In:
FEBS Letters, Wiley, Vol. 580, No. 27 ( 2006-11-27), p. 6413-6422
Abstract:
A simple model is put forward to explain the long‐known three‐base periodicity in coding DNA. We propose the concept of same ‐ phase triplet clustering , i.e. a condition wherein a triplet appears several times in one phase without interruption by the two other possible phases. For instance, in the sequence (i): NTT_GNN_NTT_GNN_NTT_GNN_NNN_NTT_GNN (where N is any nucleotide but combinations producing TTG are excluded) there would be clustering of same‐phase TTG because this triplet appears uninterruptedly in phase 2. In contrast, in the sequence (ii): TTG_NTT_GNN_NNT_TGN_NNN_NTT_GNN there is no same‐phase clustering because neighboring TTGs are all in different phases. Observe also that in sequence (i) TTG triplets are separated by 3, 3 and 6 nucleotides (3 n distances), while in sequence (ii) they are separated by 1, 4 and 5 nucleotides (non‐3 n distances). In this work, we demonstrate that in coding DNA the 3 n distances generated by (i)‐type sequences proportionally outnumber the non‐3 n distances generated by (ii)‐type sequences, this condition would be the basis of three‐base periodicity. Randomized sequences had (i)‐ and (ii)‐type sequences too but clustering was statistically different. To prove our model we generated (i)‐type sequences in a randomized sequence by inducing clustering of same‐phase triplets. In agreement with the model this sequence displayed three‐base periodicity. Furthermore, two‐ and four‐base periodicities could also be induced by artificially inducing clustering of duplets and tetraplets.
Type of Medium:
Online Resource
ISSN:
0014-5793
,
1873-3468
DOI:
10.1016/j.febslet.2006.10.056
Language:
English
Publisher:
Wiley
Publication Date:
2006
detail.hit.zdb_id:
212746-5
detail.hit.zdb_id:
1460391-3
SSG:
12
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