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These data suggest that short hydrophobic sequences adopt a more extended conformation.
For many years it was thought the TAS sequences adopt a heterochromatin-like conformation[17], [38], [50] [52] that acts as a buffer between the chromosome termini and euchromatic regions.
This detection can be achieved by adsorbing the sequences nonspecifically through the nucleotide side chains onto the enhancing surface of silver colloids, where the sequences adopt a flattened configuration.
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At lower temperatures, the thermosensing region in these sequences adopts a secondary structure that sequesters the ribosome binding site (RBS) of a gene, hence interfering with translation initiation by the ribosome.
Thus, excluding C1d, the time frame is restricted to 18 21 ky and these estimates are about 1.4-fold higher than the larger time frame of 11 17 ky (A2: 13.9±2.0 ky; B2: 16.5±2.7 ky; C1b: 14.7±4.7 ky; C1c: 15.8±4.7 ky; D1: 10.8±2.0 ky) that was recently estimated [14] in a smaller dataset (105 mtDNA sequences) adopting a different calibration [26].
Concentrations of DNA < 30 μM traveled as a single band, suggesting that at pH 5.4 and at a concentration of 2 to 3 μM (those used in our studies) the sequences adopted an intramolecular iM structure.
We believe this is most likely the case, since we previously showed that the underlying mannosylated STR sequence adopts a rigid, nanospring structure [14], i.e. the flexibility between the CRD domain and the transmembrane domain (TMD) of the sensor should be very limited and provides a physical constraint to the lateral movement within the membrane.
One possibility consistent with these results is that the GGW sequence adopts a structured turn [30].
This implies that the DNA sequence adopts a G-quadruplex configuration when complementary strands are separated in the DNA duplex during transcription.
These data suggest that the T=T-containing human telomere sequence adopted a fold slightly different from the propeller fold in high molar concentrations of LiCl (5 M).
In this article, we described a novel algorithm, IncaRNAtion, for the RNA secondary structure design problem, i.e. the design of an RNA sequence adopting a predefined secondary structure as its minimal free-energy fold.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com