Designs of Inter-Group Complementary Sequence Set from Interleaving Z-Periodic Complementary Sequences

2016 ◽  
Vol E99.A (5) ◽  
pp. 987-993 ◽  
Author(s):  
Longye WANG ◽  
Xiaoli ZENG ◽  
Hong WEN
Keyword(s):  
Complementary Sequence ◽  
Complementary Sequences

Comparison of a + T-Rich Oligonucleotides with and without Self-Complementary Sequence Using Ion-Pair Reversed-Phase High-Performance Liquid Chromatography/Tandem Electrospray Ionization Mass Spectrometry

2005 ◽  
Vol 11 (1) ◽  
pp. 83-91 ◽  
Author(s):  
Renfang Song ◽  
Wenbing Zhang ◽  
Huayong Chen ◽  
Huimin Ma ◽  
Yulian Dong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Electrospray Ionization ◽  
Charge State ◽  
Reversed Phase ◽  
Ion Pair ◽  
Buffer System ◽  
Ionization Mass ◽  
Complementary Sequence ◽  
Complementary Sequences ◽  
Lower Charge

Both A + T-rich oligonucleotides with and without self-complementary sequences were analyzed using ion-pair reversed-phase liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) by tryethylammonium acetate (TEAA) and hexafluoroisopropanol (HFIP) buffer systems to study the characteristics of their retention behavior and electrospray ionization tandem mass spectrometry (ESI-MS/MS) response. The results indicated that the chain length had the same effect on the retention of A + T-rich oligonucleotides in both of TEAA and HFIP buffer systems but the sequence had a different impact on the retention in the two buffer systems. A + T-rich oligonucleotides with a self-complementary sequence were much shorter than those without in the TEAA buffer system whereas a slight difference was observed in the HFIP buffer system. Similar total ion current (TIC) intensity was observed both in oligonucleotides with or without self-complementary sequence. The opposite trend of a change in the TIC intensities with increasing chain length were observed in both the TEAA and HFIP buffer systems. A lower charge state was predominant in the TEAA buffer system whereas a higher charge state was mainly distributed in the HFIP buffer system. The oligonucleotides without self-complementary sequences had a higher charge state than those with self-complementary sequences. A- and T- are more esily formed at a higher charge state whereas the sequence fragments will be formed more easily at a lower charge state in both A + T-rich oligonucleotides with and without self-complementary sequences.

scholarly journals Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5’ untranslated region

2020 ◽  
Author(s):  
Xin Ee Yong ◽  
Palur Venkata Raghuvamsi ◽  
Ganesh S. Anand ◽  
Thorsten Wohland ◽  
Kamal K. Sharma
Keyword(s):  
Dengue Virus ◽  
Capsid Protein ◽  
Virus Strain ◽  
Untranslated Region ◽  
Structural Protein ◽  
Complementary Sequence ◽  
Rna Chaperone ◽  
Complementary Sequences ◽  
Rna Formation ◽  
Kissing Loop

ABSTRACTThe capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5’ untranslated region (5’UTR) to either its complementary sequence or to the 3’ untranslated region (3’UTR) occurs during (+)/(−) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5’UTR region (21-nt upstream AUG region (5’UAR) and 23-nt capsid-coding hairpin (5’cHP)) to their complementary sequences during (+)/(−) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(−) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5’UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(−) ds-RNA formation and (+) RNA circularization.

scholarly journals The RNA–RNA base pairing potential of human Dicer and Ago2 proteins

2019 ◽  
Vol 77 (16) ◽  
pp. 3231-3244 ◽  
Author(s):  
Maria Pokornowska ◽  
Marek C. Milewski ◽  
Kinga Ciechanowska ◽  
Agnieszka Szczepańska ◽  
Marta Wojnicka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Binding Sites ◽  
Rna Structure ◽  
Small Interfering Rnas ◽  
Base Pairing ◽  
Complementary Sequence ◽  
Control Of Gene Expression ◽  
Complementary Sequences

Abstract The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.

Inter-Group Complementary Sequence Set Based on Interleaved Periodic Complementary Sequences

2016 ◽  
Vol 91 (3) ◽  
pp. 1051-1064 ◽  
Author(s):  
Zhenyu Zhang ◽  
Fengchun Tian ◽  
Fanxin Zeng ◽  
Lijia Ge ◽  
Guixin Xuan
Keyword(s):  
Complementary Sequence ◽  
Complementary Sequences

Aperiodic Complementary Sequences

2014 ◽  
Vol E97.A (9) ◽  
pp. 1998-2004 ◽  
Author(s):  
Zhimin SUN ◽  
Xiangyong ZENG ◽  
Yang YANG
Keyword(s):  
Complementary Sequences

16-QAM Golay, Periodic and Z- Complementary Sequence Sets

2012 ◽  
Vol E95.A (11) ◽  
pp. 2084-2089 ◽  
Author(s):  
Fanxin ZENG ◽  
Xiaoping ZENG ◽  
Zhenyu ZHANG ◽  
Guixin XUAN
Keyword(s):  
Complementary Sequence

Synthesis of multilevel complementary sequences

1988 ◽  
Vol 24 (19) ◽  
pp. 1251 ◽  
Author(s):  
M. Darnell ◽  
A.H. Kemp
Keyword(s):  
Complementary Sequences

New Constructions of General QAM Golay Complementary Sequences

2013 ◽  
Vol 59 (11) ◽  
pp. 7684-7692 ◽  
Author(s):  
Zilong Liu ◽  
Ying Li ◽  
Yong Liang Guan
Keyword(s):  
Complementary Sequences ◽  
Golay Complementary Sequences
Sign in / Sign up

Export Citation Format

Share Document