TY - JOUR
T1 - Sequence context of oligomer tracts in eukaryotic dna
T2 - Biological and conformational implications
AU - Nussinov, Ruth
AU - Sarai, Akinori
AU - Smythers, Gary W.
AU - Jemigan, Robert L.
N1 - Funding Information:
This project has been funded at least in part with Federal funds from the Department of Health and Human Services under contact number NOl-C0-74102. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Service, nor does mention of trade names, commercial products, or organizations imply endorsement by the U. S. Government.
PY - 1988/12
Y1 - 1988/12
N2 - Recent studies of homooligomer tracts suggest different characteristics from random sequence DNA. (dA) · (dT) and (dG) · (dC) tracts are frequent in upstream regions and in some cases have been shown to be essential for regulation. Here we examine homooligomer occurrences in non-coding and coding eukaryotic sequences, focusing on the context in which the homooligomers occur. This analysis of sequences in the junction areas yields distinct and consistent characteristics. In particular, the nucleotide interrupting a run is most frequently complementary to the run. The base next to it is most frequently identical to the one constituting the run. For A or T runs the least frequent nearest and next to nearest neighbors are G or C. For G or C tracts the least frequent are A or T. Complementary oligomers behave similarly. These and additional trends are strongest for run lengths >3. The computations are carried out on the whole eukaryotic database of >4×l06 nucleotides, separately for coding and noncoding regions. These same trends are evident for both groups, but are somewhat stronger for the non-coding regions. The context in which the homooligomers occur may yield some clues to DNA conformation and its biological implications.
AB - Recent studies of homooligomer tracts suggest different characteristics from random sequence DNA. (dA) · (dT) and (dG) · (dC) tracts are frequent in upstream regions and in some cases have been shown to be essential for regulation. Here we examine homooligomer occurrences in non-coding and coding eukaryotic sequences, focusing on the context in which the homooligomers occur. This analysis of sequences in the junction areas yields distinct and consistent characteristics. In particular, the nucleotide interrupting a run is most frequently complementary to the run. The base next to it is most frequently identical to the one constituting the run. For A or T runs the least frequent nearest and next to nearest neighbors are G or C. For G or C tracts the least frequent are A or T. Complementary oligomers behave similarly. These and additional trends are strongest for run lengths >3. The computations are carried out on the whole eukaryotic database of >4×l06 nucleotides, separately for coding and noncoding regions. These same trends are evident for both groups, but are somewhat stronger for the non-coding regions. The context in which the homooligomers occur may yield some clues to DNA conformation and its biological implications.
UR - https://www.scopus.com/pages/publications/0024204477
U2 - 10.1080/07391102.1988.10506506
DO - 10.1080/07391102.1988.10506506
M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???
AN - SCOPUS:0024204477
SN - 0739-1102
VL - 6
SP - 543
EP - 562
JO - Journal of Biomolecular Structure and Dynamics
JF - Journal of Biomolecular Structure and Dynamics
IS - 3
ER -