Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization

Journal Article · Tue May 03 00:00:00 EDT 1988 · Biochemistry; (United States)

DOI:https://doi.org/10.1021/bi00409a004· OSTI ID:6999719

Woodson, S A; Crothers, D M

The authors present three-dimensional structural models for a DNA oligomer containing a bulged guanosine based on proton NMR data and energy minimization computations. The nonexchangeable proton resonances of the duplex /sup 5'/d(GATGGGCAG) x d(CTGCGCCATC) are assigned by nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy connectivities, and the NMR spectrum is compared with that of a regular 8-mer of similar sequence, /sup 5'/d(GATGGCAG) x d(CTGCCATC). Experimental proton-proton distances are obtained from NOESY spectra acquired with mixing times of 100, 150, and 200 ms. A refined three-dimensional structure for the bulge-containing duplex is calculated from regular B DNA starting coordinates by using the AMBER molecular mechanics program. They compare structures obtained by building the helix in three and four base pair increments with structures obtained by direct minimization of the entire nine base sequence,with and without experimental distance constraints. The general features of all the calculated structures are very similar. The helix is of the B family, with the extra guanine stacked into the helix, and the helix axis is bent by 18-23/sup 0/, in agreement with gel mobility data for bulge-containing sequences.

• Research Organization: Yale Univ., New Haven, CT (USA)
• OSTI ID: 6999719
• Journal Information: Biochemistry; (United States), Vol. 27:9
• Country of Publication: United States
• Language: English

Related Subjects

62 RADIOLOGY AND NUCLEAR MEDICINE
OLIGONUCLEOTIDES
MOLECULAR STRUCTURE
NUCLEAR MAGNETIC RESONANCE
GUANOSINE
OVERHAUSER EFFECT
PROTONS
STEREOCHEMISTRY
AROMATICS
AZAARENES
BARYONS
ELEMENTARY PARTICLES
FERMIONS
HADRONS
HETEROCYCLIC COMPOUNDS
MAGNETIC RESONANCE
NUCLEIC ACIDS
NUCLEONS
NUCLEOSIDES
NUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PURINES
RESONANCE
RIBOSIDES
550601* - Medicine- Unsealed Radionuclides in Diagnostics