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Nucleic Acids Research Advance Access originally published online on September 26, 2006
Nucleic Acids Research 2006 34(19):5353-5360; doi:10.1093/nar/gkl693
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Nucleic Acids Research, 2006, Vol. 34, No. 19 5353-5360
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus

Sherwin P. Montaño, Marie L. Coté1, Monica J. Roth1 and Millie M. Georgiadis*

Department of Biochemistry and Molecular Biology, Indiana University School of Medicine 635 Barnhill Dr., Indianapolis, IN 46202, USA 1 Department of Biochemistry, University of Medicine and Dentistry of New Jersey–Robert Wood Johnson Medical School 675 Hoes Lane, Piscataway, NJ 08854, USA

*To whom correspondence should be addressed. Tel: +1 317 278 8486; Fax: +1 317 274 4686; Email: mgeorgia{at}iupui.edu

Received June 19, 2006. Revised August 22, 2006. Accepted September 7, 2006.

In the first step of retroviral integration, integrase cleaves the linear viral DNA within its long terminal repeat (LTR) immediately 3' to the CA dinucleotide step, resulting in a reactive 3' OH on one strand and a 5' two base overhang on the complementary strand. In order to investigate the structural properties of the 3' end processing site within the Moloney murine leukemia virus (MMLV) LTR d(TCTTTCATT), a host-guest crystallographic method was employed to determine the structures of four self-complementary 16 bp oligonucleotides including LTR sequences (underlined), d(TTTCATTGCAATGAAA), d(CTTTCATTAATGAAAG), d(TCTTTCATATGAAAGA) and d(CACAATGATCATTGTG), the guests, complexed with the N-terminal fragment of MMLV reverse transcriptase, the host. The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice. Properties unique to the CA dinucleotide step within the LTR sequence, independent of its position from the end of the duplex, include a positive roll angle and negative slide value. This propensity for the CA dinucleotide step within the MMLV LTR sequence to adopt only positive roll angles is likely influenced by the more rigid, invariable 3' and 5' flanking TT dinucleotide steps and may be important for specific recognition and/or cleavage by the MMLV integrase.


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