrium statistical mechanical properties. Several important physical properties, such as temperature-dependent helix ratio, distribution of the helix-residue number, position-dependent helix ratio, and pair-correlation between residue states were taken up as the proving grounds on which we made a comparison between the all-atom model simulation and the Ising-based theory. As an overall trend, we realized that the Ising-based theoretical results agreed with the all-atom simulation r...

The Fidelity of the Tag-Antitag System

In the universal DNA chip method, target RNAs are mapped onto a set of DNA tags. Parallel hybridization of these tags with an indexed, complementary antitag array then provides an estimate of the relative RNA concentrations in the original solution. Although both error estimation and error reduction are important to process application, a physical model of hybridization fidelity for the TAT system has yet to be proposed. In this work, an equilibrium chemistry model of TAT hybridation is used to estimate the error probability per hybridized tag (?). The temperature dependence of ? is then discussed in detail, and compared with the predictions of the stringency picture. In combination with a modified statistical zipper model of duplex formation, implemented by the Mjolnir software package, ? is applied to investigate the error behavior of small to moderate sized TAT sets. In the first simulation, the fidelities of (1) 105 random encodings, (2) a recently reported Hamming encoding, and (3) an ?-based, evolved encoding of a 32-strand, length- 16 TAT system are estimated, and discussed in detail. In the second simulation, the scaling behavior of the mean error rate of random TAT encodings is investigated. Results are used to discuss the ability of a random strategy to generate high fidelity TAT sets, as a function of set size and encoding length.

PNA-mediated Whiplash PCR

In Whiplash PCR( WPCR), autonomous molecular computation is achieved by the recursive, self-directed polymerase extension of a mixture of DNA hairpins. A barrier confronting efficient implementation, however, is a systematic tendency for encoded molecules towards backhybridization, a simple form of self-inhibition. In order to examine this effect, the length distribution of extended strands over the course of the reaction is examined by modeling the process of recursive extension as a Markov chain. The extension efficiency per polymerase encounter of WPCR is then discussed within the framework of a statistical thermodynamic model. The efficiency predicted by this model is consistent with the premature halting of computation reported in a recent in vitro WPCR implementation. The predicted scaling behavior also indicates that completion times are long enough to render WPCR-based massive parallelism infeasible. A modified architecture, PNA-mediated WPCR (PWPCR) is then proposed in which the formation of backhybridized structures is inhibited by targeted PNA2/DNA triplex formation. The efficiency of PWPCR is discussed, using a modified form of the model developed for WPCR. Application of PWPCR is predicted to result in an increase in computational efficiency sufficient to allow the implementation of autonomous molecular computation on a massive scale.