PDBsum entry 1k5e

DNA

PDB id: 1k5e

Contents

DNA/RNA

PDB id:

1k5e

Name:

DNA

Title:

Solution structure of r-styrene adduct in the ras61 sequence

Structure:

5'-d( Cp Gp Gp Ap Cp (Abr)p Ap Gp Ap Ap G)-3'. Chain: a. Engineered: yes. Other_details: n-ras protooncogene. 5'-d( Cp Tp Tp Cp Tp Tp Gp Tp Cp Cp G)-3'. Chain: b. Engineered: yes. Other_details: n-ras protooncogene

Source:

Synthetic: yes. Other_details: this sequence was generated by an oligonucleotide synthesizer. Synthesizer

NMR struc:

1 models

Authors:

C.Hennard,J.Finneman,C.M.Harris,T.M.Harris,M.P.Stone

Key ref:

C.Hennard et al. (2001). The nonmutagenic (R)- and (S)-beta-(N(6)-adenyl)styrene oxide adducts are oriented in the major groove and show little perturbation to DNA structure. Biochemistry, 40, 9780-9791. PubMed id: 11502171 DOI: 10.1021/bi010564v

Date:

10-Oct-01 Release date: 23-Jan-02

DNA/RNA chains

C-G-G-A-C-X-A-G-A-A-G 11 bases

C-T-T-C-T-T-G-T-C-C-G 11 bases

DOI no: 10.1021/bi010564v

Biochemistry 40:9780-9791 (2001)

PubMed id: 11502171

The nonmutagenic (R)- and (S)-beta-(N(6)-adenyl)styrene oxide adducts are oriented in the major groove and show little perturbation to DNA structure.

C.Hennard, J.Finneman, C.M.Harris, T.M.Harris, M.P.Stone.

ABSTRACT

Conformations of (R)-beta-(N(6)-adenyl)styrene oxide and (S)-beta-(N(6)-adenyl)styrene oxide adducts at position X(6) in d(CGGACXAGAAG).d(CTTCTTGTCCG), incorporating codons 60, 61 (underlined), and 62 of the human N-ras protooncogene, were refined from (1)H NMR data. These were designated as the beta-R(61,2) and beta-S(61,2) adducts. A total of 533 distance restraints and 162 dihedral restraints were used for the molecular dynamics calculations of the beta-S(61,2) adduct, while 518 distances and 163 dihedrals were used for the beta-R(61,2) adduct. The increased tether length of the beta-adducts results in two significant changes in adduct structure as compared to the corresponding alpha-styrenyl adducts [Stone, M. P., and Feng, B. (1996) Magn. Reson. Chem. 34, S105-S114]. First, it reduces the distortion introduced into the DNA duplex. For both the beta-R(61,2) and beta-S(61,2) adducts, the styrenyl moiety was positioned in the major groove of the duplex with little steric hindrance. Second, it mutes the influence of stereochemistry at the alpha-carbon such that both the beta-R(61,2) and beta-S(61,2) adducts exhibit similar conformations. The results were correlated with site-specific mutagenesis experiments that revealed the beta-R(61,2) and beta-S(61,2) adducts were not mutagenic and did not block polymerase bypass.