Sequence- and structure-dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA

Journal Article · Mon Nov 27 23:00:00 EST 1989 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00450a036· OSTI ID:6921732

Spaltenstein, A; Robinson, B H; Hopkins, P B ^[1]

---

1. Univ. of Washington, Seattle (USA)

A nitroxide spin-labeled analogue of thymidine (1a), in which the methyl group is replaced by an acetylene-tethered nitroxide, was evaluated as a probe for structural and dynamics studies of sequence specifically spin-labeled DNA. Residue 1a was incorporated into synthetic deoxyoligonucleotides by using automated phosphite triester methods. {sup 1}H NMR, CD, and thermal denaturation studies indicate that 1a (T) does not significantly alter the structure of 5{prime}-d(CGCGAATT*CGCG) from that of the native dodecamer. EPR studies on monomer, single-stranded, and duplexed DNA show that 1a readily distinguishes environments of different rigidity. Comparison of the general line-shape features of the observed EPR spectra of several small duplexes (12-mer, 24-mer) with simulated EPR spectra assuming isotropic motion suggests that probe 1a monitors global tumbling of small duplexes. Increasing the length of the DNA oligomers results in significant deviation from isotropic motion, with line-shape features similar to those of calculated spectra of objects with isotropic rotational correlation times of 20-100 ns. EPR spectra of a spin-labeled GT mismatch and a T bulge in long DNAs are distinct from those of spin-labeled Watson-Crick paired DNAs, further demonstrating the value of EPR as a tool in the evaluation of local dynamic and structural features in macromolecules.

• OSTI ID: 6921732
• Journal Information: Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 28:24; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550201* -- Biochemistry-- Tracer Techniques
59 BASIC BIOLOGICAL SCIENCES
BARYONS
BIOSYNTHESIS
DICHROISM
DNA
DNA SEQUENCING
ELECTRON SPECTRA
ELECTRON SPIN RESONANCE
ELEMENTARY PARTICLES
FERMIONS
HADRONS
MAGNETIC CIRCULAR DICHROISM
MAGNETIC RESONANCE
MOLECULAR STRUCTURE
NMR SPECTRA
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACID DENATURATION
NUCLEIC ACIDS
NUCLEONS
OLIGONUCLEOTIDES
ORGANIC COMPOUNDS
PROTONS
RESONANCE
SPECTRA
STRUCTURAL CHEMICAL ANALYSIS
SYNTHESIS