Dynamic and conformational effects of structural perturbations in DNA and RNA studied by nuclear magnetic resonance and chemically induced dynamic nuclear polarization
The conformation and dynamics of oligonucleotides in solution were studied using several different NMR techniques. The oligonucleotides contain a variety of perturbations; (I) an extra cytosine: dCA/sub 3/CA/sub 3/G + dCT/sub 6/G, (II) an extra adenine: d(CGCAGAATTCGCG)/sub 2/, and (III) a G.T mismatch: d(CGTGAATTCGCG)/sub 2/. These are compared to the unperturbed duplexes, (IV) dCA/sub 6/G + dCT/sub 6/G and (V) d(CGCGAATTCGCG)/sub 2/. Through the use of nuclear Overhauser effects; the unpaired cytosine in duplex I was found to be extrahelical. Thermodynamic parameters were determined for duplexes I and IV using UV absorption melting curves. The extrahelical cytosine causes a 15/sup 0/C decrease in the duplex melting temperature. The standard free energy for duplex formation at 25/sup 0/C is 2.9 kcal mol/sup -1/ more positive for the duplex with the extra cytosine. The kinetics for exchange of the imino protons in these oligonucleotide duplexes were studied by saturation recovery techniques. In duplex I, the extra cytosine causes the exchange lifetime for one of the neighboring A.T base pairs to decrease by a factor of two over the other A.T base pairs in the duplex. The extra adenine in duplex II affects the exchange lifetimes throughout the duplex, however, the G.T mismatch in duplex III has a more local effect on the lifetimes. Also presented are solvent accessibility studies of oligonucleotides using Chemically Induced Dynamic Nuclear Polarization (CIDNP). CIDNP was observed for guanine(H8) protons and for guanine(H1') protons in dinucleotides and longer oligonucleoides.
- Research Organization:
- Lawrence Berkeley Lab., CA (USA)
- DOE Contract Number:
- AC03-76SF00098
- OSTI ID:
- 5552289
- Report Number(s):
- LBL-16811; ON: DE84004958
- Country of Publication:
- United States
- Language:
- English
Similar Records
Kinetics for exchange of imino protons in the d(C-G-C-G-A-A-T-T-C-G-C-G) double helix and in two similar helices that contain a G x T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and an extra adenine, d(C-G-C-A-G-A-A-T-T-C-G-C-G)
Chemically induced dynamic nuclear polarization studies of guanosine in nucleotides, dinucleotides, and oligonucleotides
Related Subjects
59 BASIC BIOLOGICAL SCIENCES
AMINES
AROMATICS
AZAARENES
AZINES
CYTOSINE
DNA
HETEROCYCLIC COMPOUNDS
MAGNETIC RESONANCE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
ORGANIC OXYGEN COMPOUNDS
OVERHAUSER EFFECT
POLYCYCLIC AROMATIC AMINES
PYRIMIDINES
RESONANCE
RNA
STRUCTURAL CHEMICAL ANALYSIS
THERMODYNAMICS