A fast and reliable method for detecting SNP rs67384697 (Hsa-miR-148a binding site) by a single run of allele-specific real-time PCR
Authors: Malnati, Mauro S.; Biswas, Priscilla; Ugolotti, Elisabetta; Di Marco, Eddi; Sironi, Francesca; Parolini, Francesca; Garbarino, Lucia; Mazzocco, Michela; Zipeto, Donato; Biassoni, Roberto
Surface expression of human leukocyte antigen (HLA)-class I molecules is critical for modulating T/natural killer lymphocytes' effector functions. Among HLA molecules, HLA-C, the most recently evolved form of class I antigens, is subjected to both transcriptional and multiple post-transcriptional regulation mechanisms affecting its cell surface expression. Among the latter a region placed in the 30 untranslated region of HLA-C transcript contains the single nucleotide polymorphism (SNP) rs67384697 "G-ins/del" that has been found to be strictly associated with surface levels of HLA-C allomorphs because of the effect on the binding site of a microRNA (Hsa-miR-148a). Higher expression of HLA-C has been proved to influence HIV-1 infection via a better control of viremia and a slower disease progression. More importantly, the analysis of SNP rs67384697 "G-ins/del" combined with the evaluation of the HLA-Bw4/-Bw6 C1/C2 supratype, as well as the killer immunoglobulin-like receptor genetic asset, has proved to be pivotal in defining the status of Elite Controllers in the Caucasian population. Here we describe a new reliable and fast method of allele-specific real-time PCR to monitor the integrity/disruption of the binding site of the microRNA Hsa-miR-148a in a high-throughput format that can be easily applied to studies involving large cohorts of individuals.
Impact of low-cost methods in the description of excimer and exciplex formation: pyrene-pyrene and pyrene-naphthalene case studies
THEORETICAL CHEMISTRY ACCOUNTS
Authors: do Casal, Mariana T.; Cardozo, Thiago M.
The formation of excimers and exciplexes is relevant to a number of photochemical and photophysical processes such as fluorescence quenching and exciton trapping. Theoretical evaluation of the properties and dynamics of such systems often relies on approximate methods to reduce computational time. In this work, we present an assessment of calculations of the excited states of pyrene-pyrene and pyrene-naphthalene pairs with RI-SOS-ADC(2) and the TD-DFT functionals CAM-B3LYP-D3 and omega B97-XD. We find that ADC(2) yields dissociation energies with relatively small errors for the pyrene-pyrene excimer inS(1)and a consistent picture of the splitting of monomerL(a)andL(b)states into theLa-,La+,Lb-, andLb+ states as the rings approach. TD-DFT, on the other hand, predicts too large dissociation energies for the excimer and is unfit for the description of the pyrene-pyrene dimer. The pyrene-naphthalene exciplex is predicted by RI-SOS-ADC(2) to have a very small dissociation energy, comparable to that of the benzene-benzene excimer.