Terminator T2 in the same locus has similar characteristics: it is located between genes petD and rpoA in chloroplasts of Arabidopsis thaliana and contains a palindrome of 44 bases length with coordinates 77719...77762 (whereas the complete intergenic region is 77673...77900 according to the GenBank annotation of NC_000932.1) and three non-complementary pairs (an imperfect palindrome).
The molecular self assembly process involved in 2, 3 and 4, facilitates the formation of some base pair motifs with graph-set of R22 8) and a rare non-complementary base pair motif with graph-set R22(10).
For the sake of clarity of presentation, assume that w(F) = e| F |, where | F| is the number of base-pairs in F, and assume that non-complementary base-pairs are not allowed to occur.
Because of a quite good knowledge of the complementary base pairs, we believe that those structures could be found in the non-canonical non-complementary nucleobase pairs.
Our prediction model considers existence of two opposing forces: positive effect corresponding to the formation of complementary base pairs (which is quantified by the reward function), and negative effect due to the existence of non-complementary base pairs (quantified by the penalty function).
This oligodeoxynucleotide contains 15 base-pairs of non-complementary region at both 5' and 3' ends.
Adaptors consisting of ~50 bp oligonucleotide pairs with a non-complementary mid-portion were ligated on to the ends of each fragment after the digest (16 hr ligation using T4 ligase at room temperature).
In their design scheme, each pair of primers contained non-complementary sequences at their 3′ terminus and primer-primer complementary sequences at the 5′ terminus.
Yet, even in the absence of recombination, a part of the colonies showed no specialization, owing to the pairing of individuals with non-complementary thresholds.
The sensor surface clearly distinguished between complementary and non-complementary target ssDNA.
The fabricated biosensor was able to specifically distinguish complementary, non-complementary and mismatched oligonucleotides.
