Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

Watkins, Norman E.; Kennelly, William J.; Tsay, Mike J.; Tuin, Astrid; Swenson, Lara; Lee, Nana; Morosyuk, Svetlana; Hicks, Donald A.; SantaLucia, John

doi:10.1093/nar/gkq905

Cited by 35 publications

(74 citation statements)

References 51 publications

(93 reference statements)

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“…The superior capabilities of the above monomers to increase mismatch discrimination within DNA*/RNA duplexes makes them relevant molecular tools in the design of antisense ONs [21] and for detection and analysis of pathogenic genes. [22] Steady-state fluorescence emission spectra of ON1-ON8 and the corresponding matched or singly mismatched duplexes were recorded. The fluorescence intensities were generally increased upon hybridization to DNA or RNA, and to the best of our knowledge this is the first report in which ONs modified with acyclic pyrene-nucleotides have been shown to generate increased fluorescence intensities upon hybridization.…”

Section: Discussionmentioning

confidence: 99%

Pyrene‐Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties

et al. 2012

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Two pyrene-modified UNA monomers were synthesized and incorporated into 21-mer DNA oligonucleotides. Melting temperatures and thermodynamic properties of the modified duplexes were measured, and the fluorescence properties of single strands and duplexes containing one or more pyrene-UNA modifications were studied. It was found that incorporation of pyrene-UNA monomers increased duplex stability relative to UNA monomers, and thermodynamic studies revealed significant mismatch discriminative capabilities of the pyrene-UNA modified oligonucleotides. Furthermore, the steady-state fluorescence emission intensities of pyrene-UNA modified oligonucleotides were increased upon hybridization to DNA, which to the best of our knowledge is unprecedented for an acyclic pyrene modification in DNA. Interestingly, pyrene excimer emission was observed for single-stranded oligonucleotides containing three pyrene-UNA modifications, whereas this excimer emission disappeared after hybridization to DNA. In view of both the pyrene monomer and the excimer fluorescence emission, the triply modified oligonucleotides show intriguing properties relating to the development of new DNA/RNA detection tools.

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Section: Discussionmentioning

confidence: 99%

Pyrene‐Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties

et al. 2012

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“…Perhaps the best characterized RGN system is the Type-II CRISPR associated Streptococcus Pyogenes Cas9 (Figure 6A, S5). This bias is about a factor two lower than the average gain per correct base pair for RNA:DNA hybrids in solution (75,76), indicating that association with the RGN destabilizes the hybrid. This is in line with recent studies demonstrating that the protein has a strong contribution to the energetics of the resulting bound complex (53,54,57).…”

Section: Comparison To Experimental Data For a Broad Class Of Rna Guimentioning

confidence: 89%

The kinetic basis of CRISPR-Cas off-targeting rules

Klein

Eslami-Mossallam

et al. 2017

Preprint

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Cas nucleases are popular tools for genome editing applications due to their ability to introduce DNA breaks at desired genomic locations. Such differential targeting is achieved through loading an RNA guide complimentary to the intended target sequence. As it turns out, sequences with only a partial match to the guide can also be cleaved. A large number of experiments have shed light on this off-targeting, outlining a number of rather peculiar empirical rules that detail the effect of mismatches at various positions and at various relative distances. We construct a kinetic model predicting on-target cleavage efficiency as well as offtarget specificity. Our model explains a unified targeting rule for any target harboring mismatches, independent of their abundance and placing, and the observed decoupling between efficiency and specificity when protein-DNA interactions are weakened. We favorably compare our model to

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“…In addition, our algorithm can probe DNA-RNA bonds using the parameter sets from Refs. [103,104], and interpolating between the DNA and RNA cases for those parameters that have not yet been tabulated from experimental data. The inclusion of DNA strands may require slight modification to the two entropy parameters (b and v s ) which are based on data from RNA experiments.…”

Section: S2 Probing Multiple Interacting Strandsmentioning

confidence: 99%

RNA structure prediction including pseudoknots through direct enumeration of states

Kimchi

Cragnolini

Brenner

et al. 2018

Preprint

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The accurate prediction of RNA secondary structure from primary sequence has had enormous impact on research from the past forty years. While many algorithms are available to make these predictions, the inclusion of non-nested loops, termed pseudoknots, still poses challenges. Here, we describe a new method to compute the entire free energy landscape of secondary structures of RNA resulting from a primary RNA sequence, by combining a polymer physics model for the entropy of pseudoknots with exhaustive enumeration of the set of possible structures. Our polymer physics model can address arbitrarily complex pseudoknots and has only two free loop entropy parameters that correspond to concrete physical quantities, over an order of magnitude fewer than even the sparsest state-of-the-art algorithms. Our model outperforms previously published methods in predicting pseudoknots, while performing on par with current methods in the prediction of nonpseudoknotted structures. For RNA sequences of ∼ 45 nucleotides, or ∼ 90 with minimal heuristics, the complete enumeration of possible secondary structures can be accomplished quickly despite the NP-complete nature of the problem. * Electronic address: okimchi@g.harvard.edu † Electronic address: ljc37@cam.ac.uk 1 More generally, we can define a probability q( R) of a nucleotide at the origin being base paired with a nucleotide a vector R away. Then, vs is defined as vs = d R q( R) and rs is the value of | R| for which q( R) is non-negligible.

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Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

Cited by 35 publications

References 51 publications

Pyrene‐Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties

Pyrene‐Modified Unlocked Nucleic Acids: Synthesis, Thermodynamic Studies, and Fluorescent Properties

The kinetic basis of CRISPR-Cas off-targeting rules

RNA structure prediction including pseudoknots through direct enumeration of states

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