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

Montaño SP, Coté ML, Roth MJ, Georgiadis MM - Nucleic Acids Res. (2006)

Bottom Line: 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.The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.

ABSTRACT
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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Related in: MedlinePlus

Hydration of LTR-A DNA. The water molecules that interact with the minor groove of the LTR-A DNA are represented as blue spheres. Only one half of the LTR-A DNA, the unique 8mer, is shown for clarity.
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fig3: Hydration of LTR-A DNA. The water molecules that interact with the minor groove of the LTR-A DNA are represented as blue spheres. Only one half of the LTR-A DNA, the unique 8mer, is shown for clarity.

Mentions: For the MMLV LTR CA dinucleotide steps, we note a correlation of positive roll angle and negative slide that is independent of its position within the oligonucleotide for this particular dinucleotide within the LTR sequences. In each case, the positive roll value for the CA dinucleotide step exceeds that of the average roll angle for that step. The largest roll angle is observed in the LTR-A structure with a value of 9.9°. The magnitude of this value may in part result from the presence of ordered water molecules in the minor groove in this structure as shown in Figure 3 and discussed below. The combination of positive roll and negative slide has specific consequences for the positioning of hydrogen bonding atoms present within the CA step. In the minor groove of a CA dinucleotide step with negative roll and positive slide, O2 of C points towards the 3′ A. Whereas, for the CA dinucleotide with positive roll and negative slide, the O2 points away from the 3′A in the minor groove (Figure 2C) resulting in an O2 of C to N3 of A distance that is ∼0.7 Å longer (in LTR-A) than that for the same atoms in the CA dinucleotide with negative roll. Within the major groove, the opposite trends are seen for the positioning of hydrogen-bonding atoms, namely that for the CA step with positive roll, the hydrogen bonding atoms in C and A are closer together than are those in the CA step with negative roll. The structural properties imparted by the positive roll angle and negative slide value of the CA dinucleotide step may provide a basis for recognition of the MMLV LTR by integrase.


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

Montaño SP, Coté ML, Roth MJ, Georgiadis MM - Nucleic Acids Res. (2006)

Hydration of LTR-A DNA. The water molecules that interact with the minor groove of the LTR-A DNA are represented as blue spheres. Only one half of the LTR-A DNA, the unique 8mer, is shown for clarity.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636480&req=5

fig3: Hydration of LTR-A DNA. The water molecules that interact with the minor groove of the LTR-A DNA are represented as blue spheres. Only one half of the LTR-A DNA, the unique 8mer, is shown for clarity.
Mentions: For the MMLV LTR CA dinucleotide steps, we note a correlation of positive roll angle and negative slide that is independent of its position within the oligonucleotide for this particular dinucleotide within the LTR sequences. In each case, the positive roll value for the CA dinucleotide step exceeds that of the average roll angle for that step. The largest roll angle is observed in the LTR-A structure with a value of 9.9°. The magnitude of this value may in part result from the presence of ordered water molecules in the minor groove in this structure as shown in Figure 3 and discussed below. The combination of positive roll and negative slide has specific consequences for the positioning of hydrogen bonding atoms present within the CA step. In the minor groove of a CA dinucleotide step with negative roll and positive slide, O2 of C points towards the 3′ A. Whereas, for the CA dinucleotide with positive roll and negative slide, the O2 points away from the 3′A in the minor groove (Figure 2C) resulting in an O2 of C to N3 of A distance that is ∼0.7 Å longer (in LTR-A) than that for the same atoms in the CA dinucleotide with negative roll. Within the major groove, the opposite trends are seen for the positioning of hydrogen-bonding atoms, namely that for the CA step with positive roll, the hydrogen bonding atoms in C and A are closer together than are those in the CA step with negative roll. The structural properties imparted by the positive roll angle and negative slide value of the CA dinucleotide step may provide a basis for recognition of the MMLV LTR by integrase.

Bottom Line: 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.The structures of the LTR-containing oligonucleotides were compared to those of non-LTR oligonucleotides crystallized in the same lattice.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus