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  • 1
    Electronic Resource
    Electronic Resource
    Modified nucleoside-dependent transition metal binding to DNA analogs of the tRNA anticodon stem/loop domain (1995)
    Springer
    BioMetals 8 (1995), S. 290-296 
    Details
    ISSN: 1572-8773
    Keywords: tRNA ; tDNA ; anticodon domain ; transition metal ion effects ; spectroscopic characterization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract Biologically active DNA analogs of tRNAPhe (tDNAPhe) were used to investigate metal ion interaction with tRNA-like structures lacking the 2′OH. Binding of Mg2+ to the 76 oligonucleotide tDNAPhe, monitored by circular dichroism spectroscopy, increased base stacking and thus the conformational stability of the molecule. Mg2+ binding was dependent on a d(m5C) in the anticodon region. In contrast to Mg2+, Cd2+ decreased base stacking interactions, thereby destabilizing the molecule. Since alterations in the anticodon region contributed to most of the spectral changes observed, detailed studies were conducted with anticodon hairpin heptadecamers (tDNAAC Phe). The conformation of tDNAAC Phe-d(m5C) in the presence of 1 mm Cd2+, Co2+, Cr2+, Cu2+, Ni2+, Pb2+, VO2+ or Zn2+ differed significantly from that of the biologically active structure resulting from interaction with Mg2+, Mn2+ or Ca2+. Nanomolar concentrations of the transition metals were sufficient to denature the tDNAAC Phe-d(m5C) structure without catalyzing cleavage of the oligonucleotide. In the absence of Mg2+ and at [Cd2+] to [tDNAAc Phe-d(m5C)] ratios of approximately 0.2–1.0, tDNAAC Phe-d(m5C40) formed a stable conformation with one Cd2+ bound with a K d = 3.7 × 10-7. In contrast to Mg2+, Cd2+ altered the DNA analogs without discriminating between modified and unmodified tDNAAC Phe. This ability of transition metals to disrupt higher order DNA structures, and possibly RNA, at μM concentrations, in vitro, demonstrates that these structures are potential targets in chronic metal exposure, in vivo.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00141601
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Experimental Models of Protein–RNA Interaction: Isolation and Analyses of tRNAPhe and U1 snRNA-Binding Peptides from Bacteriophage Display Libraries (1999)
    Springer
    The protein journal 18 (1999), S. 425-435 
    Details
    ISSN: 1573-4943
    Keywords: Phage peptide display library ; peptide–RNA binding ; tRNA ; U1 snRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Peptides that bind either U1 small nuclear RNA (U1 snRNA) or the anticodon stem and loop of yeast tRNAPhe (tRNA AC Phe ) were selected from a random-sequence, 15-amino acid bacteriophage display library. An experimental system, including an affinity selection method, was designed to identify primary RNA-binding peptide sequences without bias to known amino acid sequences and without incorporating nonspecific binding of the anionic RNA backbone. Nitrocellulose binding assays were used to evaluate the binding of RNA by peptide-displaying bacteriophage. Amino acid sequences of RNA-binding bacteriophage were determined from the foreign insert DNA sequences, and peptides corresponding to the RNA-binding bacteriophage inserts were chemically synthesized. Peptide affinities for the RNAs (K d ≍ 0.1–5.0 μM) were analyzed successfully using fluorescence and circular dichroism spectroscopies. These methodologies demonstrate the feasibility of rapidly identifying, isolating, and initiating the analyses of small peptides that bind to RNAs in an effort to define better the chemistry, structure, and function of protein–RNA complexes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1020688609121
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  • 3
    Electronic Resource
    Electronic Resource
    Ribosome-independent anticodon to codon binding assessed by circular dichroism: Roles of base modifications, Mg2+ and 2′OH (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biospectroscopy 2 (1996), S. 205-217 
    Details
    ISSN: 1075-4261
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Physics
    Notes: Modified nucleoside contributions to tRNA's binding of mRNA codons are not differentiated from that of tRNA's interactions with the ribosome in ribosome-mediated binding assays. Circular dichroism spectrapolarimetry (CD) proved to be a sensitive method for detection of anticodon-codon interaction in the absence of ribosomes. The binding of the yeast tRNAPhe anticodon stem and loop (tRNAPheAC) to coding triplets was studied. Unmodified tRNAPheAC interacted specifically with r(UUC). Mg2+ was not critical to codon binding. Codon binding was accompanied by a change in anticodon domain conformation that was stable below 17°C. In contrast, tRNAPheAC with m5C40 has an anticodon loop closed by two intra-loop base pairs and did not bind codon. The importance of the ribose 2′OH relative to that of modified nucleosides and Mg2+ was investigated using DNA analogs of tRNAPheAC, tDNAPheAC. An open anticodon loop conformation and Mg2+ binding were necessary for tDNAPheAC interaction with d(TTC). The binding of d(TTC) was accompanied by a change in tDNAPheAC conformation, stable below 17°C. With d(m1G)37 maintaining an open loop conformation, tDNAPheAC base paired with d(TTC), but not with d(TCTTC), providing the first physical evidence of how position-37 modifications may maintain the translational reading frame. Position-37 modifications occur in 72% of tRNAs; only one third promote an open loop by negating intra-loop base pairing. Thus, position-37 modifications may have evolved to impart an open and dynamic anticodon loop conformation that is important for effective and correct codon binding. © 1996 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 4
    Electronic Resource
    Electronic Resource
    Conformation of the hypermodified purine queuine: Substrate for the enzyme transfer RNA - guanine transglycosylase (1988)
    Chichester : Wiley-Blackwell
    Organic Magnetic Resonance 26 (1988), S. 4-7 
    Details
    ISSN: 0749-1581
    Keywords: Queuine ; Hypermodified purine ; Structure and conformation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The hypermodified nucleotidyl purine queuine [7-(3,4-trans-4,5-cis-dihydroxycyclopent-1-en-3-ylaminomethyl)-7-deazaguanine] is a substrate for transfer ribonucleic acid (tRNA) enzymes replacing guanine at nucleotide position 34 of tRNAs for the amino acids aspartic acid, asparagine, bistidine and tyrosine. The structure and conformation of native queuine was studied by one-dimensional 13C and 1H NMR spectroscopy and by two-dimensional NMR spectroscopy (COSY and NOESY). The structure in solution was found to be the 3,4-trans-4,5-cis-dihydroxycyclopent-1-ene form. The plane of the cyclopentene ring is probably perpendicular to that of the purine ring structure.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/mrc.1260260103
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    Paper (German National Licenses)
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