Effect of hairpin loop structure on reactivity, sequence preference and adduct orientation of a DNA-interactive pyrrolo[2,1-c][1,4]benzodiazepine (PBD) antitumour agent

2015 ◽  
Vol 13 (13) ◽  
pp. 4031-4040 ◽  
Author(s):  
David E. Thurston ◽  
Higia Vassoler ◽  
Paul J. M. Jackson ◽  
Colin H. James ◽  
Khondaker M. Rahman
Keyword(s):  
Structural Flexibility ◽  
Loop Structure ◽  
Hairpin Loop ◽  
Dna Hairpins ◽  
Sequence Preference ◽  
Antitumour Agent

Pyrrolobenzodiazepine (PBD) monomer GWL-78 reacts faster with DNA hairpins containing a hexaethylene glycol (HEG) loop compared to hairpins containing a TTT loop due to the greater structural flexibility of the HEG.

scholarly journals Cloning and Analysis of the Telomere and Terminal Inverted Repeat of the Linear Chromosome of Streptomyces griseus

2002 ◽  
Vol 184 (12) ◽  
pp. 3411-3415 ◽  
Author(s):  
Kohei Goshi ◽  
Tetsuya Uchida ◽  
Alexander Lezhava ◽  
Masayuki Yamasaki ◽  
Keiichiro Hiratsu ◽  
...  
Keyword(s):  
Inverted Repeat ◽  
Streptomyces Griseus ◽  
Open Reading Frames ◽  
Terminal Inverted Repeat ◽  
Loop Structure ◽  
Hairpin Loop ◽  
Cloning And Sequencing ◽  
Linear Chromosome ◽  
Palindromic Sequences ◽  
Reading Frames

ABSTRACT Cloning and sequencing of the telomere of Streptomyces griseus revealed five palindromic sequences in the terminal 116 nucleotides, all of which can make a hairpin loop structure. However, the end sequence cannot form the foldback secondary structure that is common in Streptomyces telomeres and is suggested to be necessary for terminal replication. Both inside ends of the terminal inverted repeat (TIR) were also cloned and sequenced. The results confirmed the size of the TIR to be 24 kb and identified two almost identical open reading frames that might have been involved in the formation of the TIR.

The stem hairpin loop structure of p2Sp1 RNA is required for RNA-cleaving activity

1999 ◽  
Vol 1489 (2-3) ◽  
pp. 374-382 ◽  
Author(s):  
Kazumi Hosono ◽  
Hideo Hosaka ◽  
Gota Kawai ◽  
Kazuyuki Takai ◽  
Hiroshi Takaku
Keyword(s):  
Loop Structure ◽  
Hairpin Loop

scholarly journals A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52.

1997 ◽  
Vol 17 (5) ◽  
pp. 2649-2657 ◽  
Author(s):  
H Shi ◽  
B E Hoffman ◽  
J T Lis
Keyword(s):  
Rna Binding ◽  
Rna Recognition ◽  
Loop Structure ◽  
Hairpin Loop ◽  
Structural Element ◽  
Rna Sequences ◽  
Sr Protein ◽  
Rna Recognition Motifs ◽  
Splicing Regulators ◽  
Recognition Motifs

B52, also known as SRp55, is a member of the Drosophila melanogaster SR protein family, a group of nuclear proteins that are both essential splicing factors and specific splicing regulators. Like most SR proteins, B52 contains two RNA recognition motifs in the N terminus and a C-terminal domain rich in serine-arginine dipeptide repeats. Since B52 is an essential protein and is expected to play a role in splicing a subset of Drosophila pre-mRNAs, its function is likely to be mediated by specific interactions with RNA. To investigate the RNA-binding specificity of B52, we isolated B52-binding RNAs by selection and amplification from a pool of random RNA sequences by using full-length B52 protein as the target. These RNAs contained a conserved consensus motif that constitutes the core of a secondary structural element predicted by energy minimization. Deletion and substitution mutations defined the B52-binding site on these RNAs as a hairpin loop structure covering about 20 nucleotides, which was confirmed by structure-specific enzymatic probing. Finally, we demonstrated that both RNA recognition motifs of B52 are required for RNA binding, while the RS domain is not involved in this interaction.

Hairpin Loop Structure at the Termini of the Chlorella Virus PBCV-1 Genome

Virology ◽  
1994 ◽  
Vol 202 (2) ◽  
pp. 1079-1082 ◽  
Author(s):  
Yanping Zhang ◽  
Peter Strasser ◽  
Reingard Grabherr ◽  
James L. Van Etten
Keyword(s):  
Loop Structure ◽  
Hairpin Loop ◽  
Chlorella Virus

scholarly journals Hairpin Loop Structure in the 3′ Arm of the Influenza A Virus Virion RNA Promoter Is Required for Endonuclease Activity

2001 ◽  
Vol 75 (15) ◽  
pp. 7042-7049 ◽  
Author(s):  
Michael B. Leahy ◽  
Helen C. Dobbyn ◽  
George G. Brownlee
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Influenza A ◽  
Point Mutations ◽  
Nucleotide Position ◽  
Loop Structure ◽  
Endonuclease Activity ◽  
Hairpin Loop ◽  
Virus Rna ◽  
Rna Promoter

ABSTRACT Previous studies have shown that the 5′ arm of the influenza A virus virion RNA promoter requires a hairpin loop structure for efficient endonuclease activity of influenza virus RNA polymerase, an activity that is required for the cap-snatching activity of primers from host pre-mRNA. Here we examine whether a hairpin loop is also required in the 3′ arm of the viral RNA promoter. We study point mutations at each nucleotide position (1 to 12) within the 3′ arm of the promoter as well as complementary “rescue” mutations which restored base pairing in the stem of a potential hairpin loop. Our results suggest that endonuclease activity is absolutely dependent on the presence of a 3′ hairpin loop structure. This is the first direct evidence for RNA secondary structure within the 3′ arm being required for a specific stage, i.e., endonuclease cleavage, in the influenza virus replicative cycle.

scholarly journals Hairpin loop structure of African swine fever virus DNA

1986 ◽  
Vol 14 (17) ◽  
pp. 6835-6844 ◽  
Author(s):  
Antonio González ◽  
Antonio Talavera ◽  
José M. Almendral ◽  
Eladio Viñuela
Keyword(s):  
African Swine Fever Virus ◽  
African Swine Fever ◽  
Fever Virus ◽  
Loop Structure ◽  
Hairpin Loop

Intramolecular G-quadruplex-hairpin loop structure competition of a GC-rich exon region in the TMPRSS2 gene

2021 ◽  
Author(s):  
Wataru Sugimoto ◽  
Natsuki Kinoshita ◽  
Minori Nakata ◽  
Tatsuya Ohyama ◽  
Hisae Minatojima-Minaminachi ◽  
...  
Keyword(s):  
Loop Structure ◽  
Hairpin Loop ◽  
G Quadruplex ◽  
Structural Competition ◽  
Exon Region

We identified cytosine-rich regions adjacent to guanine-rich regions in protease genes. A typical GC-rich sequence derived from the TMPRSS2 gene showed structural competition between a G-quadruplex and a hairpin loop,...

Sign in / Sign up

Export Citation Format

Share Document