The DNA d(GGGGGTTTTT)[center dot]d(AAAAACCCCC) and Bam H1 d(GGATCC)[sub 2] structure investigation by 1-D and 2-D NMR spectroscopy. [NMR (nuclear magnetic resonance)]
Two-dimensional NMR techniques Correlated (COSY) and Nuclear Overhauser Effect Spectroscopy (NOESY) have been used with one-dimensional NMR results to complete the assignment of the proton NMR spectrum of double-stranded B DNA duplex, d(G[sub 5]T[sub 5]).d(A[sub 5]C[sub 5]) and restriction endonuclease Bam H1 duplex d(GGATCC)[sub 2]. A general method of assigning the non-exchangeable and exchangeable protons in the NMR spectra of DNA duplexes in D[sub 2]O or H[sub 2]O respectively is discussed. COSY and NOESY measurements have been combined to systematically assign many of the resonances from the H1[prime], H2[prime], H2[double prime] and H3[prime] sugar protons to specific nucleotides in the duplex. This method relies on the fact that sugar protons within a specific nucleotide are scalar coupled and that base protons H8/H6 in right-handed helices can interact simultaneously with their own H2[prime], H2[double prime] sugar protons and those of the adjacent nucleotide attached to its 5[prime] end. COSY experiments are used to identify sugar resonances within a residue, NOESY experiments determination of linkage to adjacent residues. The base protons H5 and H6 resonances of cytosines in the spectrum can immediately be identified by the COSY experiment. The methyl protons of thymine exhibit strong through-space interbase interaction. This establishes that the nucleotides have an anti conformation of the bases relative to the sugar. The self-complementary decanucleotide sequence d(G[sub 5]T[sub 5])[center dot]d(A[sub 5]C[sub 5]) forms a ten base-paired duplex in solution. The five Watson-Crick imino protons are resolved between 12 and 14 ppm and have been assigned to positions in the sequence using sequential nearest-neighbor NOE connectivity. At 1[degrees]C the imino proton of the terminal base pair 1 has broadened out. The interproton distances obtained from 2-D Nuclear Overhauser Effect (NOESY) data is examined by simulation to derive structures for DNA helices.
- Research Organization:
- State Univ. of New York, Albany, NY (United States)
- OSTI ID:
- 7077954
- Resource Relation:
- Other Information: Thesis (Ph.D.)
- Country of Publication:
- United States
- Language:
- English
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