NMR studies of the deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA)ter dot oligo(Dt) tract

Journal Article · Tue Sep 18 04:00:00 EDT 1990 · Biochemistry; (USA)

DOI:https://doi.org/10.1021/bi00489a047· OSTI ID:5762407

Morden, K M; Gunn, B M; Maskos, K ^[1]

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1. Louisiana State Univ., Baton Rouge (USA)

One- and two-dimensional NMR experiments were carried out on a decamer, d-(CGCTTTTCGC){center dot}d(GCGAAAAGCG), and on the same sequence with the addition of an unpaired thymidine, d(CGCTTTTCGC){center dot}d(GCGAATAAGCG), which will be referred to as the T-bulge decamer. Evidence from one-dimensional NOE experiments on the exchangeable protons indicates that the unpaired thymidine is extrahelical. This conclusion is also supported by numerous cross-peaks in the two-dimensional NOESY spectrum of the nonexchangeable protons. Assignments for all of the resonances, with the exception of the H5{prime} and H5{double prime} resonances, have been made for both oligonucleotide duplexes through the use of 2D NOESY, COSY, and relayed COSY experiments. Temperature dependence of the methyl resonance chemical shifts indicates that the unpaired thymidine shows unusual behavior compared to other thymidines in the duplex. Two-dimensional NOESY experiments carried out from 5 to 35{degree}C indicate the unpaired thymidine remains extrahelical throughout this temperature range. A similar temperature dependence for the methyl chemical shift is found in the corresponding single-strand d(GCGAATAAGCG). The oligo-(dA){center dot}oligo(dT) tracts in both the decamer and the T-bulge decamer have structures different from B-form DNA and exhibit NOEs similar to those observed in other oligonucleotides containing A{center dot}T tracts. The formation of this unusual A{center dot}T tract structure may induce the extrahelical conformation of the unpaired thymidine.

• OSTI ID: 5762407
• Journal Information: Biochemistry; (USA), Journal Name: Biochemistry; (USA) Vol. 29:37; ISSN 0006-2960; ISSN BICHA
• Country of Publication: United States
• Language: English

Related Subjects

550601* -- Medicine-- Unsealed Radionuclides in Diagnostics
62 RADIOLOGY AND NUCLEAR MEDICINE
AMINO ACIDS
AZINES
CARBOXYLIC ACIDS
CHELATING AGENTS
CHEMICAL SHIFT
DNA
EDTA
HETEROCYCLIC COMPOUNDS
MAGNETIC RESONANCE
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEOSIDES
NUCLEOTIDES
OLIGONUCLEOTIDES
ORGANIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
OVERHAUSER EFFECT
PYRIMIDINES
RESONANCE
RIBOSIDES
TEMPERATURE DEPENDENCE
THYMIDINE