scholarly journals Rational Design of a Photoswitchable DNA Glue Enabling High Regulatory Function and Supramolecular Chirality Transfer

2021 ◽  
Author(s):  
Nadja Simeth ◽  
Shotaro Kobayashi ◽  
Piermichele Kobauri ◽  
Stefano Crespi ◽  
Wiktor Szymanski ◽  
...  
Keyword(s):  
Rational Design ◽  
Regulatory Function ◽  
Duplex Dna ◽  
Base Pairs ◽  
Chirality Transfer ◽  
Complementary Dna ◽  
Spontaneous Formation ◽  
Supramolecular Chirality

Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the...

scholarly journals Chiroptical Sensing of Amino Acid Derivatives by Host–Guest Complexation with Cyclo[6]aramide

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4064
Author(s):  
Xuebin Wang ◽  
Jiecheng Ji ◽  
Zejiang Liu ◽  
Yimin Cai ◽  
Jialiang Tang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Density Functional ◽  
Cd Spectroscopy ◽  
Functional Theory ◽  
Chirality Transfer ◽  
Supramolecular Chirality ◽  
New Strategy ◽  
Spectroscopy Studies ◽  
Effective Component ◽  
Acid Esters

A hydrogen-bonded (H-bonded) amide macrocycle was found to serve as an effective component in the host–guest assembly for a supramolecular chirality transfer process. Circular dichroism (CD) spectroscopy studies showed that the near-planar macrocycle could produce a CD response when combined with three of the twelve L-α-amino acid esters (all cryptochiral molecules) tested as possible guests. The host–guest complexation between the macrocycle and cationic guests was explored using NMR, revealing the presence of a strong affinity involving the multi-point recognition of guests. This was further corroborated by density functional theory (DFT) calculations. The present work proposes a new strategy for amplifying the CD signals of cryptochiral molecules by means of H-bonded macrocycle-based host–guest association, and is expected to be useful in designing supramolecular chiroptical sensing materials.

scholarly journals Transient Hoogsteen base pairs in canonical duplex DNA

Nature ◽  
2011 ◽  
Vol 470 (7335) ◽  
pp. 498-502 ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Eunae Kim ◽  
Abigail A. Wise ◽  
Patrick J. O’Brien ◽  
Ioan Andricioaei ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Base Pairs

scholarly journals A historical account of hoogsteen base-pairs in duplex DNA

Biopolymers ◽  
2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Evgenia N. Nikolova ◽  
Huiqing Zhou ◽  
Federico L. Gottardo ◽  
Heidi S. Alvey ◽  
Isaac J. Kimsey ◽  
...  
Keyword(s):  
Duplex Dna ◽  
Historical Account ◽  
Base Pairs

scholarly journals Rational design of minimal synthetic promoters for plants

2020 ◽  
Vol 48 (21) ◽  
pp. 11845-11856 ◽  
Author(s):  
Yao-Min Cai ◽  
Kalyani Kallam ◽  
Henry Tidd ◽  
Giovanni Gendarini ◽  
Amanda Salzman ◽  
...  
Keyword(s):  
Rational Design ◽  
Plant Pathogens ◽  
Critical Role ◽  
Experimental System ◽  
Computational Design ◽  
Regulatory Elements ◽  
Regulatory Function ◽  
Synthetic Promoters ◽  
Sequence Elements ◽  
Plant Promoters

Abstract Promoters serve a critical role in establishing baseline transcriptional capacity through the recruitment of proteins, including transcription factors. Previously, a paucity of data for cis-regulatory elements in plants meant that it was challenging to determine which sequence elements in plant promoter sequences contributed to transcriptional function. In this study, we have identified functional elements in the promoters of plant genes and plant pathogens that utilize plant transcriptional machinery for gene expression. We have established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of a suite of synthetic promoters of different strengths. These have been used to regulate the relative expression of output genes in simple genetic devices.

Positive cooperativity of the specific binding between Hg2+ ion and T:T mismatched base pairs in duplex DNA

2012 ◽  
Vol 532 ◽  
pp. 28-35 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Yukako Miyakawa ◽  
Akira Ono ◽  
Tetsuo Kozasa
Keyword(s):  
Specific Binding ◽  
Duplex Dna ◽  
Base Pairs ◽  
Positive Cooperativity

scholarly journals DNA polymerase β: effects of gapped DNA substrates on dNTP specificity, fidelity, processivity and conformational changes1

1998 ◽  
Vol 331 (1) ◽  
pp. 79-87 ◽  
Author(s):  
Jinwoo AHN ◽  
Vadim S. KRAYNOV ◽  
Xuejun ZHONG ◽  
Brian G. WERNEBURG ◽  
Ming-Daw TSAI
Keyword(s):  
Conformational Change ◽  
Dna Polymerase ◽  
Catalytic Efficiency ◽  
Duplex Dna ◽  
Gap Filling ◽  
Dna Polymerase Β ◽  
Base Pairs ◽  
Single Nucleotide ◽  
Dna Substrates ◽  
Gapped Dna

Pre-steady-state kinetic analysis was used to compare the catalytic properties of DNA polymerase β (Pol β) for single-base gap-filling and regular duplex DNA synthesis. The rate of polymerization (kpol) and the apparent equilibrium dissociation constant of dNTP (Kd) were determined with single-nucleotide gapped DNA substrates for all four possible correct base pairs and twelve possible incorrect base pairs, and the results were compared with those obtained previously with non-gapped primer/template duplex DNA substrates. For correct dNTP incorporation, the use of single-nucleotide gapped DNA led to significant decreases in the Kd of dNTP. Although kpol was little affected, the catalytic efficiency kpol/Kd increased significantly owing to the decreases in Kd. In contrast, for incorrect dNTP incorporation, the use of single-nucleotide gapped DNA substrates did not affect the Kd of dNTP appreciably but caused the kpol (and thus kpol/Kd) for incorrect dNTP incorporation to increase. As a consequence the fidelity of Pol β was not significantly affected by the use of single-nucleotide gapped DNA substrates. In addition we show that under processive polymerization conditions the processivity of Pol β increases in the gap-filling synthesis owing to a decreased rate of DNA dissociation. Finally, with a single-nucleotide gapped DNA substrate the rate-limiting conformational change step before chemistry was also observed. However, the preceding fast conformational change observed with duplex DNA substrates was not clearly detected. A possible cause is that in the complex with the gapped DNA, the 8 kDa N-terminal domain of Pol β already exists in a closed conformation. This interpretation was supported by tryptic digestion experiments.

scholarly journals Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Heidi S. Alvey ◽  
Federico L. Gottardo ◽  
Evgenia N. Nikolova ◽  
Hashim M. Al-Hashimi
Keyword(s):  
Duplex Dna ◽  
Base Pairs
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