The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.
Thermodynamic Parameters To Predict Stability of RNA/DNA Hybrid Duplexes
Abstract
The thermodynamic parameters (delta H degree, delta S degree, and delta G degree 37) for 16 nearest-neighbor sets and one initiation factor are presented here in order to predict stability of RNA/DNA hybrid duplexes. To determine the nearest-neighbor parameters, thermodynamics for 68 different hybrid sequences (136 single-stranded oligonucleotides) with 5-13 nucleotide length including several duplexes with identical nearest-neighbors were measured by UV melting procedure. These sequences were selected to have many different combinations of nearest-neighbor pairs, and so that the number of the 16 nearest-neighbor sequences in the oligomers were as equal as possible. The structures of the hybrids were also investigated by measuring circular dichroism spectra. Comparing delta G degree 37 values of the hybrids with DNA/DNA and RNA/RNA parameters reported previously (Breslauer, K.J., Frank, R., Blöcker, H., & Marky, L.A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750; Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T., & Turner, D.H. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9373-9377), RNA/RNA double helix is the most stable of the three kinds of helixes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA hybrid duplexes depends on its sequence. Calculated thermodynamic values of hybrid formation with the present parameters reproduce the experimental values within reasonable errors.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“These energy terms have an error of around 5–10% (32,33,35).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [35]
Citations
Cites
Predicting DNA duplex stability from the base sequence
Breslauer, K. J., Frank, R., Blöcker, H., & Marky, L. A. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.11.3746 · Cited by 1,837
Improved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
Self-citationAntisense Oligonucleotides as Therapeutic Agents—Is the Bullet Really Magical?
Stein, C., & Cheng, Y. C. (1993) · Science · doi:10.1126/science.8351515 · Cited by 1,300
Ivanov, V. I., Minchenkova, L. E., Schyolkina, A. K., et al. (1973) · Biopolymers · doi:10.1002/bip.1973.360120109 · Cited by 936
Form and Function of Retroviral Proviruses
VARMUS, H. E. (1982) · Science · doi:10.1126/science.6177038 · Cited by 577
Free energy of imperfect nucleic acid helices
Gralla, J. D., & Crothers, D. M. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90096-x · Cited by 503
Petersheim, M., & Turner, D. H. (1983) · Biochemistry · doi:10.1021/bi00271a004 · Cited by 497
Martin, F. H., & Tinoco, I. (1980) · Nucleic Acids Research · doi:10.1093/nar/8.10.2295 · Cited by 304
Ogawa, T., & Okazaki, T. (1980) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.49.070180.002225 · Cited by 223
A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli
Yager, T. D., & von Hippel, P. H. (1991) · Biochemistry · doi:10.1021/bi00218a032 · Cited by 193
Cited by
Sorted by citations
High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
RNAstructure: software for RNA secondary structure prediction and analysis
Reuter, J. S., & Mathews, D. H. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-129 · Cited by 2,018
“DNA-RNA hybridization parameters are also used by OligoWalk [93].”
MethodA general purpose RNA-cleaving DNA enzyme
Santoro, S. W., & Joyce, G. F. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4262 · Cited by 1,546
The microRNAs of Caenorhabditis elegans
Lim, L. P., Lau, N. C., Weinstein, E. G., Abdelhakim, A., Yekta, S., Rhoades, M. W., Burge, C. B., & Bartel, D. P. (2003) · Genes & Development · doi:10.1101/gad.1074403 · Cited by 1,259
“To maintain hybridization specificity without varying hybridization or washing conditions, the length of probes for different sequences was adjusted so that the predicted melting temperatures of the miRNA-probe duplexes did not exceed 60°C (Sugimoto et al. 1995).”
BackgroundXia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
Zuker, M., Mathews, D. H., & Turner, D. H. (1999) · Springer eBooks · doi:10.1007/978-94-011-4485-8_2 · Cited by 1,139
“Parameters are also available for predicting the formation of RNA/DNA duplexes [37].”
BackgroundInactivation of the SR Protein Splicing Factor ASF/SF2 Results in Genomic Instability
Xialu Li, C., & Manley, J. L. (2005) · Cell · doi:10.1016/j.cell.2005.06.008 · Cited by 772
The emerging field of RNA nanotechnology
Guo, P. (2010) · Nature Nanotechnology · doi:10.1038/nnano.2010.231 · Cited by 726
“Among the three helices (RNA/RNA, RNA/DNA and DNA/DNA), the RNA/RNA double helix is the most stabl”
Lin, Y., Cradick, T. J., Brown, M. T., Deshmukh, H., Ranjan, P., Sarode, N., Wile, B. M., Vertino, P. M., Stewart, F. J., & Bao, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku402 · Cited by 634
“We believe that high GC-content, which makes the RNA/DNA hybrids more stable (39), may be responsible for increased tolerance of DNA bulges and sgRNA bulges.”
Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids
Nakano, S., Miyoshi, D., & Sugimoto, N. (2013) · Chemical Reviews · doi:10.1021/cr400113m · Cited by 578
Self-citationChemical Etiology of Nucleic Acid Structure: The α-Threofuranosyl-(3'→2') Oligonucleotide System
Schöning, K.-U., Scholz, P., Guntha, S., Wu, X., Krishnamurthy, R., & Eschenmoser, A. (2000) · Science · doi:10.1126/science.290.5495.1347 · Cited by 556
Duquette, M. L., Handa, P., Vincent, J. A., Taylor, A. F., & Maizels, N. (2004) · Genes & Development · doi:10.1101/gad.1200804 · Cited by 528
“A hybrid of G-rich RNA and C-rich DNA would be predicted to be quite stable, reflecting the high stability of the rG/dC base pair and stacking of adjacent guanines in the RNA (Sugimoto et al. 1995).”
BackgroundIDT SciTools: a suite for analysis and design of nucleic acid oligomers
Owczarzy, R., Tataurov, A. V., Wu, Y., Manthey, J. A., McQuisten, K. A., Almabrazi, H., Pedersen, K. F., Lin, Y., Garretson, J. S., McEntaggart, N. O., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn198 · Cited by 570
“These three tools assist in the design of effective siRNAs, as there are several properties that discriminate between effective and ineffective siRNA duplexes (46,47).”
BackgroundInfluentialSkourti-Stathaki, K., & Proudfoot, N. J. (2014) · Genes & Development · doi:10.1101/gad.242990.114 · Cited by 552
“The increased thermodynamic stability of a G-rich RNA strand bound to C-rich DNA could be a reason for this sequence specificity (Sugimoto et al. 1995).”
BackgroundSfold web server for statistical folding and rational design of nucleic acids
Ding, Y.-B., Chan, C. Y., & Lawrence, C. E. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh449 · Cited by 524
“The antisense oligo binding energy is a weighted sum of the DNA/RNA stacking energies (21) for the hybrid formed by the antisense oligo and the targeted sequence.”
BackgroundChen, Y.-J., Liu, P., Nielsen, A. A. K., Brophy, J. A. N., Clancy, K., Peterson, T., & Voigt, C. A. (2013) · Nature Methods · doi:10.1038/nmeth.2515 · Cited by 477
Improved Thermodynamic Parameters and Helix Initiation Factor to Predict Stability of DNA Duplexes
Sugimoto, N., Nakano, S., Yoneyama, M., & Honda, K.-I. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.22.4501 · Cited by 468
Self-citationR-loop-mediated genomic instability is caused by impairment of replication fork progressionPreprint
Gan, W., Guan, Z., Liu, J., Gui, T., Shen, K., Manley, J. L., & Xialu Li, C. (2011) · Genes & Development · doi:10.1101/gad.17010011 · Cited by 459
“For example, it has been known for some time that G-rich regions in nascent transcripts favor R-loop formation due to the exceptional stability of rG:dC base pairs (Sugimoto et al. 1995).”
BackgroundIncreasing the specificity of CRISPR systems with engineered RNA secondary structures
Kocak, D. D., Josephs, E. A., Bhandarkar, V., Adkar, S. S., Kwon, J. B., & Gersbach, C. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0095-1 · Cited by 351
Gene Designer: a synthetic biology tool for constructing artificial DNA segments
Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., & Govindarajan, S. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-285 · Cited by 379
“The DNA melting temperature calculation is performed using the nearest neighbor method[47,48].”
MethodChen, L., Chen, J., Zhang, X., Gu, Y., Xiao, R., Shao, C., Tang, P., Qian, H., Luo, D., Li, H., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.008 · Cited by 373
“…debate whether a postulated G-quadruplex is involved (Duquette et al., 2004; Roy et al., 2008), whereas C-rich template sequences are thought to permit stronger RNA/DNA base-pairing to compete with DNA/DNA base-pairing in order to enhance and stabilize R-loop formation (Sugimoto et al., 1995).”
InfluentialAdvancement of the emerging field of RNA nanotechnology
Jasinski, D., Haque, F., Binzel, D. W., & Guo, P. (2017) · ACS Nano · doi:10.1021/acsnano.6b05737 · Cited by 352
Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a
Strohkendl, I., Saifuddin, F. A., Rybarski, J. R., Finkelstein, I. J., & Russell, R. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.043 · Cited by 357
Hydration Regulates Thermodynamics of G-Quadruplex Formation under Molecular Crowding Conditions
Miyoshi, D., Karimata, H. T., & Sugimoto, N. (2006) · Journal of the American Chemical Society · doi:10.1021/ja061267m · Cited by 346
Self-citationModulation of the Helicase Activity of eIF4A by eIF4B, eIF4H, and eIF4F
Rogers, G. W., Richter, N. J., Lima, W. F., & Merrick, W. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m100157200 · Cited by 339
A model of molecular interactions on short oligonucleotide microarrays
Zhang, L., Miles, M. F., & Aldape, K. (2003) · Nature Biotechnology · doi:10.1038/nbt836 · Cited by 320
In vitro selection, characterization, and application of deoxyribozymes that cleave RNA
Silverman, S. K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki930 · Cited by 306
“A proposed rule of thumb for designing the binding arms is that each arm should have a binding free energy (DG ) of at least 10– 12 kcal/mol (72), as calculated on the basis of tabulated RNA:DNA interaction energies (79).”
BackgroundMolecular crowding effects on structure and stability of DNA
Miyoshi, D., & Sugimoto, N. (2008) · Biochimie · doi:10.1016/j.biochi.2008.02.009 · Cited by 290
“Short oligomer nucleic acids are suitable for quantitative studies because their structure association and dissociation are often in a two-state transition, which allows us to evaluate thermodynamic parameters under various conditions [61,62].”
BackgroundSelf-citationDwight, Z., Palais, R. A., & Wittwer, C. T. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr065 · Cited by 258
“Gotoh, 1983; Markham and Zuker, 2005; Poland, 1974; Steger, 1994; Tostesen, 2003; Zimm, 1960) to predict fluorescent melting analysis of PCR products in a rich web application.”
BackgroundPredicting oligonucleotide affinity to nucleic acid targets
Mathews, D. H., Burkard, M. E., Freier, S. M., Wyatt, J. R., & Turner, D. H. (1999) · RNA · doi:10.1017/s1355838299991148 · Cited by 247
Stable RNA nanoparticles as potential new generation drugs for cancer therapy
Shu, Y., Pi, F., Sharma, A. K., Rajabi, M., Haque, F., Shu, D., Leggas, M. L., Evers, B. M., & Guo, P. (2013) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2013.11.006 · Cited by 247
“varieties of RNA motifs such as helices, loops, bulges, stems, hairpins, and pseudoknots to specify rich 3D architectures; 2) it possesses both canonical and noncanonical base pairings [43–45], as well as base stacking capabilities for inter- or intra-molecular interaction [46,47]; 3) it displays unique features in tr…”
Prediction of rho-independent transcriptional terminators in Escherichia coli
Lesnik, E. A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.17.3583 · Cited by 239
“The free energy of hybrid duplex formation mirrors this observed inhibition, with stability as follows: rGG:dCC > rCC:dGG >> rAA:dTT >> rUU:dAA (24).”
MethodCDK9-dependent RNA polymerase II pausing controls transcription initiation
Gressel, S., Schwalb, B., Decker, T.-M., Qin, W., Leonhardt, H., Eick, D., & Cramer, P. (2017) · eLife · doi:10.7554/elife.29736 · Cited by 247
“DNA-RNA and DNA-DNA melting temperature calculation The gene-wise mean melting temperature of the DNA-RNA and DNA-DNA hybrid was calculated from subsequent melting temperature estimates of 8-base pair DNA-RNA and DNA-DNA duplexes tiling the respective area according to (SantaLucia, 1998; Sugimoto et al., 1995).”
MethodThermodynamics of internal C.T mismatches in DNA
Allawi, H. T. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.11.2694 · Cited by 235
The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwinding
Pang, P. S., Jankowsky, E., Planet, P. J., & Pyle, A. M. (2002) · The EMBO Journal · doi:10.1093/emboj/21.5.1168 · Cited by 222
Drolet, M. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.05006.x · Cited by 213
LaFleur, T. L., Hossain, A., & Salis, H. M. (2022) · Nature Communications · doi:10.1038/s41467-022-32829-5 · Cited by 202
“For example, for all UP sequences, we calculate the minor groove width of the distal and proximal UP sites 45 ; for all ITR sequences, we calculate the thermodynamic stability of the R-loop 46,47 ; for all spacer sequences, we calculate the local DNA rigidity 48 .”
MethodNaef, F., & Magnasco, M. O. (2003) · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics · doi:10.1103/physreve.68.011906 · Cited by 201
The newly discovered Q motif of DEAD‐box RNA helicases regulates RNA‐binding and helicase activity
Cordin, O., Tanner, N. K., Doère, M., et al. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600272 · Cited by 199
“The duplex stability was calculated according to Sugimoto et al (1995) and Turner et al (1988).”
MethodYilmaz, L. S., Parnerkar, S., & Noguera, D. R. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01733-10 · Cited by 196
“The supporting software (UNAFold [15]) and parameter database (20) of mathFISH are publicly available, as well as the description of the mathematical models used (8, 24–26).”
MethodR loops stimulate genetic instability of CTG·CAG repeats
Lin, Y., Dent, S., Wilson, J. H., Wells, R. D., & Напиерала, М. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909740107 · Cited by 199
Sequence-Dependent Thermodynamic Parameters for Locked Nucleic Acid (LNA)−DNA Duplex Formation
McTigue, P. M., Peterson, R. J., & Kahn, J. D. (2004) · Biochemistry · doi:10.1021/bi035976d · Cited by 194
Applied Force Reveals Mechanistic and Energetic Details of Transcription Termination
Larson, M. H., Greenleaf, W. J., Landick, R. C., & Block, S. M. (2008) · Cell · doi:10.1016/j.cell.2008.01.027 · Cited by 190
“It is computed to form the weakest duplex: 4 kBT, based on nearest-neighbor interaction energies (Sugimoto et al., 1995).”
Determining the influence of structure on hybridization using oligonucleotide arrays
Mir, K. U., & Southern, E. M. (1999) · Nature Biotechnology · doi:10.1038/11732 · Cited by 177
“In these cases, duplex stability, and hence, melting behavior, can be calculated with reasonable accuracy from nearest-neighbor thermodynamic parameter”
MethodUi‐Tei, K., Naito, Y., Zenno, S., Nishi, K., Yamato, K., Takahashi, F., Juni, A., & Saigo, K. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn042 · Cited by 180
“Melting temperature (Tm) was calculated based on the nearest-neighbor model (26) and the thermodynamic values for RNA–RNA (27) and RNA–DNA (28).”
BackgroundMethodEffects of RNA secondary structure on cellular antisense activity
Vickers, T. A. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.6.1340 · Cited by 177
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry
Lalanne, J., Taggart, J., Guo, M. S., Herzel, L., Schieler, A., & Li, G. (2018) · Cell · doi:10.1016/j.cell.2018.03.007 · Cited by 175
“…see below), stability of the U-tract’s RNA/DNA hybrid ΔGU (for the 8 nt immediately upstream of the 3’ end, computed with a nearest-neighbor model (Sugimoto et al., 1995)), number of U’s in the U-tract nU (total number of U’s in the 8 nt upstream of the 3’ end), hairpin free energy (see…”
MethodPrykhozhij, S. V., Rajan, V., Gaston, D., & Berman, J. N. (2015) · PLoS ONE · doi:10.1371/journal.pone.0119372 · Cited by 173
“We implemented the thermodynamical nearest-neighbor Tm prediction originally provided by Sugimoto et al.,1995 [31] and based on a previous implementation in MELTING [32].”
BackgroundMethodCRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Alkan, F., Wenzel, A., Anthon, C., Havgaard, J. H., & Gorodkin, J. (2018) · Genome biology · doi:10.1186/s13059-018-1534-x · Cited by 174
Interactions between RNA polymerase and the “core recognition element” counteract pausing
Vvedenskaya, I. O., Vahedian-Movahed, H., Bird, J. G., Knoblauch, J. G., Goldman, S. R., Zhang, Y., Ebright, R. H., & Nickels, B. E. (2014) · Science · doi:10.1126/science.1253458 · Cited by 178
Biosensor-based microRNA detection: techniques, design, performance, and challenges
Johnson, B. N., & Mutharasan, R. (2014) · The Analyst · doi:10.1039/c3an01677c · Cited by 172
The yeast Pif1p DNA helicase preferentially unwinds RNA DNA substrates
Boulé, J.-B., & Zakian, V. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm613 · Cited by 163
“hybrids of high GC content are predicted to be more stable in solution than their DNA–DNA counterparts (18).”
BackgroundDeoxyribozymes with 2‘−5‘ RNA Ligase Activity
Flynn-Charlebois, A., Wang, Y., Prior, T. K., Rashid, I., Manthei, K. A., Coppins, R. L., Wolf, A. C., & Silverman, S. K. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028774y · Cited by 163
Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level
Herrero‐Galán, E., Fuentes-Perez, M. E., Carrasco, C., Valpuesta, J., Carrascosa, J. L., Moreno‐Herrero, F., & Arias‐Gonzalez, J. R. (2012) · Journal of the American Chemical Society · doi:10.1021/ja3054755 · Cited by 161
Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosomePreprint
Tanaka, N., Aronova, A., & Schwer, B. (2007) · Genes & Development · doi:10.1101/gad.1580507 · Cited by 159
Stability and Mismatch Discrimination of Locked Nucleic Acid–DNA Duplexes
Owczarzy, R., You, Y., Groth, C. L., & Tataurov, A. V. (2011) · Biochemistry · doi:10.1021/bi200904e · Cited by 164
Cotranscriptional processes and their influence on genome stabilityPreprint
Xialu Li, C., & Manley, J. L. (2006) · Genes & Development · doi:10.1101/gad.1438306 · Cited by 158
“This is consistent with the fact that the exceptional stability of the rG/dC base pairs (Sugimoto et al. 1995) facilitates R-loop formation by favoring RNA:DNA over DNA:DNA hybrids in regions where the nontemplate strand is G-rich, such as the S regions (Gritzmacher 1989).”
BackgroundSimulation-guided DNA probe design for consistently ultraspecific hybridization
Wang, J. S., & Zhang, D. Y. (2015) · Nature Chemistry · doi:10.1038/nchem.2266 · Cited by 156
“ΔΔG° values for RNA are incomplete in literature [37, 38].”
Time-resolved structural analysis of an RNA-cleaving DNA catalyst
Borggräfe, J., Victor, J., Rosenbach, H., et al. (2021) · Nature · doi:10.1038/s41586-021-04225-4 · Cited by 156
Kumar, R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.6.1272 · Cited by 152
Sequence-dependent Kinetic Model for Transcription Elongation by RNA Polymerase
Bai, L., Shundrovsky, A., & Wang, M. D. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.08.107 · Cited by 150
“An additional contribution to this discrepancy could arise from the uncertainties in the state energy calculations (w1 kBT), which are due to uncertainties in the available experimental thermodynamic values for DNA–DNA or RNA–DNA duplexes.(11,12) Biochemically, it has been difficult to identify unique or consensus pau…”
BackgroundCairns, M. J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg378 · Cited by 146
“In the case of the rU-dA pairing there is a relatively weak interaction consisting of two hydrogen bonds (13).”
BackgroundOptimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays
Urakawa, H., Fantroussi, S. E., Smidt, H., et al. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.5.2848-2856.2003 · Cited by 146
“0001), indicate that the stability of DNA-DNA duplexes and RNA-DNA duplexes is sequence dependent (20, 23) and underscore the difficulty in a priori prediction of duplex stability using currently available models (H.”
MethodFurther Characterization of the Helicase Activity of eIF4A
Rogers, G. W., Lima, W. F., & Merrick, W. C. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m007560200 · Cited by 145
Effects of single-walled carbon nanotubes on the polymerase chain reaction
Cui, D., Tian, F., Kong, Y., et al. (2003) · Nanotechnology · doi:10.1088/0957-4484/15/1/030 · Cited by 145
Josephs, E. A., Koçak, D. D., Fitzgibbon, C. J., McMenemy, J., Gersbach, C. A., & Marszałek, P. E. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv892 · Cited by 147
“Sequence-dependent DNA:DNA hybridization free energies G◦(x)DNA:DNA were obtained from (30); sequence-dependent RNA:DNA hybridization free energies G◦(x)RNA:DNA were obtained from (31); and G◦(x)RNA:DNA values in cases of introduced point mismatches rG·dG, rC·dC, rA·dA and rU·dT were obtained from (32) (under slightly…”
BackgroundTemperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation
Wu, P., Nakano, S., & Sugimoto, N. (2002) · European Journal of Biochemistry · doi:10.1046/j.1432-1033.2002.02970.x · Cited by 142
“It should be noted that the published NN-model parameters were generally extracted from the temperature-independent thermodynamic data [17,19,21,22,25].”
InfluentialSelf-citationMELTING, computing the melting temperature of nucleic acid duplex
Novère, N. G. L. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.12.1226 · Cited by 143
“…et al. (1986); SantaLucia et al. (1996); Sugimoto et al. (1996), and Allawi and SantaLucia (1997) (the default) for the homoduplexes DNA/DNA, of Freier et al. (1986) and Xia et al. (1998) (the default) for the homoduplexes RNA/RNA, and of Sugimoto et al. (1995) for the heteroduplexes DNA/RNA.”
Target site selection for an RNA-cleaving catalytic DNA
Cairns, M. J., Hopkins, T. M., Witherington, C., et al. (1999) · Nature Biotechnology · doi:10.1038/8658 · Cited by 140
“To gain some appreciation of the relationship between heteroduplex stability and cleavage activity, the ΔG° was predicted for each deoxyribozyme (by the nearest neighbor metho”
MethodRoberts, C. C., Bandaru, R., & Switzer, C. (1997) · Journal of the American Chemical Society · doi:10.1021/ja970123s · Cited by 139
Mitigating off-target effects in CRISPR/Cas9-mediated in vivo gene editing
Han, H. A., Pang, J. K. S., & Soh, B.-S. (2020) · Journal of Molecular Medicine · doi:10.1007/s00109-020-01893-z · Cited by 134
“The underlying mechanism behind this change in specificity is unknown and intriguing given that an increase in GC content usually stabilises the hybridisation of RNA to DNA [51].”
BackgroundGuo, P., Haque, F., Hallahan, B. J., Reif, R. D., & Li, H. (2012) · Nucleic Acid Therapeutics · doi:10.1089/nat.2012.0350 · Cited by 132
“, 2010), base stacking properties (Searle and Williams, 1993; Sugimoto et al., 1995), and various in vivo attributes (Chang and Tinoco, 1994; Guo et al.”
InfluentialInterplay between DNA sequence and negative superhelicity drives R-loop structures
Stolz, R., Sulthana, S., Hartono, S. R., Malig, M., Benham, C., & Chédin, F. (2019) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1819476116 · Cited by 118
Structure, stability and behaviour of nucleic acids in ionic liquids
Tateishi‐Karimata, H., & Sugimoto, N. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku499 · Cited by 130
“Buffer containing 4 M NaCl was used, given that previous quantitative analyses of DNA duplex stabilities were performed in this solution (56).”
MethodSelf-citationLi, H., Lee, T., Dziubla, T. D., Pi, F., Guo, S., Xu, J., Li, C., Haque, F., Liang, X., & Guo, P. (2015) · Nano Today · doi:10.1016/j.nantod.2015.09.003 · Cited by 129
Yang, S., Chen, S., Liu, S., Tang, X., Qin, L., Qiu, G.-H., Chen, J.-X., & Chen, W. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03084 · Cited by 124
Catalytic Nucleic Acids: From Lab to Applications
Sun, L., Cairns, M. J., Saravolac, E. G., Baker, A., & Gerlach, W. L. (2000) · Pharmacological Reviews · doi:10.1016/s0031-6997(24)01455-8 · Cited by 121
“Factors other than length that tend to increase the heteroduplex stability include the general GC content and specific pyrimidine’s content of the DNA component (Ratmeyer et al., 1994; Sugimoto et al., 1995; Gyi et al., 1998).”
Lin, Y., & Wilson, J. H. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00739-07 · Cited by 120
“Due to the exceptional stability of rG:dC base pairs (68), R-loops tend to form when the template FIG.”
BackgroundA Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies
Culviner, P. H., Guegler, C. K., & Laub, M. T. (2020) · mBio · doi:10.1128/mbio.00010-20 · Cited by 121
“We used the default nearest-neighbor calculation table for RNA-DNA 218 hybrids(12).”
MethodFelder, S., Meierhoff, K., Sane, A. P., et al. (2001) · The Plant Cell · doi:10.1105/tpc.010090 · Cited by 121
“Because RNA-RNA hybrids are more stable than DNA-RNA hybrids under the chosen hybridization conditions (Sugimoto et al., 1995), this concurrent reaction results in psbT-psbH nonprocessed RNAs that have hybridized both the psbN RNA and the 5 psbH single-stranded DNA probe.”
BackgroundToulokhonov, I., & Landick, R. C. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00439-8 · Cited by 119
“…termination and bypass ( G‡, Flap Domain Mediates Pause Hairpin Action 1131 Molecular Cell 1132 (A) Structures of intrinsic terminators with the G of formation (in kcal/mol at 1 M NaCl and 37 C) for the terminator hairpin alone (red; Zuker, 2003) and the 8 bp hybrid (black; Sugimoto et al., 1995).”
BackgroundActivation of different split functionalities on re-association of RNA–DNA hybrids
Afonin, K. A., Viard, M., Martins, A. N., Lockett, S., Maciag, A. E., Freed, E. O., Heldman, E., Jaeger, L., Blumenthal, R. P., & Shapiro, B. A. (2013) · Nature Nanotechnology · doi:10.1038/nnano.2013.44 · Cited by 118
Jang, K., Jeong, S., Kang, D. Y., Sp, N., Yang, Y. M., & Kim, D. (2020) · Scientific Reports · doi:10.1038/s41598-020-61432-1 · Cited by 113
Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent In Situ Hybridization
Yilmaz, L. S., & Noguera, D. R. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.12.7126-7139.2004 · Cited by 113
Farasat, I., & Salis, H. M. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004724 · Cited by 114
“These nearest-neighbor free energies are designated as ΔG and ΔG, and may be calculated using previously developed free energy models that have been parameterized using calorimetry measurements [52,53,54,55].”
BackgroundMethodInfluentialDeveloping RT-LAMP assays for rapid diagnosis of SARS-CoV-2 in saliva
Huang, X., Tang, G., Ismail, N., & Wang, X. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103736 · Cited by 110
“25,26 To avoid potential primer cross-reactivity due to low sequence complexity, a stretch of continuous same nucleotides was not allowed (4 C’s, 4 G’s, 5 A’s, or 5 T’s).”
Hu, Y., Rolfs, A., Bhullar, B., Murthy, T. V. S., Zhu, C., Berger, M. F., Camargo, A. A., Kelley, F., McCarron, S., Jepson, D., et al. (2007) · Genome Research · doi:10.1101/gr.6037607 · Cited by 112
“For Phases Three and Four, first-step PCR, optimal gene-specific primers were designed using a modified nearestneighbor algorithm (Sugimoto et al. 1995).”
MethodTranscriptional Pausing at +62 of the HIV-1 Nascent RNA Modulates Formation of the TAR RNA Structure
Palangat, M., Meier, T. I., Keene, R. G., & Landick, R. C. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80103-3 · Cited by 108
“2 kcal/mol more stable than Does the HIV-1 Pause Play a Rolea 39-terminal hybrid (Sugimoto et al., 1995).”
BackgroundA Boost for the Emerging Field of RNA Nanotechnology
Shukla, G. C., Haque, F., Tor, Y., Wilhelmsson, L. M., Toulmé, J., Isambert, H., Guo, P., Rossi, J. J., Tenenbaum, S. A., & Shapiro, B. A. (2011) · ACS Nano · doi:10.1021/nn200989r · Cited by 109
Poliovirus RNA-dependent RNA Polymerase (3Dpol) Is Sufficient for Template Switchingin Vitro
Arnold, J. J., & Cameron, C. E. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.5.2706 · Cited by 106
Thermodynamics of base pairing
Turner, D. H. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80047-9 · Cited by 104
Microarrays for identifying binding sites and probing structure of RNAs
Kierzek, R., Turner, D. H., & Kierzek, E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1303 · Cited by 104
“In this approach: (i) the probes are 5- or 6-nucleotides long and based on the natural 2′-O-methylated backbone because single-stranded regions within natural RNAs are short and 2′-O-methylRNA/RNA duplexes are more stable (38) than RNA/RNA (39) or DNA/RNA (40) duplexes, and (ii) the probes are modified to make hybridi…”
BackgroundInfluentialRNA nanotechnology for computer design and in vivo computation
Meikang Qiu, A., Khisamutdinov, E. F., Zhao, Z. J., Pan, C., Choi, J., Leontis, N. B., & Guo, P. (2013) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2012.0310 · Cited by 103
“RNA secondary structures are stabilized largely by nearest-neighbour interactions that can be measured in model systems [77,78].”
BackgroundManaging the sequence-specificity of antisense oligonucleotides in drug discovery
Hagedorn, P., Hansen, B. R., Koch, T., & Lindow, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx056 · Cited by 109
“Thermodynamic parameters are different for DNA– RNA binding compared with DNA–DNA binding (82,83) and DNA–RNA binding is also affected by chemical modifications such as LNA (84,85).”
BackgroundKankia, B. I., & Marky, L. A. (1999) · The Journal of Physical Chemistry B · doi:10.1021/jp991614x · Cited by 103
Chen, S. X., & Seelig, G. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b00277 · Cited by 103
CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context
Corsi, G. I., Qu, K., Alkan, F., Pan, X., Luo, Y., & Gorodkin, J. (2022) · Nature Communications · doi:10.1038/s41467-022-30515-0 · Cited by 104
The α‐ L ‐Threofuranosyl‐(3′→2′)‐oligonucleotide System (‘TNA'): Synthesis and Pairing Properties
Schöning, K., Scholz, P., Wu, X., Guntha, S., Delgado, G., Krishnamurthy, R., & Eschenmoser, A. (2002) · Helvetica Chimica Acta · doi:10.1002/hlca.200290000 · Cited by 102
Hendrix, D. A. (2019) · doi:10.5399/osu/1140 · Cited by 100
Suppression of Smooth Muscle Cell Proliferation by a c-myc RNA-cleaving Deoxyribozyme
Sun, L., Cairns, M. J., Gerlach, W. L., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.24.17236 · Cited by 99
Metadata
- Authors
- Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M.
- Affiliations
- Konan University (JP)
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 1995-09-05
- Volume
- 34
- Issue
- 35
- Pages
- 11211-11216
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- OpenAlex
- W2010759469
- Semantic Scholar
- 5a5921b07eda10a7cfa0f9410e5f8048ae2d9247
- Cited by
- 697
- References
- 23
- Citations by year
- 2026: 23 · 2025: 21 · 2024: 35 · 2023: 19 · 2022: 23 · 2021: 23 · 2020: 25 · 2019: 27 · 2018: 17 · 2017: 23 · 2016: 23 · 2015: 23 · 2014: 27 · 2013: 30 · 2012: 26
- FWCI
- 2.85
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced biosensing and bioanalysis techniques
- Keywords
- hybrid stability, oligonucleotide duplexes, UV melting, circular dichroism, initiation factors
- MeSH terms
- Base Sequence, Circular Dichroism, DNA, Drug Stability, Molecular Sequence Data, Nucleic Acid Conformation, Nucleic Acid Hybridization, Oligodeoxyribonucleotides, Oligoribonucleotides, RNA, Thermodynamics, Molecular Structure
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
