The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.

In this paper we consider a single server queueing model with under general bulk service rule with infinite upper bound on the batch size which we call group clearance. The arrivals occur according to a batch Markovian point process and the services are generally distributed. The customers arriving after the service initiation cannot enter the ongoing service. The service time is independent on the batch size. First, we employ the classical embedded Markov renewal process approach to study the model. Secondly, under the assumption that the services are of phase type, we study the model as a continuous-time Markov chain whose generator has a very special structure. Using matrix-analytic methods we study the model in steady-state and discuss some special cases of the model as well as representative numerical examples covering a wide range of service time distributions such as constant, uniform, Weibull, and phase type.