GNA Trinucleotide Loop Sequences Producing Extraordinarily Stable DNA Minihairpins

Yoshizawa, Satoko; Kawai, Gota; Watanabe, Kimitsuna; Miura, Kin‐ichiro; Hirao, Ichiro

doi:10.1021/bi961738p

Cited by 141 publications

(143 citation statements)

References 37 publications

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“…The occurrence of A in the middle of a short palindromic sequence causes the formation of a hairpin structure [7]. Replacement of A by G decreases the stability of this structure [7], and it may be responsible for the observed low frequency of the G allele. However, it does not by itself explain how this may play a role in b-thalassemia.…”

Section: Resultsmentioning

confidence: 99%

Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human β‐globin locus control region (LCR) in Indian population

et al. 2001

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LCR, a genetic regulatory element, was examined in b-thalassemia patients who do not show any mutation in the b-globin genes. We sequenced LCR-HS2, HS3, and HS4 in samples from 16 such patients from the Indian population and found only one SNP A-G in the inverted repeat in HS4. A signi®cant association was observed between the G allele and occurrence of b-thalassemia by Fisher's exact test. The AG and GG genotypes showed higher relative risk as compared to the AA genotype. We also observed linkage disequilibrium between the A/G polymorphism and the AT-rich motif of the LCR HS2 region, suggesting that the G allele could be an evolutionarily new mutation in the study population. Am.

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Section: Resultsmentioning

confidence: 99%

Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human β‐globin locus control region (LCR) in Indian population

et al. 2001

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“…The hairpin formation and stability is extremely dependent on both the central base sequence of the loop and the sequence of the stem region (3,14). The effect of different nucleotide compositions on the loop stability have recently been studied (15,16). Less stable loop structures with proper length of the stem might be preferable because a structure with a too stable stem can compete with the PCR-primer hybridization and the polymerase extension in the PCR step, thereby decreasing the efficiency of the PCR.…”

Section: Discussionmentioning

confidence: 99%

PCR-Introduced Loop Structure as Primer in DNA Sequencing

et al. 1998

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“…vRNAP promoter hairpins are unusually stable because of specific sequences of the loop (Ϫ12A and Ϫ10G) and the loop-closing base pair (3Ј-G:C-5Ј) (9,(14)(15)(16). This sequence-dependent stability is reflected in the increased electrophoretic mobility in the presence of 6 M urea of oligonucleotides containing these unusually stable DNA hairpins (Fig.…”

Section: -mentioning

confidence: 99%

Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin

Davydova

Santangelo²,

Rothman-Denes³

2007

Proc. Natl. Acad. Sci. U.S.A.

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Bacteriophage N4 minivirion RNA polymerase (mini-vRNAP), the RNA polymerase (RNAP) domain of vRNAP, is a member of the T7-like RNAP family. Mini-vRNAP recognizes promoters that comprise conserved sequences and a 3-base loop-5-base pair (bp) stem DNA hairpin structure on single-stranded templates. Here, we defined the DNA structural and sequence requirements for minivRNAP promoter recognition. Mini-vRNAP binds a 20-nucleotide (nt) N4 P2 promoter deoxyoligonucleotide with high affinity (K d ‫؍‬ 2 nM) to form a salt-resistant complex. We show that mini-vRNAP interacts specifically with the central base of the hairpin loop (؊11G) and a base at the stem (؊8G) and that the guanine 6-keto and 7-imino groups at both positions are essential for binding and complex salt resistance. The major determinant (؊11G), which must be presented to mini-vRNAP in the context of a hairpin loop, appears to interact with mini-vRNAP Trp-129. This interaction requires template single-strandedness at positions ؊2 and ؊1. Contacts with the promoter are disrupted when the RNA product becomes 11-12 nt long. This detailed description of vRNAP interaction with its promoter hairpin provides insights into RNAPpromoter interactions and explains how the injected vRNAP, which is present in one or two copies, recognizes its promoters on a single copy of the injected genome.T7-like RNA polymerase B acteriophage N4 virion RNA polymerase (vRNAP), which is responsible for the transcription of the phage early genes, is present in virions in one or two copies and is injected into the host together with the phage genome at the onset of infection (1, 2). vRNAP is a 3,500-aa polypeptide that lacks extensive sequence similarity to either of the two known families of DNA-dependent RNAPs (3). Using controlled trypsin proteolysis and catalytic autolabeling, we defined a stable and transcriptionally active 1,106-aa domain (mini-vRNAP) located at the center of the vR-NAP polypeptide (3). Mini-vRNAP possesses the same initiation, elongation, termination, and product displacement properties as full-length vRNAP (3, 4).Mutational, biochemical, and phylogenetic analyses indicated that mini-vRNAP is a highly diverged member of the T7 RNAP family (3). However, although T7 RNAP recognizes its promoters in double-stranded templates (5), vRNAP transcribes promotercontaining, single-stranded templates with in vivo specificity (6), recognizing a 3-base loop-5-bp stem hairpin structure and specific sequences at the promoter (7). In vivo, vRNAP promoter recognition requires template supercoiling (8) to drive extrusion of the promoter hairpins from the double-stranded N4 genome (9, 10) and Escherichia coli single-stranded DNA-binding protein to stabilize single-stranded regions surrounding the site of transcription initiation (11). We have used single-stranded templates to identify unambiguously the site of transcription initiation as well as the sequence and structural DNA determinants of vRNAP-promoter interaction. The results reveal two major determinants of vRNAP hairpin rec...

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GNA Trinucleotide Loop Sequences Producing Extraordinarily Stable DNA Minihairpins

Cited by 141 publications

References 37 publications

Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human β‐globin locus control region (LCR) in Indian population

Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS)4 of the human β‐globin locus control region (LCR) in Indian population

PCR-Introduced Loop Structure as Primer in DNA Sequencing

Bacteriophage N4 virion RNA polymerase interaction with its promoter DNA hairpin

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