The hydrogen-bonding structure in parallel-stranded duplex DNA is reverse Watson-Crick

Journal Article · Tue Mar 26 00:00:00 EST 1991 · Biochemistry; (United States)

DOI:https://doi.org/10.1021/bi00226a012· OSTI ID:5510864

Peticolas, W L ^[1]; Rippe, K; Jovin, T M ^[2]

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1. Univ. of Oregon, Eugene (USA)
2. Max Planck Institute for Biophysical Chemistry, Goettingen (Germany)

Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5{prime}-d-((A){sub 10}TAATTTTAAATATTT)-3{prime} (D1) and 5{prime}-d((T){sub 10}ATTAAAATTTATAAA)-3{prime} (D2) in H{sub 2}O and D{sub 2}O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the deoxyoligonucleotides D1 and 5{prime}-d(AAATATTTAAAATTA-(T){sub 10})-3{prime} (D3). The Raman spectra of the antiparallel-stranded (aps) duplex are reminiscent of the spectra of poly(d(A)){center dot}poly(d(T)) and a B-form structure similar to that adopted by the homopolymer duplex is assigned to the antiparallel double helix. The spectra of the parallel-stranded (ps) and antiparallel-stranded duplexes differ significantly due to changes in helical organization, i.e., base pairing, base stacking, and backbone conformation. Large changes observed in the carbonyl stretching region implicate the involvement of the C(2) carbonyl of thymine in base pairing. The interaction of adenine with the C(2) carbonyl of thymine is consistent with formation of reverse Watson-Crick base pairing in parallel-stranded DNA. Phosphate-furanose vibrations similar to those observed for B-form DNA of heterogeneous sequence and high A,T content are observed at 843 and 1,092 cm{sup {minus}1} in the spectra of the parallel-stranded duplex.

• OSTI ID: 5510864
• Journal Information: Biochemistry; (United States), Vol. 30:12; ISSN 0006-2960
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
DNA
CHEMICAL BONDS
OLIGONUCLEOTIDES
RAMAN SPECTRA
ADENINES
CARBONYLATION
HEAVY WATER
MOLECULAR STRUCTURE
AMINES
ANTIMETABOLITES
AROMATICS
AZAARENES
CHEMICAL REACTIONS
DRUGS
HETEROCYCLIC COMPOUNDS
HYDROGEN COMPOUNDS
NUCLEIC ACIDS
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
OXYGEN COMPOUNDS
PURINES
SPECTRA
WATER
550201* - Biochemistry- Tracer Techniques