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Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles.
The principal sequence feature responsible for intrinsic DNA curvature is generally assumed to be runs of adenines. However, according to the wedge model of DNA curvature, each dinucleotide step isExpand
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The Triplet Code From First Principles
  • E. Trifonov
  • Biology, Medicine
  • Journal of biomolecular structure & dynamics
  • 1 August 2004
Abstract Temporal order (“chronology”) of appearance of amino acids and their respective codons on evolutionary scene is reconstructed. A consensus chronology of amino acids is built on the basis ofExpand
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The pitch of chromatin DNA is reflected in its nucleotide sequence.
A correlation analysis of chromatin DNA nucleotide sequences reveals the clear tendency of some of the dinucleotides to be repeated along the sequences with periods of 3 and about 10.5 bases. ThisExpand
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CURVATURE: software for the analysis of curved DNA
TLDR
Software is presented to plot the sequence-dependent spatial trajectory of the DNA double helix and/or distribution of curvature along the DNA molecule using nearest-neighbor wedge model. Expand
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Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences.
Five different algorithms have been applied for detecting DNA sequence pattern hidden in 204 DNA sequences collected from the literature which are experimentally found to be involved in nucleosomeExpand
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3-, 10.5-, 200- and 400-base periodicities in genome sequences
The above periodicities are the main hidden oscillating patterns detected so far in the genomic sequences. The 3-base periodicity is characteristic for the protein-coding sequences only. The sourceExpand
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Consensus temporal order of amino acids and evolution of the triplet code.
Forty different single-factor criteria and multi-factor hypotheses about chronological order of appearance of amino acids in the early evolution are summarized in consensus ranking. All availableExpand
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Linguistics of nucleotide sequences: morphology and comparison of vocabularies.
The concept of "words" in continuous languages devoid of blanks is introduced and an operational definition of words given. With this novel concept nucleotide sequences become object for linguisticExpand
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Curved DNA: design, synthesis, and circularization.
Curved DNA molecules and unusually small circles have been obtained by ligation of synthetic 21-base precursors: (sequence in text). The ligation resulted in the formation of double-strandedExpand
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10-11 bp periodicities in complete genomes reflect protein structure and DNA folding
TLDR
MOTIVATION Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Expand
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