In this set of experiments the targets are single stranded RNA molecules where some of the pyrimidines (the U and C bases) carry a biotin, while the probes are single stranded DNA molecules.
Comment on: ``Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
In brief, while drawing a DNA walk, the corresponding mappings assign a direction/unit vector to each nucleotide, to dinucleotide or to purine (pyrimidine).
Determinative degree and nucleotide sequence analysis by trianders
There are 8 unmixed families (all 4 codons encode the same amino acid), and 8 mixed families for which several patterns of assignment exist, in 6 of the latter the pyrimidine codons (Z = C, U) determine one amino acid, and the purine codons (Z = A, G) determine other ones or termination signals (in one family).
Determinative degree and nucleotide sequence analysis by trianders
The one-dimensional (purine/pyrimidine) DNA walks are deﬁned by only one coordinate, while x is chosen as position, i.e.
Determinative degree and nucleotide sequence analysis by trianders
But for simplicity, people usually take them to be binary variables which can be considered as distinguishing only between purines and pyrimidines.
Quasispecies distribution of Eigen model
Analytical expression of purine/pyrimidine autocorrelation function after and before random mutations.
Chaos in DNA inversions (Draft paper)
We make the simulations for K = 4 symbols (A, C, G, T) and K = 2 symbols (purines, pyrimidines).
Markov Chain Order estimation with Conditional Mutual Information
Table 3: Same format of results as for Table 1, but for transition matrices of given order L estimated from a DNA sequence of genes of length N = 6000 in the form of purines and pyrimidines (K = 2) and all the four nucleotides (K = 4).
Markov Chain Order estimation with Conditional Mutual Information
We make the computations for both genes and intergenic regions of length N = 10000 and N = 100000 and for K = 2 (purines, pyrimidines), and the estimated orders from all criteria are shown in Figure 3.
Markov Chain Order estimation with Conditional Mutual Information
This form is determined by two forces – complementary interactions and stacking (interaction of neighboring nucleotides). Stacking is a nonspecific event as there is a well-known formula: purine-purine>purine-pyrimidine>pyrimidine-pyrimidine.
Evolution of the genetic code. Why are there strong and weak letter doublets? The first gene, the first protein. Early (ancient) biosynthesis of protein
As the purine and the pyrimidine bases significantly differ in their sizes, the above statement seem nearly obvious.
Evolution of the genetic code. From the CG- to the CGUA-alphabet, from RNA double helix to DNA
This mutation leads to the replacement of purine by pyrimidine, significantly changing the shape of the codon if the damage occurs in the second letter. Table 7 shows that the oxidative guanine damage in the first letter is not so significant.
Evolution of the genetic code. From the CG- to the CGUA-alphabet, from RNA double helix to DNA
To represent the evolution of nucleic acid and protein sequence, we express the parallel and Eigen models for molecular evolution in terms of a functional integral representation with an h-letter alphabet, lifting the two-state, purine/pyrimidine assumption often made in quasi-species theory.
Solution of the Crow-Kimura and Eigen models for alphabets of arbitrary size by Schwinger spin coherent states
The general result for the parallel model reduces to known results for the purine/pyrimidine h = 2 alphabet and the nucleic acid h = 4 alphabet for the Kimura 3 ST mutation scheme.
Solution of the Crow-Kimura and Eigen models for alphabets of arbitrary size by Schwinger spin coherent states
The choice of a binary alphabet, which simpliﬁes the mathematical and numerical analysis of the theory, represents a coarse graining of the fourletter alphabet of the nucleic acids DNA/RNA (A,C,G,T/U), by considering the two basic chemical structures of nitrogenated bases, purines (A,G) and pyrimidines (C,T/U).
Solution of the Crow-Kimura and Eigen models for alphabets of arbitrary size by Schwinger spin coherent states
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