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)

Journal Article · Thu Dec 31 23:00:00 EST 1981 · Biochemistry; (United States)

DOI:https://doi.org/10.1021/bi00268a038· OSTI ID:5809105

Pardi, A; Morden, K M; Patel, D J; Tinoco, I Jr

The relaxation lifetimes of imino protons from individual base pairs were measured in (I) a perfect helix, d(C-G-C-G-A-T-T-C-G-C-G), (II) this helix with a G x C base pair replaced with a G x T base pair, d(C-G-T-G-A-A-T-T-C-G-C-G), and (III) the perfect helix with an extra adenine base in a mismatch, d(C-G-C-A-G-A-A-T-T-C-G-C-G). The lifetimes were measured by saturation recovery proton nuclear magnetic resonance experiments performed on the imino protons of these duplexes. The measured lifetimes of the imino protons were shown to correspond to chemical exchange lifetimes at higher temperatures and spin-lattice relaxation times at lower temperatures. Comparison of the lifetimes in these duplexes showed that the destabilizing effect of the G x T base pair in II affected the opening rate of only the nearest-neighbor base pairs. For helix III, the extra adenine affected the opening rates of all the base pairs in the helix and thus was a larger perturbation for opening of the base pairs than the G x T base pair. The temperature dependence of the exchange rates of the imino proton in the perfect helix gives values of 14-15 kcal/mol for activation energies of A x T imino protons. The effects of a perturbation in helix on the exchange rates and the mechanisms for exchange of imino protons from oligonucleotide helices are discussed.

• Research Organization: Univ. of California, Berkeley
• DOE Contract Number: AC03-76SF00098
• OSTI ID: 5809105
• Journal Information: Biochemistry; (United States), Journal Name: Biochemistry; (United States) Vol. 24:25; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
ACTIVATION ENERGY
BARYONS
BIOCHEMICAL REACTION KINETICS
CONFIGURATION
DNA
ELEMENTARY PARTICLES
ENERGY
EXCHANGE INTERACTIONS
FERMIONS
HADRONS
HELICAL CONFIGURATION
INTERACTIONS
KINETICS
MAGNETIC RESONANCE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
ORGANIC COMPOUNDS
PROTONS
REACTION KINETICS
RELAXATION
RELAXATION TIME
RESONANCE
SPIN-LATTICE RELAXATION
TEMPERATURE DEPENDENCE