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,...

scholarly journals Locking up the AS1411 Aptamer with a Flanking Duplex: Towards an Improved Nucleolin-Targeting

2021 ◽  
Vol 14 (2) ◽  
pp. 121
Author(s):  
André Miranda ◽  
Tiago Santos ◽  
Eric Largy ◽  
Carla Cruz
Keyword(s):  
Loop Structure ◽  
Binding Properties ◽  
Stem Loop ◽  
Affinity Ligand ◽  
Stem Loop Structure ◽  
Topology Maintenance ◽  
G Quadruplex ◽  
Dimeric Form ◽  
Biophysical Techniques ◽  
Melting Experiments

We have designed AS1411-N6, a derivative of the nucleolin (NCL)-binding aptamer AS1411, by adding six nucleotides to the 5′-end that are complementary to nucleotides at the 3′-end forcing it into a stem-loop structure. We evaluated by several biophysical techniques if AS1411-N6 can adopt one or more conformations, one of which allows NCL binding. We found a decrease of polymorphism of G-quadruplex (G4)-forming sequences comparing to AS1411 and the G4 formation in presence of K+ promotes the duplex folding. We also studied the binding properties of ligands TMPyP4, PhenDC3, PDS, 360A, and BRACO-19 in terms of stability, binding, topology maintenance of AS1411-N6, and NCL recognition. The melting experiments revealed promising stabilizer effects of PhenDC3, 360A, and TMPyP4, and the affinity calculations showed that 360A is the most prominent affinity ligand for AS1411-N6 and AS1411. The affinity determined between AS1411-N6 and NCL denoting a strong interaction and complex formation was assessed by PAGE in which the electrophoretic profile of AS1411-N6 showed bands of the dimeric form in the presence of the ligands and NCL.

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

Structural Competition Involving G-Quadruplex DNA and Its Complement†

Biochemistry ◽  
2003 ◽  
Vol 42 (40) ◽  
pp. 11736-11744 ◽  
Author(s):  
Wei Li ◽  
Daisuke Miyoshi ◽  
Shu-ichi Nakano ◽  
Naoki Sugimoto
Keyword(s):  
Quadruplex Dna ◽  
G Quadruplex ◽  
Structural Competition

scholarly journals A New G-Quadruplex with Hairpin Loop Immediately Upstream of the Human BCL2 P1 Promoter Modulates Transcription

2016 ◽  
Vol 138 (8) ◽  
pp. 2563-2570 ◽  
Author(s):  
Buket Onel ◽  
Megan Carver ◽  
Guanhui Wu ◽  
Daria Timonina ◽  
Salil Kalarn ◽  
...  
Keyword(s):  
Hairpin Loop ◽  
G Quadruplex

Abstract 2130: The novel G-quadruplex with hairpin loop formed immediately upstream of the human BCL-2 P1 promoter represses BCL-2 transcription

2016 ◽  
Author(s):  
Buket Onel ◽  
Guanhui Wu ◽  
Megan Carver ◽  
Daria Timonina ◽  
Marti Larriva ◽  
...  
Keyword(s):  
The Novel ◽  
Hairpin Loop ◽  
G Quadruplex
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