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A recurrent DNA sequence at sites of protein interaction
Advances in Biophysics, 1985Variation in the observed spin lattice relaxation rate (Robs) interpreted as proton exchange dominated in sequences corresponding to part of promoters where RNA polymerase initiates mRNA synthesis has been observed by both Patel et al. and Reid and co-workers.
P, Lu, S, Cheung, M, Donlan
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|DNA bending by sequence and proteins
1995Abstract A fundamental problem confronting any living organism is how to package an immense length of DNA in an organised manner into a small volume. One solution is to compact the DNA by the tight bending of the duplex in the form of a superhelix which can itself then be folded into a more compact structure. Because the DNA double helix
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Thermodynamics of sequence-specific protein-DNA interactions
Biophysical Chemistry, 1996The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics.
T, Härd, T, Lundbäck
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Identification of Sequence-Specific DNA Binding Proteins
2004Publisher Summary This chapter describes methods for the identification of nuclear proteins that bind specific DNA sequences within the cis -regulatory domains of genes. Protocols for the preparation of nuclear extract, quantitative electrophoretic mobility shift analysis, oligonucleotide affinity chromatography, and protein preparation for amino ...
James A, Coffman, Chiou-Hwa, Yuh
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Dual Function of DNA Sequences: Protein-Coding Sequences Function as Transcriptional Enhancers
Perspectives in Biology and Medicine, 2015Most of our genome comprises noncoding sequences that include diverse transcriptional regulatory elements, such as enhancers, while only ~1.5% of the genome codes for proteins. Nevertheless, DNA sequences that code for protein (exons) can also function as enhancers (eExons) that regulate transcription.
Naama, Hirsch, Ramon Y, Birnbaum
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A program to optimize DNA sequences for protein expression
Bioinformatics, 1990THOYO is a program that combines sequence feature identification with automatic editing to allow the rapid optimization of «reverse translation» sequence. Data, entered as amino acid sequence in single or triple letter code, is automatically reverse translated using the most frequent codons of man, Saccharomyces cerevisiae or Escherichia ...
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Interaction of regulator proteins with recognition sequences of DNA
Cell, 1974Benjamin Lewin The MIT Press 28 Carleton Street Cambridge, Mass 02142 Although models for the control of gene expression have for some time focused on the concept that regulator proteins act by recognizing specific nu- cleotide sequences, only now is it becoming possi- ble to define the molecular basis of such interac- tions. The existence of two sites
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From Genes to Proteins: Genotypic and Phenotypic Analysis of DNA Sequences by Protein Sequencing
1983Sequences of genes, and gene products such as proteins, provide a detailed and largely self-consistent context for discussion of molecular phylogenies and taxonomic relationships. Analysis at the DNA level, an alternative and often more rapid approach for protein sequence analysis, requires identification of codogenic regions.
K. Beyreuther +9 more
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DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences
Briefings in Bioinformatics, 2021Sina Ghadermarzi +2 more
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