AN OPTIMIZED PROTOCOL FOR IN VACUO MOLECULARDYNAMICS SIMULATION AND TRAJECTORYANALYSIS OF MODIFIED DNA DUPLEXES

This paper presents an optimized protocol for in vacuo molecular dynamics studies of short DNAduplexes containing modified nucleosides. The example studied is an 11 base pair DNA duplex modifiedwith l,N6-ethenodeoxyadenosine (dεA) located opposite deoxyguanosine. A complex moleculardynamics trajectory was subjected to statistical cluster analysis. Groups (clusters) of similarconformations, which can be statistically identified after energy minimization of the trajectory results,have been analyzed with particular regard to the estimation of intrinsic stability of the duplex (hydrogenbonding and base stacking). The modified residue was found to form two hydrogen bonds within thed ε A / d G base pair, which stabilize the duplex, thus allowing its conformation to remain close to regularB-DNA.Pozna

SU(2) Cosmological Solitons

We present a class of numerical solutions to the SU(2) nonlinear $\sigma$-model coupled to the Einstein equations with cosmological constant $\Lambda\geq 0$ in spherical symmetry. These solutions are characterized by the presence of a regular static region which includes a center of symmetry. They are parameterized by a dimensionless ``coupling constant'' $\beta$, the sign of the cosmological constant, and an integer ``excitation number'' $n$. The phenomenology we find is compared to the corresponding solutions found for the Einstein-Yang-Mills (EYM) equations with positive $\Lambda$ (EYM$\Lambda$). If we choose $\Lambda$ positive and fix $n$, we find a family of static spacetimes with a Killing horizon for $0 \leq \beta < \beta_{max}$. As a limiting solution for $\beta = \beta_{max}$ we find a {\em globally} static spacetime with $\Lambda=0$, the lowest excitation being the Einstein static universe. To interpret the physical significance of the Killing horizon in the cosmological context, we apply the concept of a trapping horizon as formulated by Hayward. For small values of $\beta$ an asymptotically de Sitter dynamic region contains the static region within a Killing horizon of cosmological type. For strong coupling the static region contains an ``eternal cosmological black hole''.Comment: 20 pages, 6 figures, Revte

New, extended hairpin form of the TAR-2 RNA domain points to the structural polymorphism at the 5′ end of the HIV-2 leader RNA

The HIV-2 TAR RNA domain (TAR-2) plays a key role in the trans-activation of HIV-2 transcription as it is the target for the Tat-2 protein and several cell factors. Here, we show that the TAR-2 domain exists in vitro in two global, alternative forms: a new, extended hairpin form with two conformers and the already proposed branched hairpins form. This points strongly to the structural polymorphism of the 5′ end of the HIV-2 leader RNA. The evidence comes from the non-denaturing PAGE mobility assay, 2D structure prediction, enzymatic and Pb(2+)- or Mg(2+)-induced RNA cleavages. Existence of the TAR-2 extended form was further proved by the examination of engineered TAR-2 mutants stabilized either in the branched or extended structure. The TAR-2 extended form predominates with an increasing magnesium concentration. Gel retardation assays reveal that both TAR-2 wt and its mutant, unable to form branched structure, bind Tat-2 protein with comparable, high affinity, while RNA hairpins I and II, derived from TAR-2 branched structure model, show much less protein binding. We propose that an internal loop region of the TAR-2 extended hairpin form is a potential Tat-2 binding site

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Background: Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description: RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl webcite. Conclusions: RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the ‘dot-bracket’ notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb)

The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

RNA dimerization is an essential step in the retroviral life cycle. Dimerization and encapsidation signals, closely linked in HIV-2, are located in the leader RNA region. The SL1 motif and nucleocapsid protein are considered important for both processes. In this study, we show the structure of the HIV-2 leader RNA (+1–560) captured as a loose dimer. Potential structural rearrangements within the leader RNA were studied. In the loose dimer form, the HIV-2 leader RNA strand exists in vitro as a single global fold. Two kissing loop interfaces within the loose dimer were identified: SL1/SL1 and TAR/TAR. Evidence for these findings is provided by RNA probing using SHAPE, chemical reagents, enzymes, non-denaturing PAGE mobility assays, antisense oligonucleotides hybridization and analysis of an RNA mutant. Both TAR and SL1 as isolated domains are bound by recombinant NCp8 protein with high affinity, contrary to the hairpins downstream of SL1. Foot-printing of the SL1/NCp8 complex indicates that the major binding site maps to the SL1 upper stem. Taken together, these data suggest a model in which TAR hairpin III, the segment of SL1 proximal to the loop and the PAL palindromic sequence play specific roles in the initiation of dimerization