Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.

Non-B DNA structures show diverse conformations and complex transition kinetics comparable to RNA or proteins--a perspective from mechanical unfolding and refolding experiments.

Abstract: With the firm demonstration of the in vivo presence and biological functions of many non-B DNA structures, it is of great significance to understand their physiological roles from the perspective of structural conformation, stability, and transition kinetics. Although relatively simple in primary sequences compared to proteins, non-B DNA species show rather versatile conformations and dynamic transitions. As the most-studied non-B DNA species, the G-quadruplex displays a myriad of conformations that can interconvert between each other in different solutions. These features impose challenges for ensemble-average techniques, such as X-ray crystallography, NMR spectroscopy, and circular dichroism (CD), but leave room for single-molecular approaches to illustrate the structure, stability, and transition kinetics of individual non-B DNA species in a solution mixture. Deconvolution of the mixture can be further facilitated by statistical data treatment, such as iPoDNano (integrated population deconvolution with nanometer resolution), which resolves populations with subnanometer size differences. This Personal Account summarizes current mechanical unfolding and refolding methods to interrogate single non-B DNA species, with an emphasis on DNA G-quadruplexes and i-motifs. These single-molecule studies start to demonstrate that structures and transitions in non-B DNA species can approach the complexity of those in RNA or proteins, which provides solid justification for the biological functions carried out by non-B DNA species.

DNA at membrane surfaces: An experimental overview

Abstract: Atomic force microscopy studies of DNA attached to rigid surfaces were initially motivated by the development-of methods which would stretch DNA for the purposes of rapid sequencing. Currently there is much interest in studies of multilayers of DNA chains self-assembled on membranes which form spontaneously when DNA adsorbs onto oppositely charged cationic liposomes (CLs). A major motivation for elucidating the structures and interactions in these CL-DNA complexes arises for two reasons. The first is that they are known to mimic certain characteristics of viruses by being efficient chemical carriers of genes (DNA sections) for delivery in cells. The second is that they are models of studies of DNA condensation phases in two dimensions. DNA-membrane interactions should also provide clues for the relevant molecular forces in the condensation of DNA in chromosomes and viral capsids. The particular complexes described in this review contain linear DNA forming a new ‘hybrid’ phase of matter; that is, the DNA chains form a finite size two dimensional smectic coupled to the three dimensional smectic phase of membranes.

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer in crystal environment: comparison of atomic point-charge, extra-point, and polarizable force fields.

Abstract: Molecular dynamics simulations of the DNA duplex d(CCAACGTTGG)2 were used to study the relationship between DNA sequence and structure in a crystal environment. Three different force fields were used: a traditional description based on atomic point charges, a polarizable force field, and an “extra-point” force field (with additional charges on extranuclear sites). It is found that all the force fields reproduce fairly well the sequence-dependent features of the experimental structure. The polarizable force field, however, provides the most accurate representation of the crystal structure and the sequence-dependent effects observed in the experiment. These results point out to the need of the inclusion of polarization for accurate descriptions of DNA.

Functional Materials Derived from DNA

Abstract: DNA has special properties and its unique double-helical structure offers excellent prospects forcreating novel DNA-based materials. In recent years, DNA has been shown to be an ideal molecule in thematerial world. This review is intended to provide an overview of functional materials derived from DNAbased on the double-helical structure. Various DNA-based materials are reviewed according to the basicDNA structural properties, including the electrostatic properties of DNA as a highly charged polyelectrolyte,complementary base pairing, and intercalation and groove binding interaction with small molecules. Finally,attempts to produce biomaterials based on DNA are also summarized.