Showing papers on "Molecular models of DNA published in 2003"

Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices

Abstract: The programmed self-assembly of patterned aperiodic molecular structures is a major challenge in nanotechnology and has numerous potential applications for nanofabrication of complex structures and useful devices. Here we report the construction of an aperiodic patterned DNA lattice (barcode lattice) by a self-assembly process of directed nucleation of DNA tiles around a scaffold DNA strand. The input DNA scaffold strand, constructed by ligation of shorter synthetic oligonucleotides, provides layers of the DNA lattice with barcode patterning information represented by the presence or absence of DNA hairpin loops protruding out of the lattice plane. Self-assembly of multiple DNA tiles around the scaffold strand was shown to result in a patterned lattice containing barcode information of 01101. We have also demonstrated the reprogramming of the system to another patterning. An inverted barcode pattern of 10010 was achieved by modifying the scaffold strands and one of the strands composing each tile. A ribbon lattice, consisting of repetitions of the barcode pattern with expected periodicity, was also constructed by the addition of sticky ends. The patterning of both classes of lattices was clearly observable via atomic force microscopy. These results represent a step toward implementation of a visual readout system capable of converting information encoded on a 1D DNA strand into a 2D form readable by advanced microscopic techniques. A functioning visual output method would not only increase the readout speed of DNA-based computers, but may also find use in other sequence identification techniques such as mutation or allele mapping.

A glossary of DNA structures from A to Z.

Abstract: The right-handed double-helical Watson-Crick model for B-form DNA is the most commonly known DNA structure. In addition to this classic structure, several other forms of DNA have been observed and it is clear that the DNA molecule can assume different structures depending on the base sequence and environment. The various forms of DNA have been identified as A, B, C etc. In fact, a detailed inspection of the literature reveals that only the letters F, Q, U, V and Y are now available to describe any new DNA structure that may appear in the future. It is also apparent that it may be more relevant to talk about the A, B or C type dinucleotide steps, since several recent structures show mixtures of various different geometries and a careful analysis is essential before identifying it as a 'new structure'. This review provides a glossary of currently identified DNA structures and is quite timely as it outlines the present understanding of DNA structure exactly 50 years after the original discovery of DNA structure by Watson and Crick

Thermal denaturation of a helicoidal DNA model.

Abstract: We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e., the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's "universality class" strongly suggests the presence of an "underlying" continuous transition.

Branching DNA machines based on transitions of hairpin structures

Abstract: We constructed a DNA machine, the state branches of which depend on input DNA oligomers. The machine is a single DNA oligomer consisting of two hairpin structures connected by a single-stranded section. The input DNA oligomers can invade a hairpin's stem via branch migration, opening the hairpin. The branching state is represented by which of the hairpins is opened. This paper describes the design of the DNA machine, an analysis of secondary structure transitions, and experimental results.

Controlling the speed and direction of molecular motors that replicate DNA

Abstract: The advent of techniques to detect and manipulate individual molecules has revealed that mechanical tension on a DNA polymer can control both the speed and direction of the DNA polymerase (DNAp) motor. Reconciling the interpretation of these single molecule experiments with crystal structural data has been the focus of our previous work. In more recent work, we are developing a more broadly applicable conceptual framework to describe how tension on a DNA polymer can produce both the "tuning" and "switching" phenomena observed in DNA polymerase motors. The chief aims are to elucidate the mechanism by which DNA replication is controlled in cells and to seek novel strategies for controlling molecular scale processes and the function of nanodevices.

New Structural Motifs Isohelical to DNA

Abstract: Currently, significant progress has been made in the design and synthesis of site-specific DNA-binding agents that are analogues of the natural pyrrolecarboxamide antibiotics netropsin and distamycin and the bis benzimidazole dye Hoechst 33258 [1–7]. These compounds bind in the minor DNA groove to runs of three to five consecutive AT-base pairs. All of them contain a structural motif in which five-membered aromatic cycles are linked via two sp2-hybridized atoms (Fig. 1). Hereinafter, this structural motif will be referred to as motif I.