Stabilizing effects of the RNA 2′-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2′-O-methylated adenosines

Lubini, Paolo; Zürcher, W.; Egli, Martin

doi:10.1016/1074-5521(94)90039-6

Cited by 107 publications

(107 citation statements)

References 36 publications

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“…However, the ANA-and FANA-modified decamers crystallize in new P2 1 2 1 2 1 and P2 1 forms, respectively, unlike other decamers of the same sequence containing 2′-O-modified residues (see for example refs 49, 53-58) that crystallize in an orthorhombic form with approximate unit cell constants of 25, 44, and 45 Å. It is noteworthy that the decamer duplex with 2′-O-methyl-A at positions 5 (strand 1) and 15 (strand 2) crystallizes in the "regular" orthorhombic form (53). Therefore, the presence of the ANA and FANA modifications triggers a change in the lattice for these two decamers.…”

Section: Resultsmentioning

confidence: 99%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

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2′-Deoxy-2′-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A-and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A-and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

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Section: Resultsmentioning

confidence: 99%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

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“…Rather, the OCH 3 substitution reduced activity to the basal level seen with the all-DNA substrate D12 (data not shown). The OCH 3 ribonucleoside is expected to adopt an RNA-like 3Ј-endo-sugar pucker (28). The fact that the NHEJ ligases discriminated between a ribose and a 2Ј-OCH 3 ribose is subject to several interpretations.…”

Section: B-d)mentioning

confidence: 99%

Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide

Zhu

Shuman

2008

Journal of Biological Chemistry

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Many bacterial species have a nonhomologous end joining system of DNA repair driven by dedicated DNA ligases (LigD and LigC). LigD is a multifunctional enzyme composed of a ligase domain fused to two other catalytic modules: a polymerase that preferentially adds ribonucleotides to double-strand break ends and a phosphoesterase that trims 3 -oligoribonucleotide tracts until only a single 3 -ribonucleotide remains. LigD and LigC have a feeble capacity to seal 3 -OH/5 -PO 4 DNA nicks. Here, we report that nick sealing by LigD and LigC enzymes is stimulated by the presence of a single ribonucleotide at the broken 3 -OH end. The ribonucleotide effect on LigD and LigC is specific for the 3 -terminal nucleotide and is either diminished or abolished when additional vicinal ribonucleotides are present. No such 3 -ribonucleotide effect is observed for bacterial LigA or Chlorella virus ligase. We found that in vitro repair of a double-strand break by Pseudomonas LigD requires the polymerase module and results in incorporation of an alkalilabile ribonucleotide at the repair junction. These results illuminate an underlying logic for the domain organization of LigD, whereby the polymerase and phosphoesterase domains can heal the broken 3 -end to generate the monoribonucleotide terminus favored by the nonhomologous end joining ligases.Direct evidence that bacteria catalyze DNA double-strand break (DSB) 2 repair via nonhomologous end joining (NHEJ) emerged from studies of the repair of linear plasmid DNAs transfected into mycobacteria (1). NHEJ entails approximation of the broken DNA ends, aided by the bacterial end-binding protein Ku, followed by sealing of at least one of the broken strands by a specialized bacterial ATP-dependent DNA ligase, either LigD or LigC (1-9, 36). Unlike homologous recombination, which is generally error-free, NHEJ can be either faithful or mutagenic. The signature feature of NHEJ in mycobacteria is that half of the repair events at blunt or complementary 5Ј-overhang DSBs are unfaithful because the DSB ends are extended by polymerases or resected by nucleases prior to sealing by ligase (1,8,9,36). Because NHEJ does not rely on a homologous DNA template, it can operate when only one chromosomal copy is available, e.g. during late stationary phase or after sporulation (10 -13). Whereas mutagenic DSB repair might seem counterproductive, it can be advantageous, especially if the alternative is death of the quiescent bacterium or spore.Biochemical, structural, and genetic studies of the NHEJ ligases and Ku proteins of Mycobacterium, Pseudomonas, Bacillus, and Agrobacterium are beginning to define a pathway with unique features and distinctive enzymatic components (1, 4 -9, 14 -17, 36). Ku and LigD are critical agents of the pathway. The efficiency of plasmid-based NHEJ of blunt and 5Ј-overhang DSBs in mycobacteria is reduced several hundredfold by deletion of Ku and by ϳ100-fold by deletion of LigD (1, 36). LigC provides an efficient backup sealing function in mycobacteria when LigD sealing activity is a...

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“…32 P-Labeled DNA substrates (1.25 nM) were incubated in 20 l of the buffer with 100 nM integrase at 37°C. Aliquots were taken after 5, 10, 20, 30, 60, and 120 min.…”

Section: Methodsmentioning

confidence: 99%

Probing of HIV-1 Integrase/DNA Interactions Using Novel Analogs of Viral DNA

Agapkina

Smolov

Barbe

et al. 2006

Journal of Biological Chemistry

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The specific activity of the human immunodeficiency virus, type 1 (HIV-1), integrase on the viral long terminal repeat requires the binding of the enzyme to certain sequences located in the U3 and U5 regions at the ends of viral DNA, but the determinants of this specific DNA-protein recognition are not yet completely understood. We synthesized DNA duplexes mimicking the U5 region and containing either 2-modified nucleosides or 1,3-propanediol insertions and studied their interactions with HIV-1 integrase, using Mn 2؉ or Mg 2؉ ions as integrase cofactors. These DNA modifications had no strong effect on integrase binding to the substrate analogs but significantly affected 3-end processing rate. The effects of nucleoside modifications at positions 5, 6, and especially 3 strongly depended on the cationic cofactor used. These effects were much more pronounced in the presence of Mg 2؉ than in the presence of Mn 2؉ . Modifications of base pairs 7-9 affected 3-end processing equally in the presence of both ions. Adenine from the 3rd bp is thought to form at least two hydrogen bonds with integrase that are crucial for specific DNA recognition. The complementary base, thymine, is not important for integrase activity. For other positions, our results suggest that integrase recognizes a fine structure of the sugar-phosphate backbone rather than heterocyclic bases. Integrase interactions with the unprocessed strand at positions 5-8 are more important than interactions with the processed strand for specific substrate recognition. Based on our results, we suggest a model for integrase interaction with the U5 substrate.Following reverse transcription, a DNA copy of the human immunodeficiency virus, type 1 (HIV-1), 2 RNA is integrated into the genome of infected cells. Integration is a prerequisite for viral replication and is catalyzed by the viral enzyme integrase (IN). IN binds to sequences located at the end of U3 and U5 parts of long terminal repeats (LTRs) of viral DNA and catalyzes the trimming, or 3Ј-end processing, of the terminal dinucleotide from the 3Ј-ends of both strands of the DNA. IN then mediates a strand transfer reaction that inserts the viral DNA into the host DNA. During this reaction, IN must bind simultaneously to viral and target DNA. However, IN interacts with these two DNA molecules in different ways as follows: binding to host DNA does not depend directly on host DNA sequence, whereas interaction with the viral DNA is a sequence-specific process. Nevertheless, the U5 and U3 sequences recognized by IN are not exactly identical.Strand transfer and 3Ј-end processing reactions may be carried out in vitro, using recombinant HIV IN, DNA duplexes mimicking U3 or U5 sequences of LTRs, and divalent metal ions, such as Mg 2ϩ or Mn 2ϩ . However, the Mn 2ϩ -and Mg 2ϩ -dependent activities of IN are not equivalent, with lower specificity reported for Mn 2ϩ -dependent IN (1, 2). Moreover, the inhibition of HIV-1 IN by compounds such as ␤-diketo acids, which interact with the active site of HIV-1 IN, is also metal-de...

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Stabilizing effects of the RNA 2′-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2′-O-methylated adenosines

Cited by 107 publications

References 36 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide

Probing of HIV-1 Integrase/DNA Interactions Using Novel Analogs of Viral DNA

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Stabilizing effects of the RNA 2′-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2′-O-methylated adenosines

Cited by 107 publications

References 36 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

Bacterial Nonhomologous End Joining Ligases Preferentially Seal Breaks with a 3′-OH Monoribonucleotide

Probing of HIV-1 Integrase/DNA Interactions Using Novel Analogs of Viral DNA

Contact Info

Product

Resources

About

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,