Dataset Information

Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G*C) base-pair kinetics.

ABSTRACT: NMR magnetization transfer from water and ammonia-catalyzed exchange of the imino proton have been used to probe enhanced thermostability and conformational rearrangements induced by Mg(2+) in two key activity fragments r(CACCUGGCGACAGGUG) and r(GGCCAAAAGCC) of the encephalomyocarditis virus (EMCV) picornavirus internal ribosome entry site (IRES). We have measured some of their r(G*C) base-pair lifetimes and dissociation constants under different MgCl(2) conditions, and we compare them with those of other short RNA duplexes. The RNA fragment r(CACCUGGCGACAGGUG) adopts two topologies, a palindromic duplex with two conformations and a hairpin, whose equilibrium can be monitored: the duplex form is destabilized by Mg(2+) and temperature, a delicate balance wherein the entropic contribution of the free energy helps populate the hairpin state. For both fragments, the opening rates of the r(G*C) pairs are lower in the presence of Mg(2+) and their dissociation constants are smaller or comparable. Analysis of the results suggests that Mg(2+) has a preferential and specific effect on the r(CACCUGGCGACAGGUG) hairpin in the region close to the r(G*C) closing pair of the GCGA tetraloop, and the ion moves diffusively around r(GGCCAAAAGCC), thereby differentiating the GNRA and RAAA hairpin motifs that are both involved in the biological regulation functions of the EMCV IRES.

SUBMITTER: Dupont JA

PROVIDER: S-EPMC2710458 | biostudies-other | 2009 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Similar Datasets

Project description:Worldwide, thalassemia represents one of the most common genetic disorders. There is a prevalence of Beta-thalassemia in Kingdom of Saudi Arabia (KSA), however there is a genetic counseling availability and an existence of mandatory premarital testing policy. Few studies detect molecular mutations of thalassemia genes in different KSA governates, including Makkah, Hufuf, Qatif, and Dammam but in our peer knowledge there is no reports on high altitude Taif region. The aim of the present study is to evaluate the molecular mutation analysis of β-thalassemia gene in El Taif province (as a high-altitude area) patients of KSA and to estimate the iron overload toxicity due to thalassemia syndrome on the hotspot noncoding D-loop region (hypervariable, HV2 gene fragment) of mtDNA. Blood samples were collected from total 25 β-thalassemia patients and 25 normal control that were used for HPLC, hematological analysis and different molecular evaluations. Extracted nuclear DNA from blood sample was used to detect known mutations accompanied with β-thalassemia in other countries using PCR-ARMS technique targeting IVSII-1, IVSI-5, Codon 8/9, Cd44 and Cd5 genes' mutations. Moreover, mtDNA was used to detect point of mutation of HV2 fragment in the D-loop region using PCR-SSCP and then sequencing. Results show significant increase in the level of HbA2 and decrease of HbA in comparison to control by using HPLC. PCR-ARMS reports that all β-thalassemia patients have heterozygous alleles of wild and mutated regions with nucleotide transition/transversion of IVSI-5 (AC>AG), Codon 8/9 (CT>CC), and Cd44 (GG>GA), however no point of mutation was detected in IVSII-1 (AC>AT) Cd5 (CT>CG) genes. Moreover, PCR-SSCP shows points of mutations for β-thalassemia HV2 fragment that were confirmed by sequencing in the form of base pairs deletion, insertion and transition/transversion. For the first time, the present study reports the presence of 2 bps found in HV2 region that might be specific to KSA nations and not found in other countries. In conclusion, our results were in concurrent with other studies in the presence of specific genetic mutations in β-thalassemia patients that is accompanied with points of mutations in HV2 region of high altitude Taif governate.

Dataset Information

Mg2+ modulation of EMCV IRES key activity fragment equilibria and r(G*C) base-pair kinetics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets