MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures

One major challenge in nucleic acids analysis by hybridization probes is a compromise between the probe's tight binding and sequence‐selective recognition of nucleic acid targets folded into stable secondary structures. We have been developing a four‐way junction (4WJ)‐based sensor that consists of a universal stem‐loop (USL) probe immobilized on an electrode surface and two adaptor strands (M and F). The sensor was shown to be highly selective towards single base mismatches at room temperature, able to detect multiple targets using the same USL probe, and have improved ability to detect folded nucleic acids. However, some nucleic acid targets, including natural RNA, are folded into very stable secondary and tertiary structures, which may represent a challenge even for the 4WJ sensors. This work describes a new sensor, named MVF since it uses three probe stands M, V and F, which further improves the performance of 4WJ sensors with folded targets. The MVF sensor interrogating a 16S rRNA NASBA amplicon with calculated folding energy of ?32.82 kcal/mol has demonstrated 2.5‐fold improvement in a signal‐to‐background ratio in comparison with a 4WJ sensor lacking strand V. The proposed design can be used as a general strategy in the analysis of folded nucleic acids including natural RNA.     

On order preserving contractions

Let (Ω,Σ,μ) be a measure space and letP be an operator onL ₂(Ω,Σ,μ) with ‖P‖≦1,Pf≧0 a.e. wheneverf≧0. If the subspaceK is defined byK={x| ||P ⁿ x||=||P ^*n x||=||x||,n=1,2,...} thenK=L ₂(Ω,Σ₁,μ), where Σ₁ ⊂ Σ and onK the operatorP is “essentially” a measure preserving transformation. Thus the eigenvalues ofP of modulus one, form a group under multiplication. This last result was proved by Rota for finiteμ here finiteness is not assumed) and is a generalization of a theorem of Frobenius and Perron on positive matrices. The research reported in this document has been sponsored in part by Air Force Office of Scientific Research, OAR through the European Office, Aerospace Research, United States Air Force.     

Ergodic decomposition of a topological space

Given a positive contraction,P, onC(X) we define the conservative and dissipative parts ofP and establish divergence of ΣP ⁿf(x) on the conservative part ofX.     

A Note On Subloop Lattices

Pálfy and Pudlák (Algebra Universalis 11, 22–27, 1980) posed the question: is every finite lattice isomorphic to an interval sublattice of the lattice of subgroups of a finite group? in this paper we will look at examples of lattices that can be realized as subloop lattices but not as subgroup lattices. This is a first step in answering a new question: is every finite lattice isomorphic to an interval sublattice of the subloop lattice of a finite loop?     

Identification of archaeal proteins that affect the exosome function in vitro

Background  

The archaeal exosome is formed by a hexameric RNase PH ring and three RNA binding subunits and has been shown to bind and degrade RNA in vitro. Despite extensive studies on the eukaryotic exosome and on the proteins interacting with this complex, little information is yet available on the identification and function of archaeal exosome regulatory factors.     

Invariant subspaces of a measure preserving transformation

We consider, in this note, some invariant subspaces of a unitary operator induced by a measure preserving transformation. For these subspaces two problems are studied:

1. a.
   Is the subspace generated by characteristic functions?     

Harris operators

A method is constructed which leads to a proof for both the “zero-two” law, and the Ornstein-Métivier-Brunel Theorem for Harris operators. For the proof it is not necessary to assume that the measure space is measurable and the operator need not be given by a transition probability. We strove to make these notes self-contained.