Anne-Marie Stomp

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In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of(More)
A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, 3'-terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from(More)
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E.(More)
Interactions of the ribosome with the mRNA constitute the mechanism of translation in bacteria. We hypothesize that a variable free energy pattern arising from repeated hybridizations of the rRNA tail with a moving window of mRNA sequence could encode information required to maintain translational reading frame. If present, this signal should exist in all(More)
We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3'-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions,(More)
The exact identification of splice sites is a major functional sequence mapping task. The interaction between pre-mRNA splice sites and snRNAs suggests that thermodynamic models could provide methods for identifying splice sites. We show that the donor site position can be identified by finding the minimum binding energy calculated between a mask(More)
In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis by allowing the two molecules to hybridize and form a double-helix. Many mRNAs, however, lack SD sequences and presumably use another mechanism to(More)
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