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miRNAs exert their effects by complementary base-pair binding to a short 7 8 nucleotide seed region typically located on the 3′ untranslated region of the messenger RNA which they inhibit6,9.
First, we measured PrimPol binding to a short 13/18-mer 13/18-merubstrate, which has a five nucleotide (nt) ssDNA overhang on the template strand.
Generally, transcription factors regulate the expression of the target gene positively or negatively by binding to a short sequence of nucleotides called a transcription factor binding site (or motif) in the upstream region of their start point of transcription.
Structural analyses of the individual RRMs and of RRMs 3 and 4 together suggest that the first three RRMs could bind a consecutive sequence of at least 15 nucleotides but that the fourth RRM would require linking sequences before binding to a short pyrimidine tract (Oberstrass et al, 2005; Lamichhane et al, 2010).
Found in all animal and plant cells, as well as in viral genomes, miRNAs act as inhibitors of protein translation by binding to a short six-nucleotide region within the 3′-untranslated region (3′-UTR) of their target mRNAs (Bartel 2004; Bartel and Chen 2004).
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A much smaller complex was formed upon binding to a shorter duplex (16 bp) under the same conditions (0.3 M NaCl, pH 6.5, 55 °C).
The FP measurements indicate that MrkH binds the longer mrkA regulatory fragment (from −117 to +166) with a K d value of 3.07 μmol/L using the one site specific binding model, while MrkH binds to a shorter mrkA regulatory fragment (from −117 to −37) with a K d value of 8.24 μmol/L.
To investigate the approximate footprint of DNA recognised by Chd1-DBD, binding to a series of progressively shorter DNA fragments was tested.
After binding to 2-5A sholigoadenylatesates, a ubiquitous, latent endonuclease, RNase L, is activated through dimerization and degrades either cellular or viral RNAs, resulting in the inhibition of protein synthesis, cellular apoptosis and impaired virus propagation.
Experimental identification of the ligand proteins binding to the short, medium and long KEPEs may provide a new perspective on gene regulation.
As a result, binding to short dsRNA is kinetically unstable explaining why MDA5 is activated only by >0.5 2 kb long dsRNA [ 52].
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