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Limited By:	Subject = Base pairing;

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miR-CATCH: microRNA capture affinity technology. (2015)

Vencken, Sebastian; Hassan, Tidi; McElvaney, Noel G; Smith, Stephen GJ; Greene, Catheri...

miR-CATCH: microRNA capture affinity technology. (2015)

Vencken, Sebastian; Hassan, Tidi; McElvaney, Noel G; Smith, Stephen GJ; Greene, Catherine M

Abstract:

The final publication is available at Springer via 10.1007/978-1-4939-1538-5_23
Several experimental methods exist to explore the microRNA (miRNA) regulome. These methods almost exclusively focus on multiple targets bound to a single, or perhaps a few miRNAs of interest. Here, we describe a microRNA capture affinity technology (miR-CATCH) which uses an affinity capture oligonucleotide to co-purify a single target messenger RNA (mRNA) together with all its endogenously bound miRNAs. This bench-top method is similar to RNA immunoprecipitation (RIP) and provides an experimental alternative to computational miRNA target prediction.

https://epubs.rcsi.ie/medart/60

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On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics (2011)

Fadda, Elisa; Pomès, Régis

On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics (2011)

Fadda, Elisa; Pomès, Régis

Abstract:

Uracil (U) can be found in DNA as a mismatch paired either to adenine (A) or to guanine (G). Removal of U from DNA is performed by a class of enzymes known as uracil–DNA–glycosylases (UDG). Recent studies suggest that recognition of U–A and U–G mismatches by UDG takes place via an extra-helical mechanism. In this work, we use molecular dynamics simulations to analyze the structure, dynamics and open base pair kinetics of U–A base pairs relative to their natural T–A counterpart in 12 dodecamers. Our results show that the presence of U does not alter the local conformation of B-DNA. Breathing dynamics and base pair closing kinetics are only weakly dependent on the presence of U versus T, with open T–A and U–A pairs lifetimes in the nanosecond timescale. Additionally, we observed spontaneous base flipping in U–A pairs. We analyze the structure and dynamics for this event and compare the results to available crystallographic data of open base pair conformations. Our results are in agree...

http://mural.maynoothuniversity.ie/7826/

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Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex (2020)

Keane, Páraic M.; Poynton, Fergus E.; Hall, James P.; Quinn, Susan J.

Reversal of a Single Base-Pair Step Controls Guanine Photo-Oxidation by an Intercalating Ruthenium(II) Dipyridophenazine Complex (2020)

Keane, Páraic M.; Poynton, Fergus E.; Hall, James P.; Quinn, Susan J.

Abstract:

Small changes in DNA sequence can often have major biological effects. Here the rates and yields of guanine photo-oxidation by Λ-[Ru(TAP)2(dppz)]2+ have been compared in 5′-{CCGGATCCGG}2 and 5′-{CCGGTACCGG}2 using pico/nanosecond transient visible and time-resolved IR (TRIR) spectroscopy. The inefficiency of electron transfer in the TA sequence is consistent with the 5′-TA-3′ versus 5′-AT-3′ binding preference predicted by X-ray crystallography. The TRIR spectra also reveal the differences in binding sites in the two oligonucleotides.
Irish Research Council
Science Foundation Ireland
Royal Irish Academy/Royal Society International Exchange Scheme
UK Biotechnology and Biological Sciences Research Council
College of Science, UCD
UK Science and Technology Facilities Council

http://hdl.handle.net/10197/11605

Displaying Results 1 - 3 of 3 on page 1 of 1