The oligonucleotides containing N7-regioisomer of guanosine: influence on thermodynamic properties and structure of RNA duplexes.

During the chemical synthesis of the purine riboside, N7-regioisomer is kinetically formed, whereas N9-regioisomer is a thermodynamically formed product. We have studied the effect of substituting N9-regioisomer of guanosine with its N7-regioisomer (N7-guanosine, 7G) at a central position of several RNA duplexes. We found that this single substitution by 7G severely diminished their thermodynamic stabilities when 7G paired with C and U, but remarkably, led to a significant amount of stabilization in most of the duplexes when forming mismatches with G and A.

Predicting nearest neighbor free energies of modified RNA with LIE: results for pseudouridine and 1-methylpseudouridine within RNA duplexes.

Pseudouridine (Ψ) and 1-methylpseudouridine (mΨ) are among the key modifications in the field of mRNA therapeutics and vaccine research. The accuracy of the design and development of therapeutic RNAs containing such modifications depends on the accuracy of the secondary structure prediction, which in turn depends on the nearest neighbor (NN) thermodynamic parameters for the standard and modified residues. Here, we propose a simple approach based on molecular dynamics simulations and linear interaction energy (LIE) approximation that is able to predict the NN free energy parameters for U-A, Ψ-A and mΨ-A pairs in reasonable agreement with the recent experimental reports.

Analysis of the interaction of a non-canonical twin half-site of Cyclic AMP-Response Element (CRE) with CRE-binding protein.

Differential regulation of a gene having either canonical or non-canonical cyclic AMP response element (CRE) in its promoter is primarily accomplished by its interactions with CREB (cAMP-response element binding protein). The present study aims to delineate the mechanism of the CREB-CRE interactions at the Oncostatin-M (osm) promoter by in vitro and in silico approaches. The non-canonical CRE consists of two half-CREs separated by a short intervening sequence of 9 base pairs.

Prevention of inorganic arsenic induced squamous cell carcinoma of the skin in Swiss albino mice by black tea through epigenetic modulation.

Consumption of inorganic Arsenic (iAs) above the safe level may lead to many diseases including cancers of skin. It is known that carcinogenicity of iAs is mediated through generation of excessive reactive oxygen species and polyphenols present in black tea extract (BTE) ameliorate the deleterious effect. Epigenetics also plays vital roles in carcinogenesis.

Data-informed reparameterization of modified RNA and the effect of explicit water models: application to pseudouridine and derivatives.

Pseudouridine is one of the most abundant post-transcriptional modifications in RNA. We have previously shown that the FF99-derived parameters for pseudouridine and some of its naturally occurring derivatives in the AMBER distribution either alone or in combination with the revised γ torsion parameters (parmbsc0) failed to reproduce their conformational characteristics observed experimentally (Deb et al. in J Chem Inf Model 54:1129-1142, 2014; Deb et al.

LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations.

Modulation of structural and thermodynamic properties of nucleic acids with synthetic modifications is a promising area of research with possible applications in nanotechnology and nanotherapeutics. Locked nucleic acid (LNA) is one such modification in which the C4' and O2' atoms of the sugar moiety are connected through a methylene bridge. The LNA modified DNA aptamer RNV66, and its unmodified counterpart V7t1, both of which target the vascular endothelial growth factor (VEGF) implicated in oncogenic angiogenesis, have a G-rich tract that can fold into G-quadruplex structures.

Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA.

Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases.

Molecular Dynamics Simulation of the Conformational Preferences of Pseudouridine Derivatives: Improving the Distribution in the Glycosidic Torsion Space.

There are only four derivatives of pseudouridine (Ψ) that are known to occur naturally in RNA as post-transcriptional modifications. We have studied the conformational consequences of pseudouridylation and further modifications using replica exchange molecular dynamics simulations at the nucleoside level, and the simulated conformational preferences were compared with the available experimental (NMR) data. We found that the existing AMBER FF99-derived parameters for these nucleosides did not reproduce the observed experimental features and while the recommended bsc0 correction could be combined with these parameters leading to an improvement in the description of sugar pucker distributions, the χ correction could not be applied to these nucleosides as such because of base isomerization.

Ensemble Allosteric Model for the Modified Wobble Hypothesis.

The residue 2-thiouridine (sU) provides a remarkable example for the "modified wobble" hypothesis, which postulates that some post-transcriptional modifications at the wobble position of tRNAs restrict recognition of degenerate codons. Through extensive molecular dynamics simulations using our χ force field parameters, we demonstrate how this modification shifts the conformational ensemble from a predominantly disordered, as in the case of an RNA pentamer (GUUUC), to a substantially ordered population in GsUUUC. Our simulations clearly showed that the van der Waals interaction of sulfur played a major role in driving the disorder-to-order transition.

Comparative study of the SBP-box gene family in rice siblings.

SBP-box genes are a class of plant-specific transcription factors which have a common DNA-binding domain (SBP-domain) with an unusual zinc-finger architecture. Many of the genes in this class are thought to play a developmental role and a few are involved in the determination of plant architecture. We have made a comparative study of these genes in the genomes of rice ( and ) and its nine siblings using a recently proposed hybrid method for orthology and paralogy detection (HyPPO).

Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair.

Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context.

Probing the functional conformations of an atypical proline-rich fusion peptide.

The left-handed polyproline II (PPII) type helical structures are thought to play a very important role in many essential biological processes, particularly in recognition mechanisms. However, reliable characterisation of PPII conformation in solution can be experimentally challenging. Computational simulation of these structures offers an attractive alternative, but the accuracy of the results is dependent on the accuracy of the force field employed.

Plant Polypeptide Hormone Systemin Prefers Polyproline II Conformation in Solution.

Systemin, an 18 amino-acid-signaling peptide, was the first plant polypeptide hormone to be discovered. Earlier structural studies involving NMR spectroscopy indicated a lack of definite structure in solution while circular dichroism spectroscopy suggested the presence of left-handed polyproline II (PPII) conformation. Here, we report the results of molecular dynamics simulations of the peptide in explicit solvent with two different force fields, namely, ff99SBildn and ff99IDPs, both of which showed a large propensity for PPII-like conformations in spite of showing differing features for other conformational characteristics.

Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin.

As part of their basal immune mechanism against insect/herbivore attacks, plants have evolved systemic response mechanisms. Such a systemic wound response in tomato was found to involve an 18 amino acid polypeptide called systemin, the first polypeptide hormone to be discovered in plants. Systematic alanine scanning and deletion studies showed differential modulation in its activity, particularly a major loss of function due to alanine substitution at positions 13 and 17 and less extentive loss of function due to substitution at position 12.

Reparameterizations of the χ Torsion and Lennard-Jones σ Parameters Improve the Conformational Characteristics of Modified Uridines.

Unlabelled: The currently available force field parameters for modified RNA residues in AMBER show significant deviations in conformational properties from experimental observations. The examination of the transferability of the recently revised torsion parameters revealed that there was an overall improvement in the conformational properties for some of the modifications but the improvements were still insufficient in describing the sugar pucker preferences (J. Chem.

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.

The structural effects of the commonly occurring modified nucleoside dihydrouridine (D) observed experimentally in model oligonucleotides include a strong destabilization of the C3'-endo sugar conformation of D, the disruption of stacking interactions of neighboring residues with D and a possible destabilization of the C3'-endo sugar pucker of the 5'-neighboring nucleoside. Our simulations with a combination of a set of parameters for modified RNA residues with the recently developed AMBER FF99χ force field having reoptimized glycosidic torsion angle parameters for standard nucleosides was found to reproduce the destabilizing effect of dihydrouridine better than with the AMBER FF99 force field for nucleic acids for which the parameters for the modified residues were originally developed.

Conformational preferences of modified uridines: comparison of AMBER derived force fields.

The widespread occurrence of modified residues in RNA sequences necessitates development of accurate parameters for these modifications for reliable modeling of RNA structure and dynamics. A comprehensive set of parameters for the 107 naturally occurring RNA modifications was proposed by Aduri et al. (J.

Specificity determinants for the abscisic acid response element.

Abscisic acid (ABA) response elements (ABREs) are a group of cis-acting DNA elements that have been identified from promoter analysis of many ABA-regulated genes in plants. We are interested in understanding the mechanism of binding specificity between ABREs and a class of bZIP transcription factors known as ABRE binding factors (ABFs). In this work, we have modeled the homodimeric structure of the bZIP domain of ABRE binding factor 1 from Arabidopsis thaliana (AtABF1) and studied its interaction with ACGT core motif-containing ABRE sequences.

Genome wide gene expression regulation by HIP1 Protein Interactor, HIPPI: prediction and validation.

Background: HIP1 Protein Interactor (HIPPI) is a pro-apoptotic protein that induces Caspase8 mediated apoptosis in cell. We have shown earlier that HIPPI could interact with a specific 9 bp sequence motif, defined as the HIPPI binding site (HBS), present in the upstream promoter of Caspase1 gene and regulate its expression. We also have shown that HIPPI, without any known nuclear localization signal, could be transported to the nucleus by HIP1, a NLS containing nucleo-cytoplasmic shuttling protein.

Arabidopsis thaliana regulatory element analyzer.

Unlabelled: In the Arabidopsis thaliana regulatory element analyzer (AtREA) server, we have integrated sequence data, genome-wide expression data and functional annotation data in three application modules which will be useful to identify major regulatory targets of a user-provided cis-regulatory element (CRE), study different features of CRE distribution and evaluate the role of a set of CREs in the regulation of gene expression--independently as well as in combination with other user-provided CREs.

Availability: AtREA is freely available at http://www.bioinformatics.

TRABAS: a database for transcription regulation by ABA signaling.

The effects of abscisic acid (ABA) induction on Arabidopsis thaliana transcriptome have been investigated by various expression studies. We have assembled and analyzed data from available expression studies related to ABA signaling in Arabidopsis along with other available microarray data, functional annotations and information related to occurrence of cis-regulatory elements in promoters of Arabidopsis genes in a database called TRABAS. TRABAS is expected to provide a simple, user-friendly platform to facilitate the study of different aspects of ABA mediated transcription regulation and is freely available at http://www.