The Solution Structure of the r(gcg)d(TATACCC):d(GGGTATACGC) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected by a Junction

Salazar, Miguel; Fedoroff, Oleg Yu.; Zhu, Lianjie; Reid, Brian R.

doi:10.1006/jmbi.1994.1519

Cited by 38 publications

(66 citation statements)

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“…The location and magnitute of this bend is strikingly similar to the bend found in Okazaki-type chimeric duplexes (Salazar et al, 1994Fedoroff et al, 1996). In both cases, the bend occurs near the site of speci®c RT RNase H cleavage and may well be the structural reason for this cleavage (vide infra).…”

Section: H -H2mentioning

confidence: 80%

“…There are strong indications that a similar RT-induced structural transition also occurs in solution (Metzger et al, 1993). Previously we have determined the solution structures of several RNA-DNA chimeras (Salazar et al, 1994Fedoroff et al, 1996) and and d(GCTATAATGG):r(ccauuauagc) (Gonzalez et al, 1995) hybrids. Dotted lines show the interstrand phosphate-phosphate separation across the major grooves in these hybrids.…”

Section: Discussionmentioning

confidence: 94%

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Solution structure sf r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1(+)-strand synthesis

Fedoroff

Reid

1997

Journal of Molecular Biology

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Section: H -H2mentioning

confidence: 80%

Section: Discussionmentioning

confidence: 94%

Solution structure sf r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1(+)-strand synthesis

Fedoroff

Reid

1997

Journal of Molecular Biology

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“…Although selection and removal of the PPT primer have been accurately recapitulated in biochemical studies with wild type and mutant RT variants (7,20,(23)(24)(25)(26)(27)(28)(29)(30)(31), the structural basis for resistance to internal hydrolysis and specific cleavage at the PPT-U3 junction remains elusive. Analysis of a co-crystal of HIV-1 RT and a PPT-containing RNA/DNA hybrid (4) suggest that the altered groove width observed might not permit correct positioning of the RNA strand in the RNase H catalytic center, a notion put forward by studies of related RNA/DNA hybrids (32)(33)(34)(35)(36)(37)(38). However, our chemical footprinting studies (39) suggest an alternative hypothesis.…”

mentioning

confidence: 83%

Two Modes of HIV-1 Polypurine Tract Cleavage Are Affected by Introducing Locked Nucleic Acid Analogs into the (-) DNA Template

Dash

Yi-Brunozzi

Grice

2004

Journal of Biological Chemistry

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Unusual base-pairing in a co-crystal of reverse transcriptase (RT) and a human immunodeficiency virus type 1 (HIV-1) polypurine tract (PPT)-containing RNA/ DNA hybrid suggests local nucleic acid flexibility mediates selection of the plus-strand primer. Structural elements of HIV-1 RT potentially participating in recognition of this duplex include the thumb subdomain and the ribonuclease H (RNase H) primer grip, the latter comprising elements of the connection subdomain and RNase H domain. To investigate how stabilizing HIV-1 PPT structure influences its recognition, we modified the (؊) DNA template by inserting overlapping locked nucleic acid (LNA) doublets and triplets. Modified RNA/ DNA hybrids were evaluated for cleavage at the PPT/U3 junction. Altered specificity was observed when the homopolymeric dA⅐rU tract immediately 5 of the PPT was modified, whereas PPT/U3 cleavage was lost after substitutions in the adjacent dT⅐rA tract. In contrast, the "unzipped" portion of the PPT was moderately insensitive to LNA insertions. Although a portion of the dC⅐rG and neighboring dT⅐rA tract were minimally affected by LNA insertion, RNase H activity was highly sensitive to altering the junction between these structural elements. Using 3 -end-labeled PPT RNA primers, we also identified novel cleavage sites ahead (؉5/؉6) of the PPT/U3 junction. Differential cleavage at the PPT/U3 junction and U3 ؉ 5/؉6 site in response to LNA-induced template modification suggests two binding modes for HIV-1 RT, both of which may be controlled by the interaction of its thumb subdomain (potentially via the minor groove binding track) at either site of the unzipped region.Minus (Ϫ)-strand DNA synthesis in retroviruses is accompanied by degradation of viral RNA of the RNA/DNA replication intermediate. These are events mediated by the N-terminal DNA polymerase and C-terminal ribonuclease H (RNase H) 1 catalytic centers of the multifunctional reverse transcriptase (RT), respectively (1). Correct positioning of nucleic acids to facilitate each of these steps clearly requires its specific interaction with structural motifs of the virus-coded polymerase. Crystallographic (2-4) and biochemical analysis (5-13) of human immunodeficiency virus type 1 (HIV-1) RT identified the primer grip of the p66 thumb as a motif critical for positioning the primer 3ЈOH before nucleophilic attack on the incoming dNTP. Immediately adjacent to this motif, the minor groove binding track (MGBT) or translocation track is proposed to mediate translocation of the polymerization machinery and act as a sensor of nucleic acid geometry (14 -19). Recently, it was proposed that the RNase H primer grip (RHPG), involving portions of the p66 connection subdomain and RNase H domain, interacts with the DNA strand of an RNA/DNA hybrid, providing the RNA with a trajectory appropriate for hydrolysis within the RNase H catalytic center (4, 20, 21). These combined activities effectively prepare nascent (Ϫ) DNA for use as template for plus (ϩ)-strand, DNA-dependent DNA synthesis.A critical...

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“…Informations were obtained through: (1) quantitative measurements of J H1'-H2' and J H1'-H2" coupling constants and sums of coupling constants S1', S2' and S2". This required high-resolution P.COSY spectra with analysis of cross-sections through cross-peaks along the v2 dimension and direct reading of J coupling constants or sums of J coupling constants (Rinkel & Altona, 1987); (2) qualitative estimation of J H3'-H4' , J H2'-H3' , J H2"-H3' from P.COSY and TOCSY spectra (Kim et al, 1992;Salazar et al, 1994); (3) NOE intensities of H1'-H4' cross-peaks from the NOESY spectra recorded at 50 ms, these NOEs having been shown to be highly dependent on the pseudorotation angle (Wü thrich, 1986); (4) qualitative estimates of pseudorotation angles from H1'-H2' cross-peak patterns in P.COSY spectra as described (Mauffret et al, 1992;Gochin et al, 1990).…”

Section: Sugar Conformationsmentioning

confidence: 99%

The Hairpin Structure of a Topoisomerase II Site DNA Strand Analyzed by Combined NMR and Energy Minimization Methods

Amir-Aslani

Mauffret

Sourgen

et al. 1996

Journal of Molecular Biology

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The Solution Structure of the r(gcg)d(TATACCC):d(GGGTATACGC) Okazaki Fragment Contains Two Distinct Duplex Morphologies Connected by a Junction

Cited by 38 publications

References 0 publications

Solution structure sf r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1(+)-strand synthesis

Solution structure sf r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1(+)-strand synthesis

Two Modes of HIV-1 Polypurine Tract Cleavage Are Affected by Introducing Locked Nucleic Acid Analogs into the (-) DNA Template

The Hairpin Structure of a Topoisomerase II Site DNA Strand Analyzed by Combined NMR and Energy Minimization Methods

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