Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Nicola G A Abrescia; Andrew Thompson; Tam Huynh-Dinh; Juan A Subirana

doi:10.1073/pnas.052675499

Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing

Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2806-11. doi: 10.1073/pnas.052675499.

Authors

Nicola G A Abrescia¹, Andrew Thompson, Tam Huynh-Dinh, Juan A Subirana

Affiliation

¹ Departament d'Enginyeria Quimica, Universitat Politècnica de Catalunya, Avga Diagonal 647, E-08028 Barcelona, Spain.

Abstract

We report here an alternative double-helical structure of the DNA molecule. It has been found in the d(ATA(Br)UAT) and d(ATATAT) sequences by single-crystal x-ray crystallography. This sequence is found not only in TATA boxes, but also in other regulatory regions of DNA. Bases of the two antiparallel strands form Hoogsteen pairs, with adenines in the syn conformation. The structure is related neither to those found in triple helices nor to parallel DNA duplexes. Its conformational parameters are very similar to those of duplex DNA in the B form. Both forms may coexist under physiological conditions, although the Hoogsteen pairing greatly influences the recognition sites on DNA. Our results demonstrate that an alternative to the classical B-DNA double helix is possible.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Pairing
Crystallography, X-Ray
DNA / chemistry*
Models, Molecular
Nucleic Acid Conformation*

Substances

DNA

Associated data

PDB/1GQU