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base pair
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{{short description|Unit consisting of two nucleobases bound to each other by hydrogen bonds}}(File:DNA base-pair diagram.jpg|thumb|upright=1.4|The chemical structure of DNA base-pairs)A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, “WatsonâCrick” (or “WatsonâCrickâFranklin“) base pairs (guanineâcytosine and adenineâthymine)JOURNAL, Spencer M, The stereochemistry of deoxyribonucleic acid. II. Hydrogen-bonded pairs of bases, Acta Crystallographica, 10 January 1959, 12, 1, 66â71, 10.1107/S0365110X59000160,scripts.iucr.org/cgi-bin/paper?S0365110X59000160, en, 0365-110X, allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence.BOOK, Sequence-Dependent Variability of B-DNA, 10.1007/0-387-29148-2_2, DNA Conformation and Transcription, 18â34, 2005, Zhurkin VB, Tolstorukov MY, Xu F, Colasanti AV, Olson WK, 978-0-387-25579-8, The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes.Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA), where WatsonâCrick base pairs (guanineâcytosine and adenineâuracil) permit the formation of short double-stranded helices, and a wide variety of nonâWatsonâCrick interactions (e.g., GâU or AâA) allow RNAs to fold into a vast range of specific three-dimensional structures. In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into the amino acid sequence of proteins via the genetic code.The size of an individual gene or an organism’s entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres). The haploid human genome (23 chromosomes) is estimated to be about 3.2 billion bases long and to contain 20,000â25,000 distinct protein-coding genes.WEB, Moran LA,sandwalk.blogspot.com/2011/03/how-big-is-human-genome.html, The total size of the human genome is very likely to be ~3,200 Mb, Sandwalk.blogspot.com, 2011-03-24, 2012-07-16, WEB,www.strategicgenomics.com/Genome/index.htm, The finished length of the human genome is 2.86 Gb, Strategicgenomics.com, 2006-06-12, 2012-07-16, JOURNAL, ((International Human Genome Sequencing Consortium)), Finishing the euchromatic sequence of the human genome, Nature, 431, 7011, 931â945, October 2004, 15496913, 10.1038/nature03001, free, 2004Natur.431..931H, A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA.JOURNAL, Cockburn AF, Newkirk MJ, Firtel RA, Organization of the ribosomal RNA genes of Dictyostelium discoideum: mapping of the nontranscribed spacer regions, Cell, 9, 4 Pt 1, 605â613, December 1976, 1034500, 10.1016/0092-8674(76)90043-X, 31624366, The total number of DNA base pairs on Earth is estimated at 5.0{{e|37}} with a weight of 50 billion tonnes.NEWS, Nuwer R, Rachel Nuwer, 18 July 2015, Counting All the DNA on Earth,www.nytimes.com/2015/07/21/science/counting-all-the-dna-on-earth.html,ghostarchive.org/archive/20220101/https://www.nytimes.com/2015/07/21/science/counting-all-the-dna-on-earth.html, 2022-01-01, limited, The New York Times, New York, 0362-4331, 2015-07-18, {{cbignore}} In comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC (trillion tons of carbon).WEB,www.agci.org/classroom/biosphere/index.php, The Biosphere: Diversity of Life, Aspen Global Change Institute, Basalt, CO, 2015-07-19, 2014-11-10,www.agci.org/classroom/biosphere/index.php," title="web.archive.org/web/20141110164609www.agci.org/classroom/biosphere/index.php,">web.archive.org/web/20141110164609www.agci.org/classroom/biosphere/index.php, dead, - the content below is remote from Wikipedia
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Hydrogen bonding and stability
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Examples
The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5â²-end to the 3â²-end; thus, the bottom strand is written 3â² to 5â².
A base-paired DNA sequence:
{{code|ATCGATTGAGCTCTAGCG}}
{{code|TAGCTAACTCGAGATCGC}}
The corresponding RNA sequence, in which uracil is substituted for thymine in the RNA strand:
{{code|AUCGAUUGAGCUCUAGCG}}
{{code|UAGCUAACUCGAGAUCGC}}
Base analogs and intercalators
Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly point mutations) in DNA replication and DNA transcription. This is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its enol form.JOURNAL, Trautner TA, Swartz MN, Kornberg A, Enzymatic synthesis of deoxyribonucleic acid. X. Influence of bromouracil substitutions on replication, Proceedings of the National Academy of Sciences of the United States of America, 48, 3, 449â455, March 1962, 13922323, 220799, 10.1073/pnas.48.3.449, vanc, free, Other chemicals, known as DNA intercalators, fit into the gap between adjacent bases on a single strand and induce frameshift mutations by “masquerading” as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. Most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine.BOOK, Krebs JE, Goldstein ES, Kilpatrick ST, Lewin B, Lewin’s genes XII, Jones & Bartlett Learning, 2018, 978-1-284-10449-3, 12th, Burlington, Mass, 12, Genes are DNA and Encode RNAs and Polypeptides, Each mutagenic event in the presence of an acridine results in the addition or removal of a single base pair., {{citation needed|date=August 2022}}Mismatch repair
Mismatched base pairs can be generated by errors of DNA replication and as intermediates during homologous recombination. The process of mismatch repair ordinarily must recognize and correctly repair a small number of base mispairs within a long sequence of normal DNA base pairs. To repair mismatches formed during DNA replication, several distinctive repair processes have evolved to distinguish between the template strand and the newly formed strand so that only the newly inserted incorrect nucleotide is removed (in order to avoid generating a mutation).JOURNAL, Putnam CD, Strand discrimination in DNA mismatch repair, DNA Repair, 105, 103161, September 2021, 34171627, 8785607, 10.1016/j.dnarep.2021.103161, The proteins employed in mismatch repair during DNA replication, and the clinical significance of defects in this process are described in the article DNA mismatch repair. The process of mispair correction during recombination is described in the article gene conversion.Length measurements
File:Human karyotype with bands and sub-bands.png|thumb|Schematic karyogram of a human. The blue scale to the left of each nuclear chromosome pair (as well as the mitochondrial genomemitochondrial genomeThe following abbreviations are commonly used to describe the length of a D/RNA molecule:- bp = base pairâone bp corresponds to approximately 3.4 Ã (340 pm)BOOK, Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K, Walter P, Molecular Biology of the Cell, December 2014, Garland Science, Taylor & Francis Group, New York/Abingdon, 978-0-8153-4432-2, 177, 6th, alberts_mboc, of length along the strand, and to roughly 618 or 643 daltons for DNA and RNA respectively.
- kb (= kbp) = kiloâbase-pair = 1,000 bp
- Mb (= Mbp) = megaâbase-pair = 1,000,000 bp
- Gb (= Gbp) = gigaâbase-pair = 1,000,000,000 bp
Unnatural base pair (UBP)
{{See also|Artificial gene synthesis|Expanded genetic code|Nucleic acid analogue|Synthetic genomics}}An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base pairs found in nature, A-T (adenine â thymine) and G-C (guanine â cytosine). A few research groups have been searching for a third base pair for DNA, including teams led by Steven A. Benner, Philippe Marliere, Floyd E. Romesberg and Ichiro Hirao.NEWS,www.utsandiego.com/news/2014/may/08/tp-life-engineered-with-expanded-genetic-code/, Life engineered with expanded genetic code, Fikes BJ, May 8, 2014, San Diego Union Tribune, 8 May 2014, dead,www.utsandiego.com/news/2014/may/08/tp-life-engineered-with-expanded-genetic-code/," title="web.archive.org/web/20140509001048www.utsandiego.com/news/2014/may/08/tp-life-engineered-with-expanded-genetic-code/,">web.archive.org/web/20140509001048www.utsandiego.com/news/2014/may/08/tp-life-engineered-with-expanded-genetic-code/, 9 May 2014, Some new base pairs based on alternative hydrogen bonding, hydrophobic interactions and metal coordination have been reported.JOURNAL, Yang Z, Chen F, Alvarado JB, Benner SA, Amplification, mutation, and sequencing of a six-letter synthetic genetic system, Journal of the American Chemical Society, 133, 38, 15105â15112, September 2011, 21842904, 3427765, 10.1021/ja204910n, JOURNAL, Yamashige R, Kimoto M, Takezawa Y, Sato A, Mitsui T, Yokoyama S, Hirao I, Highly specific unnatural base pair systems as a third base pair for PCR amplification, Nucleic Acids Research, 40, 6, 2793â2806, March 2012, 22121213, 3315302, 10.1093/nar/gkr1068, JOURNAL, Takezawa Y, Müller J, Shionoya M, 2017-05-05, Artificial DNA Base Pairing Mediated by Diverse Metal Ions, Chemistry Letters, en, 46, 5, 622â633, 10.1246/cl.160985, 0366-7022, free, In 1989 Steven Benner (then working at the Swiss Federal Institute of Technology in Zurich) and his team led with modified forms of cytosine and guanine into DNA molecules in vitro.JOURNAL, Switzer C, Moroney SE, Benner SA, Enzymatic incorporation of a new base pair into DNA and RNA, 1989, J. Am. Chem. Soc., 111, 21, 8322â8323, 10.1021/ja00203a067, The nucleotides, which encoded RNA and proteins, were successfully replicated in vitro. Since then, Benner’s team has been trying to engineer cells that can make foreign bases from scratch, obviating the need for a feedstock.NEWS,www.huffingtonpost.com/2014/05/07/living-organism-artificial-dna_n_5283095.html, Scientists Create First Living Organism With ‘Artificial’ DNA, Callaway E, May 7, 2014, Nature News, Huffington Post, 8 May 2014, In 2002, Ichiro Hirao’s group in Japan developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions in transcription and translation, for the site-specific incorporation of non-standard amino acids into proteins.JOURNAL, Hirao I, Ohtsuki T, Fujiwara T, Mitsui T, Yokogawa T, Okuni T, Nakayama H, Takio K, Yabuki T, Kigawa T, Kodama K, Yokogawa T, Nishikawa K, Yokoyama S, 6, An unnatural base pair for incorporating amino acid analogs into proteins, Nature Biotechnology, 20, 2, 177â182, February 2002, 11821864, 10.1038/nbt0202-177, 22055476, In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription.JOURNAL, Hirao I, Kimoto M, Mitsui T, Fujiwara T, Kawai R, Sato A, Harada Y, Yokoyama S, 6, An unnatural hydrophobic base pair system: site-specific incorporation of nucleotide analogs into DNA and RNA, Nature Methods, 3, 9, 729â735, September 2006, 16929319, 10.1038/nmeth915, 6494156, Afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification.JOURNAL, Kimoto M, Kawai R, Mitsui T, Yokoyama S, Hirao I, An unnatural base pair system for efficient PCR amplification and functionalization of DNA molecules, Nucleic Acids Research, 37, 2, e14, February 2009, 19073696, 2632903, 10.1093/nar/gkn956, vanc, JOURNAL, Yamashige R, Kimoto M, Takezawa Y, Sato A, Mitsui T, Yokoyama S, Hirao I, Highly specific unnatural base pair systems as a third base pair for PCR amplification, Nucleic Acids Research, 40, 6, 2793â2806, March 2012, 22121213, 3315302, 10.1093/nar/gkr1068, In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated the genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins.JOURNAL, Kimoto M, Yamashige R, Matsunaga K, Yokoyama S, Hirao I, Generation of high-affinity DNA aptamers using an expanded genetic alphabet, Nature Biotechnology, 31, 5, 453â457, May 2013, 23563318, 10.1038/nbt.2556, 23329867, In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP).JOURNAL, Malyshev DA, Dhami K, Quach HT, Lavergne T, Ordoukhanian P, Torkamani A, Romesberg FE, Efficient and sequence-independent replication of DNA containing a third base pair establishes a functional six-letter genetic alphabet, Proceedings of the National Academy of Sciences of the United States of America, 109, 30, 12005â12010, July 2012, 22773812, 3409741, 10.1073/pnas.1205176109, free, 2012PNAS..10912005M, The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICSâdNaM) complex or base pair in DNA. His team designed a variety of in vitro or “test tube” templates containing the unnatural base pair and they confirmed that it was efficiently replicated with high fidelity in virtually all sequence contexts using the modern standard in vitro techniques, namely PCR amplification of DNA and PCR-based applications. Their results show that for PCR and PCR-based applications, the d5SICSâdNaM unnatural base pair is functionally equivalent to a natural base pair, and when combined with the other two natural base pairs used by all organisms, AâT and GâC, they provide a fully functional and expanded six-letter “genetic alphabet”.In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg’s laboratory had designed and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations. The transfection did not hamper the growth of the E. coli cells and showed no sign of losing its unnatural base pairs to its natural DNA repair mechanisms. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations.JOURNAL, Malyshev DA, Dhami K, Lavergne T, Chen T, Dai N, Foster JM, Corrêa IR, Romesberg FE, 6, A semi-synthetic organism with an expanded genetic alphabet, Nature, 509, 7500, 385â388, May 2014, 24805238, 4058825, 10.1038/nature13314, 2014Natur.509..385M, NEWS,www.theguardian.com/world/2014/may/07/living-organism-pass-down-artificial-dna-us-scientists, First life forms to pass on artificial DNA engineered by US scientists, Sample I, May 7, 2014, The Guardian, 8 May 2014, Romesberg said he and his colleagues created 300 variants to refine the design of nucleotides that would be stable enough and would be replicated as easily as the natural ones when the cells divide. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into E. coli bacteria. Then, the natural bacterial replication pathways use them to accurately replicate a plasmid containing d5SICSâdNaM. Other researchers were surprised that the bacteria replicated these human-made DNA subunits.The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.NEWS,www.nytimes.com/2014/05/08/business/researchers-report-breakthrough-in-creating-artificial-genetic-code.html?hpw&rref=business&_r=0, Scientists Add Letters to DNA’s Alphabet, Raising Hope and Fear, Pollack A, May 7, 2014, New York Times, 8 May 2014, Experts said the synthetic DNA incorporating the unnatural base pair raises the possibility of life forms based on a different DNA code.NEWS,www.foxnews.com/health/2014/05/08/scientists-create-organism-using-artificial-dna/, Scientists create first living organism containing artificial DNA, May 8, 2014, The Wall Street Journal, Fox News, 8 May 2014,Non-canonical base pairing
{{multiple image|image1=Wobble.svg|caption1=Wobble base pairs|width1=75|image2=Hoogsteen_Watson_Crick_pairing-en.svgSee also
References
{{Reflist|30em}}Further reading
- BOOK, Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R, 2004, Molecular Biology of the Gene, 5th, Pearson Benjamin Cummings: CSHL Press, (See esp. ch. 6 and 9)
- BOOK, Sigel A, Sigel H, Sigel RK, Interplay between Metal Ions and Nucleic Acids, Metal Ions in Life Sciences, 10, 2012, Springer, 10.1007/978-94-007-2172-2, 978-9-4007-2171-5, 92951134,
- BOOK, Clever GH, Shionoya M, Alternative DNA Base Pairing through Metal Coordination, 10.1007/978-94-007-2172-2_10, 22210343, 269â294, Interplay between Metal Ions and Nucleic Acids, 10, 2012, Metal Ions in Life Sciences, 978-94-007-2171-5,
- BOOK, Megger DA, Megger N, Mueller J, Metal-Mediated Base Pairs in Nucleic Acids with Purine- and Pyrimidine-Derived Nucleosides, 10.1007/978-94-007-2172-2_11, 22210344, 295â317, Interplay between Metal Ions and Nucleic Acids, 10, 2012, Metal Ions in Life Sciences, 978-94-007-2171-5,
External links
{{Commons category|Base pairing}}- bioweb.pasteur.fr/seqanal/interfaces/dan.html" title="web.archive.org/web/20060624093746bioweb.pasteur.fr/seqanal/interfaces/dan.html">DANâwebserver version of the EMBOSS tool for calculating melting temperatures
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