Attenuation of loop-receptor interactions with pseudoknot formation

Attenuation of loop-receptor interactions with pseudoknot formation

RNA tetraloops can recognize receptors to mediate long-range interactions in stable natural RNAs. In vitro selected GNRA tetraloop/receptor interactions are usually more 'G/C-rich' than their 'A/U-rich' natural counterparts. They are not as widespread in nature despite comparable biophysical and chemical properties. Moreover, while AA, AC and GU dinucleotide platforms occur in natural GAAA/11 n...

Covariance of complementary rRNA loop nucleotides does not necessarily represent functional pseudoknot formation in vivo.

We examined mutationally a two-hairpin structure (nucleotides 57 to 70 and 76 to 110) in a region of domain I of Escherichia coli 23S rRNA that has been implicated in specific functions in protein synthesis by other studies. On the basis of the observed covariance of several nucleotides in each loop in Bacteria, Archaea, and chloroplasts, the two hairpins have been proposed to form a pseudoknot...

Towards the Sequence Design Preventing Pseudoknot Formation

This paper addresses a pseudoknot-freeness problem of DNA and RNA sequences, motivated by biomolecular computing. WatsonCrick (WK) complementarity forces DNA strands to fold into themselves and form so-called secondary structures, which are usually undesirable for biomolecular computational purposes. This paper studies pseudoknot-bordered words, a mathematical formalization of a common secondar...

Septo-Hippocampo-Septal Loop and Memory Formation

The Cholinergic and GABAergic .bers of the medial septal/diagonal band of Broca (MS/DB) area project to the hippocampus and constitute the septo-hippocampal pathway, which has been proven to play a role in learning and memory. In addition, the hippocampus has bidirectional connections with the septum so that to self-regulate of cholinergic input. The activity of septal and hippocampal neuron...

RNA PSEUDOKNOT PREDICTION IN ENERGY BASED MODELS 3 ) Hairpin loop Hairpin loop