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  • 1
    Electronic Resource
    Electronic Resource
    Helix stability in prokaryotic promoter regions (1988)
    s.l. : American Chemical Society
    Biochemistry 27 (1988), S. 5179-5188 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00414a035
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Efficient algorithms for searching for exact repetition of nucleotide sequences (1983)
    Springer
    Journal of molecular evolution 19 (1983), S. 283-285 
    Details
    ISSN: 1432-1432
    Keywords: Sequence analysis ; Exact repetition ; Algorithm
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are several algorithms designed for searches for homologous sequences (Fitch 1966; Needleman and Wunsch 1970; Chva'tal and Sankoff 1975; Griggs 1977; Sannkoff 1972; Smith and Waterman 1981; Smith et al. 1981, Wagner and Fisher 1974; Waterman et al. 1976). This paper presents some very simple and useful high speed, “text editing” algorithms that search for exact nucleotide sequence repetition and genome duplication. The last algorithm suggested here is specifically adapted for the 4-letter alphabet of nucleotide sequences. Owing to the rapid accumulation of nucleotide sequences and the frequent need to search for sequence repetition or where a given set of nucleotides occurs in long sequences, efficient algorithms of this type are a necessity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099975
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  • 3
    Electronic Resource
    Electronic Resource
    Structural features are as important as sequence homologies inDrosophila heat shock gene upstream regions (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 106-110 
    Details
    ISSN: 1432-1432
    Keywords: Drosophila heat shock ; Protein genes ; Structural homology ; Regulatory regions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Pelham has shown that theDrosophila hsp 70 gene is not transcribed under heat shock conditions unless a given upstream region is present. Davidson et al. have recently compiled a list of sequences homologous to this region in otherDrosophila heat shock genes. They proposed that a set of unlinked genes, such as the heat shock genes, could be coordinately induced through an interaction in cis with a common regulatory molecule. That this interaction involves structural elements is suggested by the fact that these upstream regions share inverted repeats as well as areas of Z-DNA potential. Furthermore, using the Calladine-Dickerson rules for local helical parameters, we show that these regions share structural homology. This is significant because the presence of regions homologous to a derived consensus sequence does not necessarily imply structural similarity. Therefore, we suggest that these structural features are at least as important as the sequence homologies in enabling the heat shock response.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02257370
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  • 4
    Electronic Resource
    Electronic Resource
    Strong doublet preferences in nucleotide sequences and DNA geometry (1984)
    Springer
    Journal of molecular evolution 20 (1984), S. 111-119 
    Details
    ISSN: 1432-1432
    Keywords: Dinucleotides ; Sequence data ; DNA structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Analysis of the sequence data available today, comprising more than 500,000 bases, confirms the previously observed phenomenon that there are distinct dinucleotide preferences in DNA sequences. Consistent behaviour is observed in the major sequence groups analysed here in prokaryotes, eukaryotes and mitochondria. Some doublet preferences are common to all groups and are found in most sequences of the Los Alamos Library. The patterns seen in such large data sets are very significant statistically and biologically. Since they are present in numerous and diverse nucleotide sequences, one may conclude that they confer evolutionary advantages on the organism. In eukaryotes RR and YY dinucleotides are preferred over YR and RY (where R is a purine and Y a pyrimidine). Since opposite-chain nearest-neighbour purine clashes are major determinants of DNA structure, it appears that the tight packaging of DNA in nucleosomes disfavors, in general, such (YR and RY) steric repulsion.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02257371
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  • 5
    Electronic Resource
    Electronic Resource
    The distributions of nucleotides near bacterial transcription initiation and termination sites show distinct signals that may affect DNA geometry (1987)
    Springer
    Journal of molecular evolution 26 (1987), S. 187-197 
    Details
    ISSN: 1432-1432
    Keywords: Transcription initiation ; Transcription termination ; Sequence signals ; DNA geometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Compilation and analysis of all bacterial sequences which are aligned by their transcription initiation sites show a dramatic behavior of the four nucleotides. Large peaks of T and A are observed. This highly nonrandom distribution is likely to affect the DNA geometry in addition to affecting the strength of binding between the two DNA strands. Following this site, the G and C rise above their overall bacterial mean. Alignment by transcription termination sites indicates that this behavior continues till the mRNA 3′ termini. At this site the concentrations of A and T rise again above the mean. Analysis of the distributions of the 256 quartets in the 1000 nucleotide regions surrounding both transcription initiation and termination sites has been carried out. Some A/T combination sequences may serve as signals to the bacterial transcription machinery, in addition to the well-established T T G A C A and T A T A A T at positions −35 and −10, respectively, and a run of Ts at the transcription termination site. The frequent occurrences of (dA)/(dT) runs in the vicinity of these sites may result in curved DNA structures, affecting recognition and the nature of the interaction between the RNA polymerase and the DNA.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099851
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  • 6
    Electronic Resource
    Electronic Resource
    Distinct patterns in the dinucleotide nearest neighbors to G/C and A/T oligomers in eukaryotic sequences (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 259-266 
    Details
    ISSN: 1432-1432
    Keywords: DNA sequence analysis ; Frequencies ; Sequence patterns ; DNA structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The eukaryotic and prokaryotic databases are scanned for potential nearest-neighbor doublet preferences at the 5′ and 3′ flanks of some oligomers. Here we focus on oligomers containing alternating nucleotides, i.e., UV, UVUV, and UUVV where U≠V. Strong, consistent trends are observed in eukaryotic sequences. A/T alternation oligomers are preferentially flanked by A/T. G/C flanks are disfavored. G/C alternation oligomers are preferentially flanked by G/C. A/T flanks are disfavored. These trends are consistent with those observed previously for homooligomer tracts (Nussinov et al. 1989a,b). G/C tracts are preferentially flanked by G/C. A/T nearest neighbors are disfavored. The reverse holds for A/T tracts. Additional patterns are described here as well. The possible origin of these DNA composition and sequence trends is discussed. These trends are suggested to stem from protein-DNA interaction constraints.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100677
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  • 7
    Electronic Resource
    Electronic Resource
    The universal dinucleotide asymmetry rules in DNA and the amino acid codon choice (1981)
    Springer
    Journal of molecular evolution 17 (1981), S. 237-244 
    Details
    ISSN: 1432-1432
    Keywords: Dinucleotides ; Prokaryotic, Eukaryotic, DNA ; Genetic code
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Natural DNA sequences were recently found to contain distinct nearest neighbor patterns. Hetero-dinucleotides were demonstrated to appear consistently more (less) than their mirror-image counterparts. This paper shows that this assymmetric behavior does not stem from the coding requirements of the DNA. It also shows some codon patterns in prokaryotic and eukaryotic genomes which came up in the course of this work.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01732761
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  • 8
    Electronic Resource
    Electronic Resource
    Structural wrinkles and the genomic regulatory sites of eukaryotes (1985)
    Springer
    Journal of molecular evolution 22 (1985), S. 150-159 
    Details
    ISSN: 1432-1432
    Keywords: Chromatin structure ; Regulation ; Structural computations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Calculations of DNA angular parameters in 50 eukaryotic sequences reveal regions of large conformational deviations from ideal DNA around regulatory sites. Frequently, discrete peaks of structural variation are present upstream of genes. Known regulatory regions often include variants of consensus sequences. Thus, imprecise sequences and structures are recognized within large genomic stretches. The existence of structurally “wrinkled” regions in the vicinity of regulatory sequences is likely to facilitate greatly their recognition by proteins and enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101693
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  • 9
    Electronic Resource
    Electronic Resource
    A disulphide-reinforced structural scaffold shared by small proteins with diverse functions (1995)
    [s.l.] : Nature Publishing Group
    Nature structural biology 2 (1995), S. 835-837 
    Details
    ISSN: 1072-8368
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] Sir—Structural similarity between unrelated proteins has important theoretical and practical consequences. Proteins are often compared by the topology of their secondary structures12. This is difficult, however, for small proteins poor in regular secondary structures, which rely on disulphide ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nsb1095-835
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  • 10
    Electronic Resource
    Electronic Resource
    Effects of secondary structures in RNA on interlocking probabilities (1984)
    Springer
    Journal of mathematical biology 19 (1984), S. 95-107 
    Details
    ISSN: 1432-1416
    Keywords: Secondary structure ; single stranded polynucleotide ; topoisomerase ; catenane formation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract In 1967 Wang and Schwartz reported on the formation of interlocked rings between linear or circular DNA molecules by the enzyme topoisomerase. We propose viewing the secondary structured loop in RNA (or single stranded DNA) as analogous to a circular DNA molecule. Formation of a catenane between such an RNA loop with a DNA molecule may constitute a probe of the secondary and general three dimensioanl structure of the RNA molecule. The experimental results may be compared with the theoretical calculation. We suggest here a method for estimating linkage probabilities and calculate them for several cases for which secondary structures of the RNA have been proposed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00275933
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