PDBsum entry 1a9g

DNA

PDB id: 1a9g

Contents

DNA/RNA

Waters ×3

PDB id:

1a9g

Name:

DNA

Title:

Apurinic DNA with bound water at the damaged site and n3 of cytosine, beta form, nmr, 1 structure

Structure:

DNA (5'-d( Cp Gp Cp Gp Ap Aabp Ap Cp Gp Cp C)-3'). Chain: a. Engineered: yes. DNA (5'-d( Gp Gp Cp Gp Tp Cp Tp Cp Gp Cp G)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

1 models

Authors:

R.D.Beger,P.H.Bolton

Key ref:

R.D.Beger and P.H.Bolton (1998). Structures of apurinic and apyrimidinic sites in duplex DNAs. J Biol Chem, 273, 15565-15573. PubMed id: 9624147 DOI: 10.1074/jbc.273.25.15565

Date:

06-Apr-98 Release date: 15-Jul-98

DNA/RNA chains

C-G-C-G-A-AAB-A-C-G-C-C 11 bases

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

DOI no: 10.1074/jbc.273.25.15565

J Biol Chem 273:15565-15573 (1998)

PubMed id: 9624147

Structures of apurinic and apyrimidinic sites in duplex DNAs.

R.D.Beger, P.H.Bolton.

ABSTRACT

Natural and exogenous processes can give rise to abasic sites with either a purine or pyrimidine as the base on the opposing strand. The solution state structures of the apyrimidinic DNA duplex, with D6 indicating an abasic site, referred to as AD, and the apurinic DNA duplex with a dC17, referred to as CD, have been determined. A particularly striking difference is that the abasic site in CD is predominantly a beta hemiacetal, whereas in AD the alpha and beta forms are equally present. Hydrogen bonding with water by the abasic site and the base on the opposite strand appears to play a large role in determining the structure near the damaged site. Comparison of these structures with that of a duplex DNA containing a thymine glycol at the same position as the abasic site and with that of a duplex DNA containing an abasic site in the middle of a curved DNA sequence offers some insight into the common and distinct structural features of damaged DNA sites.

Selected figure(s)

Figure 7.
Fig. 7. The percentage of the accessible surface area of residues dT[18] and dC[19] as a function of probe molecule radius is shown. The percentage accessible surface area is shown for both forms of AD and both forms of CD.

Figure 9.
Fig. 9. The structures shown at the top are those of the and forms of AD with that of the DNA duplex of d(C[1]G[2] C[3]G[4]A[5]Tg[6]A[7]C[8]G[9]C[10]C[11]) paired with d(G[12]G[13]C[14]G[15]T[16]A[17]T[18]C[19]G[20]C[21]G[22]), with Tg indicating thymine glycol shown in the middle. At the bottom the and structures of AD are compared along with those of the duplex of d(C[1]G[2] C[3]A[4]A[5]A[6]A[7]A[8]T[9]G[10]C[11]G[12]) paired with d(C[13]G[14]C[15]A[16]T[17]T[18]D[19]T[20]T[21]C[22]C[23]G[24]). Only the central 5 residues of each strand are shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 15565-15573) copyright 1998.

Figures were selected by an automated process.