J Mol Biol. 1992 Jul 20;226(2):481-90.

Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.

Brown DG, Sanderson MR, Garman E, Neidle S.

Source

Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.

Abstract

The AT-selective drug berenil has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The crystal structure has been solved to a resolution of 2.0 A and an R factor of 18.3%, with the location of 65 water molecules. The drug is symmetrically bound in the 5'-AATT region of the minor groove, with its amidinium groups hydrogen-bonding to O-2 atoms of the thymine base at each end of the binding site. This arrangement is distinct from that previously found for berenil with the sequence d(CGCGAATTCGCG)2, which has the drug bound to the sequencing 5'-ATT via hydrogen bonds to adenine N-3 atoms with the involvement of a bridging water molecule at one end of the binding site. The reasons for these differences are discussed in terms of changes in helical parameters; in particular propeller twist and base-pair roll are considered to be important. The conformational and base-pair geometry of the dodecanucleotide in the structure reported here, is closely similar to that for the native structure, suggesting that the 5'-AAATTT sequence does not significantly alter during drug binding, either because of its inflexibility or because its geometry is nearly ideal for berenil binding.

PMID:: 1640462; [PubMed - indexed for MEDLINE]

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding. [EMBO J. 1990]
Crystal structure of a berenil-dodecanucleotide complex: the role of water in sequence-specific ligand binding.
Brown DG, Sanderson MR, Skelly JV, Jenkins TC, Brown T, Garman E, Stuart DI, Neidle S. EMBO J. 1990 Apr; 9(4):1329-34.
Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution. [J Mol Biol. 1992]
Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.
Edwards KJ, Brown DG, Spink N, Skelly JV, Neidle S. J Mol Biol. 1992 Aug 20; 226(4):1161-73.
Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR. [Biochemistry. 1991]
Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR.
Lane AN, Jenkins TC, Brown T, Neidle S. Biochemistry. 1991 Feb 5; 30(5):1372-85.
Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex. [Nucleic Acids Res. 1994]
Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.
Spink N, Brown DG, Skelly JV, Neidle S. Nucleic Acids Res. 1994 May 11; 22(9):1607-12.
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition. [Nucleic Acids Res. 1997]
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition.
Clark GR, Boykin DW, Czarny A, Neidle S. Nucleic Acids Res. 1997 Apr 15; 25(8):1510-5.

See reviews... See all...

Cited by 17 PubMed Central articles

The killing of African trypanosomes by ethidium bromide. [PLoS Pathog. 2010]
The killing of African trypanosomes by ethidium bromide.
Roy Chowdhury A, Bakshi R, Wang J, Yildirir G, Liu B, Pappas-Brown V, Tolun G, Griffith JD, Shapiro TA, Jensen RE, et al. PLoS Pathog. 2010 Dec 16; 6(12):e1001226. Epub 2010 Dec 16.
Structure and inhibition of human diamine oxidase. [Biochemistry. 2009]
Structure and inhibition of human diamine oxidase.
McGrath AP, Hilmer KM, Collyer CA, Shepard EM, Elmore BO, Brown DE, Dooley DM, Guss JM. Biochemistry. 2009 Oct 20; 48(41):9810-22.
A role for water molecules in DNA-ligand minor groove recognition. [Acc Chem Res. 2009]
A role for water molecules in DNA-ligand minor groove recognition.
Nguyen B, Neidle S, Wilson WD. Acc Chem Res. 2009 Jan 20; 42(1):11-21.

See all...

Structures reported by this article

Crystal Structure Of A Berenil-D(Cgcaaatttgcg) Complex; An Example Of Drug-Dna Recognition Based On Sequence- Dependent Structural Features

PDB: 1D63

Source:

Method: X-Ray Diffraction

Resolution: 2 Å

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Compound (MeSH Keyword)
PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Nucleotide
Primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Structure
Three-dimensional structure records in the NCBI Structure database for data reported in the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA r...
Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.
J Mol Biol. 1992 Jul 20 ;226(2):481-90.

PubMed
Diversity in sound pressure levels and estimated active space of resident killer...
Diversity in sound pressure levels and estimated active space of resident killer whale vocalizations.
J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2006 May ;192(5):449-59. Epub 2006 Jan 11 .

PubMed
Polymorphisms of genes coding for insulin-like growth factor 1 and its major bin...
Polymorphisms of genes coding for insulin-like growth factor 1 and its major binding proteins, circulating levels of IGF-I and IGFBP-3 and breast cancer risk: results from the EPIC study.
Br J Cancer. 2006 Jan 30 ;94(2):299-307.

PubMed
Safety aspects and cholesterol-lowering efficacy of low fat dairy products conta...
Safety aspects and cholesterol-lowering efficacy of low fat dairy products containing plant sterols.
Eur J Clin Nutr. 2006 May ;60(5):633-42.

PubMed
Driving to work and overweight and obesity: findings from the 2003 New South Wal...
Driving to work and overweight and obesity: findings from the 2003 New South Wales Health Survey, Australia.
Int J Obes (Lond). 2006 May ;30(5):782-6.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to:

Crystal structure of a berenil-d(CGCAAATTTGCG) complex. An example of drug-DNA recognition based on sequence-dependent structural features.

Source

Abstract

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

Supplemental Content

Save items

Related citations in PubMed

Cited by 17 PubMed Central articles

Structures reported by this article

Related information

Recent activity

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information