1960:
sequences containing mismatches; the number of DNA melting experiments needed to get reliable data for so many groups would be inconveniently high. However, other means exist to access thermodynamic parameters of nucleic acids: microarray technology allows hybridization monitoring of tens of thousands sequences in parallel. This data, in combination with molecular adsorption theory allows the determination of many thermodynamic parameters in a single experiment and to go beyond the nearest neighbor model. In general the predictions from the nearest neighbor method agree reasonably well with experimental results, but some unexpected outlying sequences, calling for further insights, do exist. Finally, we should also mention the increased accuracy provided by single molecule unzipping assays which provide a wealth of new insight into the thermodynamics of DNA hybridization and the validity of the nearest-neighbour model as well.
1133:°) are related to each other. From the observation of melting temperatures one can experimentally determine the thermodynamic parameters. Vice versa, and important for applications, when the thermodynamic parameters of a given nucleic acid sequence are known, the melting temperature can be predicted. It turns out that for oligonucleotides, these parameters can be well approximated by the nearest-neighbor model.
1986:
1972:
1935:
The nearest-neighbor model can be extended beyond the Watson-Crick pairs to include parameters for interactions between mismatches and neighboring base pairs. This allows the estimation of the thermodynamic parameters of sequences containing isolated mismatches, like e.g. (arrows indicating mismatch)
474:
values. Some formulas are more accurate in predicting melting temperatures of DNA duplexes. For DNA oligonucleotides, i.e. short sequences of DNA, the thermodynamics of hybridization can be accurately described as a two-state process. In this approximation one neglects the possibility of intermediate
123:
is used in laboratory practice. However, due to the different molecular geometries of the nucleotides, a single inconsistency between the two strands will make binding between them less energetically favorable. Measuring the effects of base incompatibility by quantifying the temperature at which two
1959:
A more realistic way of modeling the behavior of nucleic acids would seem to be to have parameters that depend on the neighboring groups on both sides of a nucleotide, giving a table with entries like "TCG/AGC". However, this would involve around 32 groups for Watson-Crick pairing and even more for
174:
DNA denaturation can also be used to detect sequence differences between two different DNA sequences. DNA is heated and denatured into single-stranded state, and the mixture is cooled to allow strands to rehybridize. Hybrid molecules are formed between similar sequences and any differences between
1239:
Except for the C/G initiation term, the first term represents the free energy of the first base pair, CG, in the absence of a nearest neighbor. The second term includes both the free energy of formation of the second base pair, GC, and stacking interaction between this base pair and the previous
1421:
1108:
As mentioned, this equation is based on the assumption that only two states are involved in melting: the double stranded state and the random-coil state. However, nucleic acids may melt via several intermediate states. To account for such complicated behavior, the methods of
475:
partial binding states in the formation of a double strand state from two single stranded oligonucleotides. Under this assumption one can elegantly describe the thermodynamic parameters for forming double-stranded nucleic acid AB from single-stranded nucleic acids A and B.
1638:
933:
1095:
166:
The process of DNA denaturation can be used to analyze some aspects of DNA. Because cytosine / guanine base-pairing is generally stronger than adenine / thymine base-pairing, the amount of cytosine and guanine in a genome is called its
208:
are important for determining the appropriate temperatures to use in a protocol. DNA melting temperatures can also be used as a proxy for equalizing the hybridization strengths of a set of molecules, e.g. the oligonucleotide probes of
118:
will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily. In order to reduce the diversity and obtain the most energetically preferred complexes, a technique called
783:
670:, occurs when half of the double-stranded nucleic acid has dissociated. If no additional nucleic acids are present, then , , and will be equal, and equal to half the initial concentration of double-stranded nucleic acid,
1245:
1931:
The parameters associated with the ten groups of neighbors shown in table 1 are determined from melting points of short oligonucleotide duplexes. It works out that only eight of the ten groups are independent.
1145:, the nearest-neighbor model treats a DNA helix as a string of interactions between 'neighboring' base pairs. So, for example, the DNA shown below has nearest-neighbor interactions indicated by the arrows.
183:. In the context of a single isolated region of DNA, denaturing gradient gels and temperature gradient gels can be used to detect the presence of small mismatches between two sequences, a process known as
2310:
Sponer, J; Sponer, JE; Mládek, A; Jurečka, P; Banáš, P; Otyepka, M (December 2013). "Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment".
1517:
658:
128:, also referred to as melting. In the absence of external negative factors, the processes of hybridization and melting may be repeated in succession indefinitely, which lays the ground for
1468:
155:. Both terms are used to refer to the process as it occurs when a mixture is heated, although "denaturation" can also refer to the separation of DNA strands induced by chemicals like
542:
437:
Stacking is the stabilizing interaction between the flat surfaces of adjacent bases. Stacking can happen with any face of the base, that is 5'-5', 3'-3', and vice versa.
2969:
1750:
1723:
1696:
816:
1495:
951:
2509:
Owczarzy R.; Vallone P.M.; Gallo F.J.; Paner T.M.; Lane M.J.; Benight A.S (1997). "Predicting sequence-dependent melting stability of short duplex DNA oligomers".
1141:
The interaction between bases on different strands depends somewhat on the neighboring bases. Instead of treating a DNA helix as a string of interactions between
124:
strands anneal can provide information as to the similarity in base sequence between the two strands being annealed. The complexes may be dissociated by thermal
67:
sequence. DNA, when in a state where its two strands are dissociated (i.e., the dsDNA molecule exists as two independent strands), is referred to as having been
2200:"Double-stranded cucumovirus associated RNA 5: experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophoresis"
946:° are usually given for the association and not the dissociation reaction (see the nearest-neighbor method for example). This formula then turns into:
1416:{\displaystyle \Delta G_{37}^{\circ }(\mathrm {total} )=\Delta G_{37}^{\circ }(\mathrm {initiations} )+\sum _{i=1}^{10}n_{i}\Delta G_{37}^{\circ }(i)}
679:
184:
2174:
2084:
1956:
These parameters have been fitted from melting experiments and an extension of Table 1 which includes mismatches can be found in literature.
175:
those sequences will result in a disruption of the base-pairing. On a genomic scale, the method has been used by researchers to estimate the
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2962:
2829:
282:
171:
and can be estimated by measuring the temperature at which the genomic DNA melts. Higher temperatures are associated with high GC content.
2535:
455:
Contribution of stacking to the free energy of the molecule can be experimentally estimated by observing the bent-stacked equilibrium in
226:
95:
2913:
3072:
3062:
459:. Such stabilization is dependent on the sequence. The extent of the stabilization varies with salt concentrations and temperature.
85:
2522:
190:
Methods of DNA analysis based on melting temperature have the disadvantage of being proxies for studying the underlying sequence;
3181:
3052:
3057:
2955:
2943:
Nearest
Neighbor Database: Provides a description of RNA-RNA interaction nearest neighbor parameters and examples of their use.
1633:{\displaystyle \Delta G^{\circ }(\mathrm {total} )=\Delta H_{\mathrm {total} }^{\circ }-T\Delta S_{\mathrm {total} }^{\circ }}
2890:
577:
2895:
1651:° have been determined for the ten possible pairs of interactions. These are given in Table 1, along with the value of Δ
3019:
3009:
1240:
base pair. The remaining terms are similarly defined. In general, the free energy of forming a nucleic acid duplex is
2999:
2866:
266:
140:
125:
68:
2848:
2100:
C.G. Sibley; J.E. Ahlquist (1984). "The
Phylogeny of the Hominoid Primates, as Indicated by DNA-DNA Hybridization".
3171:
3004:
2004:
258:
2250:
Protozanova E, Yakovchuk P, Frank-Kamenetskii MD (2004). "Stacked–Unstacked
Equilibrium at the Nick Site of DNA".
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2994:
262:
198:
129:
103:
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contributes and helps in formation of a helix. Stacking is the main stabilizing factor in the DNA double helix.
1429:
274:
1470:
represents the free energy associated with one of the ten possible the nearest-neighbor nucleotide pairs, and
2648:"The effects of mismatches on hybridization in DNA microarrays: Determination of nearest neighbor parameters"
2448:
1662:° for the DNA duplex shown above is calculated to be −22.4 kJ/mol. The experimental value is −21.8 kJ/mol.
2871:
3176:
3166:
3039:
3029:
2978:
2064:
Use of
Ultraviolet Absorbance-Temperature Profile for Determining the Guanine plus Cytosine Content of DNA
38:
253:
to allow proper hydrogen bonding to occur. The term annealing is often used to describe the binding of a
3047:
1110:
180:
144:
132:. Most commonly, the pairs of nucleic bases A=T and G≡C are formed, of which the latter is more stable.
269:) of reverse-complementary strands that were separated by heat (thermally denatured). Proteins such as
2780:
2565:
2411:
2109:
445:
441:
201:. Although the temperature of DNA melting is not diagnostic in the technique, methods for estimating
2611:
John SantaLucia Jr., John; Donald Hicks (June 2004). "The thermodynamics of DNA structural motifs".
486:
3108:
3077:
120:
2770:
2711:
2700:"Probing hybridization parameters from microarray experiments: Nearest-neighbor model and beyond"
2133:
928:{\displaystyle T_{m}={\frac {\Delta H^{\circ }}{\Delta S^{\circ }-R\ln {\frac {_{initial}}{2}}}}}
449:
152:
2880:
2843:
3014:
2986:
2808:
2739:
2677:
2628:
2593:
2554:"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics"
2526:
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2439:
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2180:
2170:
2158:
2152:
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2021:
1991:
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1705:
1678:
1090:{\displaystyle T_{m}={\frac {\Delta H^{\circ }}{\Delta S^{\circ }+R\ln(_{total}-_{total}/2)}}}
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2624:
2351:"Base-stacking and base-pairing contributions into thermal stability of the DNA double helix"
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Detection and
Localization of Single Base Changes by Denaturing Gradient Gel Electrophoresis
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2072:
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2062:
176:
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Huguet, J. M.; Bizarro, C. V.; Forns, N.; Smith, S. B.; Bustamante, C.; Ritort, F. (2010).
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246:
107:
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https://web.archive.org/web/20080516194508/http://www.promega.com/biomath/calc11.htm#disc
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The process of DNA melting is also used in molecular biology techniques, notably in the
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444:, specifically electrostatic attraction among aromatic rings, a process also known as
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1999:
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is the kelvin temperature of the reaction. This gives, for the nucleic acid system,
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The previous paragraph shows how melting temperature and thermodynamic parameters (Δ
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2026:
99:
91:
17:
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778:{\displaystyle T_{m}=-{\frac {\Delta G^{\circ }}{R\ln {\frac {_{initial}}{2}}}}}
148:
53:
34:
1971:
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1985:
1967:
674:. This gives an expression for the melting point of a nucleic acid duplex of
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242:
168:
64:
2759:"Single-molecule derivation of salt dependent base-pair free energies in DNA"
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2215:
2793:
2424:
2016:
1142:
544:. According to the Van´t Hoff equation, the relation between free energy, Δ
254:
156:
102:
into a single complex, which in the case of two strands is referred to as a
52:) is defined as the temperature at which half of the DNA strands are in the
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2632:
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unwinds and separates into single-stranded strands through the breaking of
2597:
2530:
2495:
2462:"Optimization of the annealing temperature for DNA amplification in vitro"
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2233:
2184:
2129:
2947:
2725:
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222:
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Table 1. Nearest-neighbor parameters for DNA/DNA duplexes in 1 M NaCl.
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can help DNA anneal. DNA strand annealing is a key step in pathways of
3098:
2904:
2121:
278:
2698:
Hadiwikarta, W. W.; Walter, J. C.; Hooyberghs, J.; Carlon, E. (2012).
2523:
10.1002/(SICI)1097-0282(1997)44:3<217::AID-BIP3>3.0.CO;2-Y
2398:
Breslauer, K.J.; Frank, R; Blöcker, H; Marky, LA; et al. (1986).
2324:
2942:
2932:
250:
2924:"Discovery of the Hybrid Helix and the First DNA-RNA Hybridization"
440:
Stacking in "free" nucleic acid molecules is mainly contributed by
143:, also called DNA melting, is the process by which double-stranded
2775:
2716:
1165:
The free energy of forming this DNA from the individual strands, Δ
270:
245:. Before annealing can occur, one of the strands may need to be
160:
2951:
1655:° calculated at 37 °C. Using these values, the value of Δ
1113:
must be used, which is especially relevant for long sequences.
3128:
3123:
1117:
Estimating thermodynamic properties from nucleic acid sequence
234:
230:
115:
111:
42:
2198:
T. Po; G. Steger; V. Rosenbaum; J. Kaper; D. Riesner (1987).
1512:°, parameters, so the change in free energy is also given by
2349:
Yakovchuk, P; Protozanova, E; Frank-Kamenetskii, MD (2006).
2937:
265:. The term is also often used to describe the reformation (
63:
depends on the length of the DNA molecule and its specific
27:
Study of how temperature affects the nucleic acid structure
2400:"Predicting DNA Duplex Stability from the Base Sequence"
2876:, melting profile, mismatches, free energy calculations
2613:
Annual Review of
Biophysics and Biomolecular Structure
2646:
Hooyberghs, J.; Van
Hummelen, P.; Carlon, E. (2009).
1735:
1708:
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1432:
1248:
954:
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682:
653:{\displaystyle \Delta G^{\circ }=-RT\ln {\frac {}{}}}
580:
489:
94:, sequence-specific interaction between two or more
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2460:Rychlik, W.; Spencer, W. J.; Rhoads, R. E. (1990).
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1462:
1415:
1089:
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448:. For biological systems with water as a solvent,
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2243:
2157:. Methods in Enzymology. Vol. 155. pp.
2067:. Methods in Enzymology. Vol. 12. pp.
285:is a major pathway of homologous recombination.
194:is generally considered a more accurate method.
90:Hybridization is the process of establishing a
2909:calculation using the Nearest-neighbour method
2344:
2342:
483:The equilibrium constant for this reaction is
294:Melting stability of base pair stacks (B DNA)
2963:
2547:
2545:
2543:
2151:R.M. Myers; T. Maniatis; L.S. Lerman (1987).
8:
2048:Tools and Techniques in Biomolecular Science
151:stacking attractions between the bases. See
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1463:{\displaystyle \Delta G_{37}^{\circ }(i)}
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2625:10.1146/annurev.biophys.32.110601.141800
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185:temperature gradient gel electrophoresis
179:between two species, a process known as
2050:. Oxford University Press. p. 243.
2038:
1941: ↓↓↓
467:Several formulas are used to calculate
1497:represents its count in the sequence.
2693:
2691:
1169:°, is represented (at 37 °C) as
463:Thermodynamics of the two-state model
7:
283:synthesis-dependent strand annealing
2872:DNA thermodynamics calculations – T
568:is the ideal gas law constant, and
1736:
1709:
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1613:
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1607:
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56:or single-stranded (ssDNA) state.
45:(dsDNA). The melting temperature (
25:
2905:AnnHyb Open Source software for T
86:Hybridization (molecular biology)
1984:
1970:
2933:uMelt: Melting Curve Prediction
2102:Journal of Molecular Evolution
1554:
1534:
1457:
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537:{\displaystyle K={\frac {}{}}}
528:
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499:
1:
2914:Sigma-aldrich technical notes
2863:calculations in OligoAnalyzer
2061:M. Mandel; J. Marmur (1968).
2849:Resources in other libraries
2552:John SantaLucia Jr. (1998).
2167:10.1016/0076-6879(87)55033-9
2077:10.1016/0076-6879(67)12133-2
1914:
1900:
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2867:Integrated DNA Technologies
1150: ↓ ↓ ↓ ↓ ↓
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31:Nucleic acid thermodynamics
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2835:Nucleic acid hybridization
2763:Proc. Natl. Acad. Sci. USA
2558:Proc. Natl. Acad. Sci. USA
2404:Proc. Natl. Acad. Sci. USA
2005:Primer (molecular biology)
1671:Nearest-neighbor sequence
241:to form a double-stranded
83:
3139:Nucleic acid double helix
2844:Resources in your library
2264:10.1016/j.jmb.2004.07.075
1915:
1901:
1887:
1873:
1859:
1845:
1831:
1817:
1803:
1789:
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663:The melting temperature,
277:. In particular, during
263:polymerase chain reaction
261:to a DNA strand during a
199:polymerase chain reaction
130:polymerase chain reaction
71:by the high temperature.
1745:{\displaystyle \Delta G}
1718:{\displaystyle \Delta S}
1691:{\displaystyle \Delta H}
275:homologous recombination
3182:Biochemical engineering
2794:10.1073/pnas.1001454107
2425:10.1073/pnas.83.11.3746
1951:3' C-C-T-G-G-C-T-G-C 5'
1946:5' G-G-A-C-T-G-A-C-G 3'
1916:Terminal G/C base pair
1902:Terminal A/T base pair
1504:° term has enthalpic, Δ
1137:Nearest-neighbor method
227:complementary sequences
3040:Nucleic acid structure
2979:Biomolecular structure
2704:Nucleic Acids Research
2652:Nucleic Acids Research
2579:10.1073/pnas.95.4.1460
2478:10.1093/nar/18.21.6409
2355:Nucleic Acids Research
2216:10.1093/nar/15.13.5069
2204:Nucleic Acids Research
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257:, or the binding of a
39:nucleic acid structure
2290:Nucleic acid database
2286:"Definition of terms"
2046:Divan, Royds (2013).
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1490:{\displaystyle n_{i}}
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1111:statistical mechanics
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249:by an enzyme such as
181:DNA-DNA hybridization
145:deoxyribonucleic acid
2007:for calculations of
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1188:(C/G initiation) + Δ
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817:
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442:intermolecular force
33:is the study of how
3109:Protein engineering
2919:Primer3 calculation
2785:2010PNAS..10715431H
2570:1998PNAS...95.1460S
2416:1986PNAS...83.3746B
2114:1984JMolE..20....2S
1667:
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229:of single-stranded
41:of double-stranded
18:Annealing (biology)
2726:10.1093/nar/gks475
2664:10.1093/nar/gkp109
2367:10.1093/nar/gkj454
2122:10.1007/BF02101980
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450:hydrophobic effect
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153:Hydrophobic effect
3172:Molecular biology
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2987:Protein structure
2830:Library resources
2472:(21): 6409–6412.
2466:Nucleic Acids Res
2410:(11): 3746–3750.
2325:10.1002/bip.22322
2210:(13): 5069–5083.
2176:978-0-12-182056-5
2086:978-0-12-181856-2
2022:Complementary DNA
1992:Technology portal
1929:
1928:
1236:(A/T initiation)
1160:3' G-C-A-A-C-T 5'
1155:5' C-G-T-T-G-A 3'
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811:is also given by
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16:(Redirected from
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3134:Structural motif
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1422:
1420:
1419:
1414:
1402:
1397:
1385:
1384:
1374:
1369:
1348:
1309:
1304:
1286:
1265:
1260:
1161:
1156:
1151:
1096:
1094:
1093:
1088:
1086:
1084:
1077:
1072:
1071:
1041:
1040:
998:
997:
984:
983:
982:
969:
964:
963:
934:
932:
931:
926:
924:
922:
921:
916:
915:
914:
877:
863:
862:
849:
848:
847:
834:
829:
828:
784:
782:
781:
776:
774:
772:
771:
766:
765:
764:
727:
715:
714:
713:
700:
692:
691:
659:
657:
656:
651:
649:
647:
633:
613:
593:
592:
543:
541:
540:
535:
533:
531:
517:
497:
296:
177:genetic distance
141:DNA denaturation
108:Oligonucleotides
21:
3197:
3196:
3192:
3191:
3190:
3188:
3187:
3186:
3152:
3151:
3148:
3143:
3087:
3034:
2981:
2976:
2908:
2899:
2884:
2875:
2862:
2855:
2854:
2853:
2838:
2837:
2833:
2826:
2821:
2820:
2769:(35): 15431–6.
2756:
2755:
2751:
2697:
2696:
2689:
2645:
2644:
2640:
2610:
2609:
2605:
2551:
2550:
2541:
2508:
2507:
2503:
2459:
2458:
2454:
2397:
2396:
2392:
2348:
2347:
2340:
2309:
2308:
2304:
2294:
2292:
2284:
2283:
2279:
2249:
2248:
2241:
2197:
2196:
2192:
2177:
2150:
2149:
2145:
2099:
2098:
2094:
2087:
2060:
2059:
2055:
2045:
2044:
2040:
2035:
2012:
1990:
1983:
1976:
1969:
1966:
1950:
1945:
1940:
1756:
1755:
1731:
1730:
1726:
1704:
1703:
1699:
1677:
1676:
1672:
1661:
1524:
1516:
1515:
1477:
1472:
1471:
1428:
1427:
1376:
1244:
1243:
1235:
1227:
1219:
1211:
1203:
1195:
1187:
1180:(predicted) = Δ
1179:
1159:
1154:
1149:
1139:
1119:
1104:
1100:
1051:
1020:
989:
985:
974:
970:
955:
950:
949:
888:
878:
854:
850:
839:
835:
820:
815:
814:
810:
738:
728:
716:
705:
701:
683:
678:
677:
673:
669:
634:
614:
584:
576:
575:
518:
498:
485:
484:
472:
465:
306:
305:
291:
219:
211:DNA microarrays
206:
138:
88:
82:
77:
61:
50:
28:
23:
22:
15:
12:
11:
5:
3195:
3193:
3185:
3184:
3179:
3174:
3169:
3164:
3154:
3153:
3145:
3144:
3142:
3141:
3136:
3131:
3126:
3121:
3116:
3111:
3106:
3104:Protein domain
3101:
3095:
3093:
3089:
3088:
3086:
3085:
3083:Thermodynamics
3080:
3075:
3070:
3065:
3060:
3055:
3050:
3044:
3042:
3036:
3035:
3033:
3032:
3030:Thermodynamics
3027:
3022:
3017:
3012:
3007:
3002:
2997:
2991:
2989:
2983:
2982:
2977:
2975:
2974:
2967:
2960:
2952:
2946:
2945:
2940:
2935:
2930:
2928:Alexander Rich
2921:
2916:
2911:
2906:
2902:
2897:
2893:
2888:
2882:
2878:
2873:
2869:
2860:
2852:
2851:
2846:
2840:
2839:
2828:
2827:
2825:
2824:External links
2822:
2819:
2818:
2749:
2687:
2638:
2603:
2539:
2517:(3): 217–239.
2501:
2452:
2390:
2338:
2319:(12): 978–88.
2302:
2277:
2258:(3): 775–785.
2239:
2190:
2175:
2143:
2092:
2085:
2053:
2037:
2036:
2034:
2031:
2030:
2029:
2024:
2019:
2014:
2010:
2002:
1996:
1995:
1981:
1978:Biology portal
1965:
1962:
1954:
1953:
1948:
1943:
1927:
1926:
1923:
1920:
1917:
1913:
1912:
1909:
1906:
1903:
1899:
1898:
1895:
1892:
1889:
1885:
1884:
1881:
1878:
1875:
1871:
1870:
1867:
1864:
1861:
1857:
1856:
1853:
1850:
1847:
1843:
1842:
1839:
1836:
1833:
1829:
1828:
1825:
1822:
1819:
1815:
1814:
1811:
1808:
1805:
1801:
1800:
1797:
1794:
1791:
1787:
1786:
1783:
1780:
1777:
1773:
1772:
1769:
1766:
1763:
1759:
1758:
1753:
1741:
1738:
1728:
1714:
1711:
1701:
1687:
1684:
1674:
1673:(5'-3'/3'-5')
1659:
1627:
1621:
1618:
1615:
1612:
1609:
1604:
1600:
1597:
1594:
1589:
1583:
1580:
1577:
1574:
1571:
1566:
1562:
1559:
1556:
1552:
1549:
1546:
1543:
1540:
1536:
1531:
1527:
1523:
1484:
1480:
1459:
1456:
1453:
1448:
1443:
1439:
1435:
1412:
1409:
1406:
1401:
1396:
1392:
1388:
1383:
1379:
1373:
1368:
1365:
1362:
1358:
1354:
1351:
1347:
1344:
1341:
1338:
1335:
1332:
1329:
1326:
1323:
1320:
1317:
1313:
1308:
1303:
1299:
1295:
1292:
1289:
1285:
1282:
1279:
1276:
1273:
1269:
1264:
1259:
1255:
1251:
1233:
1225:
1217:
1209:
1201:
1193:
1185:
1177:
1163:
1162:
1157:
1152:
1138:
1135:
1118:
1115:
1102:
1098:
1083:
1080:
1076:
1070:
1067:
1064:
1061:
1058:
1054:
1050:
1047:
1044:
1039:
1036:
1033:
1030:
1027:
1023:
1019:
1016:
1013:
1010:
1007:
1004:
1001:
996:
992:
988:
981:
977:
973:
967:
962:
958:
919:
913:
910:
907:
904:
901:
898:
895:
891:
887:
884:
881:
875:
872:
869:
866:
861:
857:
853:
846:
842:
838:
832:
827:
823:
808:
769:
763:
760:
757:
754:
751:
748:
745:
741:
737:
734:
731:
725:
722:
719:
712:
708:
704:
698:
695:
690:
686:
671:
667:
646:
643:
640:
637:
632:
629:
626:
623:
620:
617:
611:
608:
605:
602:
599:
596:
591:
587:
583:
530:
527:
524:
521:
516:
513:
510:
507:
504:
501:
495:
492:
481:
480:
470:
464:
461:
433:
432:
429:
423:
422:
419:
409:
408:
405:
395:
394:
391:
381:
380:
377:
371:
370:
367:
357:
356:
353:
343:
342:
339:
333:
332:
329:
319:
318:
315:
309:
308:
303:
300:
290:
287:
247:phosphorylated
243:polynucleotide
239:hydrogen bonds
221:Annealing, in
218:
215:
204:
192:DNA sequencing
137:
134:
84:Main article:
81:
78:
76:
73:
59:
48:
26:
24:
14:
13:
10:
9:
6:
4:
3:
2:
3194:
3183:
3180:
3178:
3177:Biotechnology
3175:
3173:
3170:
3168:
3167:Nucleic acids
3165:
3163:
3160:
3159:
3157:
3150:
3140:
3137:
3135:
3132:
3130:
3127:
3125:
3122:
3120:
3117:
3115:
3112:
3110:
3107:
3105:
3102:
3100:
3097:
3096:
3094:
3090:
3084:
3081:
3079:
3076:
3074:
3071:
3069:
3068:Determination
3066:
3064:
3061:
3059:
3056:
3054:
3051:
3049:
3046:
3045:
3043:
3041:
3037:
3031:
3028:
3026:
3023:
3021:
3018:
3016:
3015:Determination
3013:
3011:
3008:
3006:
3003:
3001:
2998:
2996:
2993:
2992:
2990:
2988:
2984:
2980:
2973:
2968:
2966:
2961:
2959:
2954:
2953:
2950:
2944:
2941:
2939:
2936:
2934:
2931:
2929:
2925:
2922:
2920:
2917:
2915:
2912:
2910:
2903:
2901:
2894:
2892:
2889:
2886:
2879:
2877:
2870:
2868:
2864:
2857:
2856:
2850:
2847:
2845:
2842:
2841:
2836:
2831:
2823:
2814:
2810:
2805:
2800:
2795:
2790:
2786:
2782:
2777:
2772:
2768:
2764:
2760:
2753:
2750:
2745:
2741:
2736:
2731:
2727:
2723:
2718:
2713:
2709:
2705:
2701:
2694:
2692:
2688:
2683:
2679:
2674:
2669:
2665:
2661:
2657:
2653:
2649:
2642:
2639:
2634:
2630:
2626:
2622:
2618:
2614:
2607:
2604:
2599:
2595:
2590:
2585:
2580:
2575:
2571:
2567:
2564:(4): 1460–5.
2563:
2559:
2555:
2548:
2546:
2544:
2540:
2537:
2532:
2528:
2524:
2520:
2516:
2512:
2505:
2502:
2497:
2493:
2488:
2483:
2479:
2475:
2471:
2467:
2463:
2456:
2453:
2450:
2445:
2441:
2436:
2431:
2426:
2421:
2417:
2413:
2409:
2405:
2401:
2394:
2391:
2386:
2382:
2377:
2372:
2368:
2364:
2361:(2): 564–74.
2360:
2356:
2352:
2345:
2343:
2339:
2334:
2330:
2326:
2322:
2318:
2314:
2306:
2303:
2291:
2287:
2281:
2278:
2273:
2269:
2265:
2261:
2257:
2253:
2246:
2244:
2240:
2235:
2231:
2226:
2221:
2217:
2213:
2209:
2205:
2201:
2194:
2191:
2186:
2182:
2178:
2172:
2168:
2164:
2160:
2156:
2155:
2147:
2144:
2139:
2135:
2131:
2127:
2123:
2119:
2115:
2111:
2107:
2103:
2096:
2093:
2088:
2082:
2078:
2074:
2070:
2066:
2065:
2057:
2054:
2049:
2042:
2039:
2032:
2028:
2025:
2023:
2020:
2018:
2015:
2013:
2006:
2003:
2001:
2000:Melting point
1998:
1997:
1993:
1987:
1982:
1979:
1973:
1968:
1963:
1961:
1957:
1949:
1944:
1939:
1938:
1937:
1933:
1924:
1921:
1918:
1910:
1907:
1904:
1896:
1893:
1890:
1882:
1879:
1876:
1868:
1865:
1862:
1854:
1851:
1848:
1840:
1837:
1834:
1826:
1823:
1820:
1812:
1809:
1806:
1798:
1795:
1792:
1784:
1781:
1778:
1770:
1767:
1764:
1739:
1729:
1712:
1702:
1685:
1675:
1670:
1669:
1663:
1658:
1654:
1650:
1646:
1641:
1625:
1602:
1595:
1592:
1587:
1564:
1557:
1529:
1525:
1513:
1511:
1507:
1503:
1498:
1482:
1478:
1454:
1446:
1441:
1437:
1424:
1407:
1399:
1394:
1390:
1381:
1377:
1371:
1366:
1363:
1360:
1356:
1352:
1306:
1301:
1297:
1290:
1262:
1257:
1253:
1241:
1237:
1231:
1223:
1215:
1207:
1199:
1191:
1183:
1175:
1170:
1168:
1158:
1153:
1148:
1147:
1146:
1144:
1136:
1134:
1132:
1128:
1124:
1116:
1114:
1112:
1106:
1078:
1074:
1068:
1065:
1062:
1059:
1056:
1048:
1042:
1037:
1034:
1031:
1028:
1025:
1017:
1008:
1005:
1002:
999:
994:
990:
979:
975:
965:
960:
956:
947:
945:
941:
936:
917:
911:
908:
905:
902:
899:
896:
893:
885:
882:
873:
870:
867:
864:
859:
855:
844:
840:
830:
825:
821:
812:
807:
803:
799:
795:
791:
786:
767:
761:
758:
755:
752:
749:
746:
743:
735:
732:
723:
720:
717:
710:
706:
696:
693:
688:
684:
675:
666:
661:
641:
638:
627:
618:
609:
606:
603:
600:
597:
594:
589:
585:
573:
571:
567:
563:
559:
555:
551:
547:
525:
522:
511:
502:
493:
490:
478:
477:
476:
473:
462:
460:
458:
453:
451:
447:
443:
438:
428:
425:
424:
418:
414:
411:
410:
404:
400:
397:
396:
390:
386:
383:
382:
376:
373:
372:
366:
362:
359:
358:
352:
348:
345:
344:
338:
335:
334:
328:
324:
321:
320:
314:
311:
310:
301:
298:
297:
288:
286:
284:
280:
276:
272:
268:
264:
260:
256:
252:
248:
244:
240:
236:
232:
228:
224:
216:
214:
212:
207:
200:
195:
193:
188:
186:
182:
178:
172:
170:
164:
162:
158:
154:
150:
146:
142:
135:
133:
131:
127:
122:
117:
113:
109:
105:
101:
100:nucleic acids
97:
96:complementary
93:
87:
80:Hybridization
79:
74:
72:
70:
66:
62:
55:
51:
44:
40:
36:
32:
19:
3149:
3119:Nucleic acid
3082:
2896:Invitrogen T
2834:
2766:
2762:
2752:
2710:(18): e138.
2707:
2703:
2655:
2651:
2641:
2616:
2612:
2606:
2561:
2557:
2514:
2510:
2504:
2469:
2465:
2455:
2407:
2403:
2393:
2358:
2354:
2316:
2312:
2305:
2293:. Retrieved
2289:
2280:
2255:
2251:
2207:
2203:
2193:
2153:
2146:
2105:
2101:
2095:
2063:
2056:
2047:
2041:
2027:Western blot
2008:
1958:
1955:
1934:
1930:
1656:
1652:
1648:
1644:
1642:
1514:
1509:
1505:
1501:
1499:
1425:
1242:
1238:
1229:
1221:
1213:
1205:
1197:
1189:
1181:
1173:
1171:
1166:
1164:
1140:
1130:
1126:
1122:
1120:
1107:
948:
943:
939:
937:
813:
805:
801:
797:
793:
789:
787:
676:
664:
662:
574:
569:
565:
561:
557:
553:
549:
545:
482:
468:
466:
454:
439:
436:
426:
416:
412:
402:
398:
388:
384:
374:
364:
360:
350:
346:
336:
326:
322:
312:
267:renaturation
225:, means for
220:
202:
196:
189:
173:
165:
139:
136:Denaturation
126:denaturation
92:non-covalent
89:
57:
46:
37:affects the
30:
29:
2900:calculation
2885:calculation
2619:: 415–440.
2511:Biopolymers
2313:Biopolymers
2108:(1): 2–15.
1643:Values of Δ
1228:(GA/CT) + Δ
1220:(TG/AC) + Δ
1212:(TT/AA) + Δ
1204:(GT/CA) + Δ
1196:(CG/GC) + Δ
938:The terms Δ
446:pi stacking
307:(Kcal/mol)
302:Melting ΔG°
237:to pair by
149:hydrophobic
98:strands of
54:random coil
35:temperature
3156:Categories
3114:Proteasome
3073:Prediction
3063:Quaternary
3020:Prediction
3010:Quaternary
2658:(7): e53.
2252:J Mol Biol
2033:References
1727:J/(mol·K)
1143:base pairs
479:AB ↔ A + B
457:nicked DNA
169:GC-content
65:nucleotide
3053:Secondary
3000:Secondary
2776:1010.1188
2717:1211.1303
2017:Base pair
1737:Δ
1710:Δ
1683:Δ
1626:∘
1599:Δ
1593:−
1588:∘
1561:Δ
1530:∘
1522:Δ
1447:∘
1434:Δ
1400:∘
1387:Δ
1357:∑
1307:∘
1294:Δ
1263:∘
1250:Δ
1129:° & Δ
1043:−
1009:
995:∘
987:Δ
980:∘
972:Δ
874:
865:−
860:∘
852:Δ
845:∘
837:Δ
788:Because Δ
724:
711:∘
703:Δ
697:−
610:
598:−
590:∘
582:Δ
255:DNA probe
217:Annealing
157:formamide
121:annealing
69:denatured
3092:See also
3058:Tertiary
3005:Tertiary
2813:20716688
2744:22661582
2682:19270064
2633:15139820
2385:16449200
2333:23784745
2272:15342236
1964:See also
1097:, where
564:, where
289:Stacking
223:genetics
75:Concepts
3099:Protein
3048:Primary
2995:Primary
2938:Tm Tool
2804:2932562
2781:Bibcode
2735:3467032
2673:2673445
2598:9465037
2566:Bibcode
2531:9591477
2496:2243783
2444:3459152
2412:Bibcode
2376:1360284
2295:4 April
2234:3601667
2185:3431470
2159:501–527
2138:6658046
2130:6429338
2110:Bibcode
2069:198–206
1757:kJ/mol
1700:kJ/mol
1647:° and Δ
942:° and Δ
672:initial
279:meiosis
3078:Design
3025:Design
2832:about
2811:
2801:
2742:
2732:
2680:
2670:
2631:
2596:
2586:
2529:
2494:
2487:332522
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2331:
2270:
2232:
2225:305948
2222:
2183:
2173:
2136:
2128:
2083:
1897:−7.66
1888:GG/CC
1883:−9.36
1880:−102.1
1874:GC/CG
1869:−9.07
1866:−113.8
1860:CG/GC
1855:−5.51
1846:GA/CT
1841:−5.40
1832:CT/GA
1827:−6.09
1818:GT/CA
1813:−6.12
1804:CA/GT
1799:−2.50
1790:TA/AT
1785:−3.67
1776:AT/TA
1771:−4.26
1762:AA/TT
1500:Each Δ
1426:where
1125:° or Δ
548:, and
431:-2.70
421:-2.04
407:-1.97
393:-1.66
379:-1.27
369:-1.04
355:-1.29
341:-1.44
331:-0.78
317:-0.12
259:primer
251:kinase
104:duplex
2771:arXiv
2712:arXiv
2589:19045
2536:(pdf)
2449:(pdf)
2134:S2CID
1925:4.05
1922:−11.7
1911:4.31
1894:−83.3
1891:−33.5
1877:−41.0
1863:−44.4
1852:−92.9
1849:−34.3
1838:−87.9
1835:−32.6
1824:−93.7
1821:−35.1
1810:−95.0
1807:−35.6
1796:−89.1
1793:−30.1
1782:−85.4
1779:−30.1
1768:−92.9
1765:−33.1
1103:total
1099:total
792:° = Δ
299:Step
271:RAD52
114:, or
2809:PMID
2740:PMID
2678:PMID
2629:PMID
2594:PMID
2527:PMID
2492:PMID
2440:PMID
2381:PMID
2329:PMID
2297:2019
2268:PMID
2230:PMID
2181:PMID
2171:ISBN
2126:PMID
2081:ISBN
1908:17.2
552:is Δ
161:urea
3162:DNA
3129:RNA
3124:DNA
2926:by
2799:PMC
2789:doi
2767:107
2730:PMC
2722:doi
2668:PMC
2660:doi
2621:doi
2584:PMC
2574:doi
2519:doi
2482:PMC
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2371:PMC
2363:doi
2321:doi
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2212:doi
2163:doi
2118:doi
2073:doi
1919:0.4
1905:9.6
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796:° -
560:ln
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427:G C
417:G T
415:or
413:A C
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401:or
399:C C
389:T C
387:or
385:G A
375:A T
365:T T
363:or
361:A A
351:C T
349:or
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337:C G
327:C A
325:or
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313:T A
235:RNA
233:or
231:DNA
159:or
116:RNA
112:DNA
43:DNA
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