I. A comparative study of ribo-, deoxyribo-, and hybrid oligonucleotide helices by nuclear magnetic resonance. II. Optical studies of ethidium binding to oligonucleotides

Technical Report · Sat Nov 01 00:00:00 EST 1980

DOI:https://doi.org/10.2172/6721445· OSTI ID:6721445

Pardi, A

The conformations and the helix-to-coil transitions in the following oligonucleotides: (I) a DNA duplex dCT/sub 5/G + dCA/sub 5/G; (II) an RNA duplex rCU/sub 5/G + rCA/sub 5/G; (III) a DNA-RNA hybrid duplex dCT/sub 5/G + rCA/sub 5/G; and (IV) a DNA-RNA hybrid triplex rCU/sub 5/G + dCA/sub 5/G were studied. The first three mixtures all form stable double helical structures at 5/sup 0/C, whereas IV forms a triple strand with a ratio of 2:1 rCU/sub 5/G:dCA/sub 5/G. The chemical shifts of the imino protons in the double strands indicate that I, II, and III have different conformations in solution. This implies a significant change in helical parameters. The chemical shift and sugar pucker data are consistent with helix I having B form geometry, whereas II and III have A (or A') geometry. The chemical shifts of the base protons in system I had transition midpoints of 28 to 30/sup 0/C indicating an all-or-none transition. The exchange lifetimes of the imino protons on helix I were a factor of two longer, for the interior A.T base pairs, than those on helix III. This reflects the greater stability of the DNA helix compared to the hybrid helix. The two terminal C.G base pairs in helix I were also found to have much different exchange rates, indicative of a sequence dependence for these exchange rates. The thermodynamic properties of ethidium binding to several oligonucleotides were investigated. The order of the stability for the 2:1 oligonucleotide:ethidium complexes was found to be rCpG > dCpG > rCpUpG approx. = rUpA > rGpUpG + rCpC. These complexes present models for a possible mechanism for frameshift mutagenesis by ethidium. A large positive induced circular dichroism (CD) has been observed for ethidium upon intercalation into nucleic acids. (ERB)

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
• DOE Contract Number: W-7405-ENG-48
• OSTI ID: 6721445
• Report Number(s): LBL-11925
• Resource Relation: Other Information: Thesis
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTANT EFFECTS ON LIVING ORGS. AND BIOL. MAT.
NUCLEOTIDES
CONFIGURATION INTERACTION
STRUCTURAL CHEMICAL ANALYSIS
BINDING ENERGY
THERMODYNAMIC PROPERTIES
MUTAGENESIS
FUNCTIONAL MODELS
MUTAGENS
EXPERIMENTAL DATA
CHEMICAL SHIFT
HELICAL CONFIGURATION
NUCLEAR MAGNETIC RESONANCE
COMPLEXES
DICHROISM
STABILITY
CONFIGURATION
DATA
ENERGY
INFORMATION
MAGNETIC RESONANCE
NUMERICAL DATA
ORGANIC COMPOUNDS
PHYSICAL PROPERTIES
RESONANCE
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