Citizendia
Your Ad Here

DNA denaturation, also called DNA melting, is the process by which double-stranded deoxyribonucleic acid unwinds and separates into single-stranded strands through the breaking of hydrogen bonding between the bases. Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen 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 urea. Urea is an Organic compound with the Chemical formula ( N[[hydrogen H]]22 C[[oxygen O]] For multiple copies of DNA molecules, the melting temperature (Tm) is defined as the temperature at which half of the DNA strands are in the double-helical state and half are in the "random-coil" states. [1] The melting temperature depends on both the length of the molecule, and the specific nucleotide sequence composition of that molecule. Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group

Contents

Applications of DNA denaturation

The process of DNA denaturation can be used to analyze some aspects of DNA. Because cytosine / guanine base-pairing is generally stronger than adenosine / thymine base-pairing, the amount of cytosine and guanine in a genome (called the "GC content") can be estimated by measuring the temperature at which the genomic DNA melts. GC-content (or guanine-cytosine content in molecular biology is the percentage of Nitrogenous bases on a DNA molecule which are either Guanine or [2] Higher temperatures are associated with high GC content.

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 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 genetic distance between two species, a process known as DNA-DNA hybridization. For 'genetic distance' in the context of a Genetic map, see Centimorgan Genetic distance is a measure of the dissimilarity of genetic DNA-DNA hybridization generally refers to a Molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences [3] 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 temperature gradient gel electrophoresis. Temperature Gradient Gel Electrophoresis ( TGGE) and Denaturing Gradient Gel Electrophoresis (DGGE are forms of Electrophoresis where there is a temperature [4][5]

Methods of DNA analysis based on melting temperature have the disadvantage of being proxies for studying the underlying sequence; DNA sequencing is generally considered a more accurate method. The term DNA sequencing encompasses biochemical methods for determining the order of the Nucleotide bases Adenine, Guanine, Cytosine

The process of DNA melting is also used in molecular biology techniques, notably in the polymerase chain reaction (PCR). Although the temperature of DNA melting is not diagnostic in the technique, methods for estimating Tm 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, eg. the oligonucleotide probes of DNA microarrays. For terminology see glossary below A DNA microarray is a High-throughput technology used in Molecular biology and in

Methods for estimating Tm

Several formulas are used to calculate Tm values. [6][7] Some formulas are more accurate in predicting melting temperatures of DNA duplexes. [8]

Wallace method

The fastest and less accurate Wallace method is suitable for oligos less than 18mers in length by counting the frequency of each nucleotide base. An oligonucleotide (or oligo) is a short segment of RNA or DNA, typically with twenty or fewer bases. The reasoning behind the method is that, because cytosine-guanine pairs form three hydrogen bonds compared to the two hydrogen bonds between adenosine and thymine, they contribute more to the stability of a double-helix.

Tm = 2(A + T) + 3(G + C)

Nearest-neighbor method

This is far more accurate method used to predict melting temperatures of nucleic acid duplexes. Although GC content plays a large factor in the hybridization energy of double-stranded DNA, interactions between neighboring bases along the helix means that stacking energies are significant. The nearest-neighbor model accounts for this by considering adjacent bases along the backbone two-at-a-time. [1] Each of these has enthalpic and entropic parameters, the sums of which determine melting temperature according to the following equation:

T_\mbox{m}=\frac{\Delta H }{\Delta S+R \ln(C_1-\frac{C_2}{2})}-273.15 \ ^\circ \mbox{C}
where
ΔH is the standard enthalpy and ΔS is the standard entropy for formation of the duplex from two single strands,
C1 is the initial concentration of the single strand that is in excess (usually probe, primer),
C2 is the initial concentration of the complementary strand that is limiting (usually target),
R is the universal gas constant \left (\mbox{1.987}\frac{\mbox{cal}}{\mbox{mol} \cdot \mbox{K}} \right). In Thermodynamics and molecular chemistry, the enthalpy (denoted as H, h, or rarely as χ) is a quotient or description of In Thermodynamics (a branch of Physics) entropy, symbolized by S, is a measure of the unavailability of a system ’s Energy Relationship with the Boltzmann constant The Boltzmann constant kB (often abbreviated k) may be used in place of the gas constant by working

Standard enthalpies and entropies are negative for the annealing reaction and are assumed to be temperature independent. If C1 > > C2 then C2 can be neglected.


Table 1. Unified nearest-neighbor parameters for DNA/DNA duplexes. [1] Note that the ΔH values are given in kilocalories per mole and that the ΔS values are given in calories per mole per kelvin.

Nearest-neighbor sequence
(5'-3'/5'-3')		 ΔH
kcal/mol		 ΔS
cal/(mol·K)
AA/TT -7. 9 -22. 2
AG/CT -7. 8 -21. 0
AT/AT -7. 2 -20. 4
AC/GT -8. 4 -22. 4
GA/TC -8. 2 -22. 2
GG/CC -8. 0 -19. 9
GC/GC -9. 8 -24. 4
TA/TA -7. 2 -21. 3
TG/CA -8. 5 -22. 7
CG/CG -10. 6 -27. 2
Terminal A-T base pair 2. 3 4. 1
Terminal G-C base pair 0. 1 -2. 8

References

  1. ^ a b c John SantaLucia Jr. (1998). "A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics". Proc. Natl. Acad. Sci. USA 95 (4): 1460–5. doi:10.1073/pnas.95.4.1460. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  [1]
  2. ^ M. Mandel and J. Marmur (1968). "Use of Ultravialet Absorbance-Temperature Profile for Determining the Guanine plus Cytosine Content of DNA". Methods in Enzymology 12 (2): 198–206. ISBN 978-0-12-181856-2.  
  3. ^ C. G. Sibley and J. E. Ahlquist (1984). "The Phylogeny of the Hominoid Primates, as Indicated by DNA-DNA Hybridization". Journal of Molecular Evolution 20: 2–15. doi:10.1007/BF02101980. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  4. ^ R. M. Myers, T. Maniatis, and L. S. Lerman (1987). "Detection and Localization of Single Base Changes by Denaturing Gradient Gel Electrophoresis". Methods in Enzymology 155: 501–527. ISBN 978-0-12-182056-5.  
  5. ^ T. Po, G. Steger, V. Rosenbaum, J. Kaper, and D. Riesner (1987). "Double-stranded cucumovirus associated RNA 5: experimental analysis of necrogenic and non-necrogenic variants by temperature-gradient gel electrophoresis". Nucleic Acids Research 15 (13): 5069–5083. doi:10.1093/nar/15.13.5069. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.  
  6. ^ Breslauer, K. J. et al. (1986). "Predicting DNA Duplex Stability from the Base Sequence". Proc. Natl. Acad. Sci. USA. 83: 3746–3750. doi:10.1073/pnas.83.11.3746. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.   (pdf)
  7. ^ Rychlik, W. et al. (1990) Nucleic Acids Res. 18, 6409-6412.
  8. ^ Owczarzy R. , Vallone P. M. , Gallo F. J. , Paner T. M. , Lane M. J. and Benight A. S (1997). "Predicting sequence-dependent melting stability of short duplex DNA oligomers". Biopolymers 44: 217–239. doi:10.1002/(SICI)1097-0282(1997)44:3<217::AID-BIP3>3.0.CO;2-Y. A digital object identifier ( DOI) is a permanent identifier given to an Electronic document.   (pdf)

See also

External links

© 2009 citizendia.org; parts available under the terms of GNU Free Documentation License, from http://en.wikipedia.org
 Dapyx Software network: MP3 Explorer | Ebook Manager | Zenithic