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Encyclopedia > Base pair

In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). In the canonical Watson-Crick base pairing, adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA. In RNA, thymine is replaced by uracil (U). Non-Watson-Crick base pairing with alternate hydrogen bonding patterns also occur, especially in RNA; common such patterns are Hoogsteen base pairs. Pairing is also the mechanism by which codons on messenger RNA molecules are recognized by anticodons on transfer RNA during protein translation. Some DNA- or RNA-binding enzymes can recognize specific base pairing patterns that identify particular regulatory regions of genes. Molecular biology is the study of biology at a molecular level. ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... On the left: nucleotides that forms the DNA and their complementary. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... For other uses, see RNA (disambiguation). ... An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... For the programming language Adenine, see Adenine (programming language). ... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... Guanine is one of the five main nucleobases found in the nucleic acids DNA and RNA; the others being adenine, cytosine, thymine, and uracil. ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at... For the similarly-spelled vitamin compound, see Thiamine Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... Uracil is a pyrimidine which is common and naturally occurring. ... A Hoogsteen base pair is a minor variation of base-pairing in nucleic acids such as the A•T pair shown in the figure. ... RNA codons. ... The life cycle of an mRNA in a eukaryotic cell. ... An anticodon is a unit made up of nucleotides that plays an important role in various DNA cycles, including DNA transcription. ... Transfer RNA Transfer RNA (abbreviated tRNA), first hypothesized by Francis Crick, is a small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ...


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 billion base pairs long and to contain 20,000-25,000 distinct genes.[1] For other uses, see Gene (disambiguation). ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... A telomere is a region of highly repetitive DNA at the end of a linear chromosome that functions as a disposable buffer. ... Haploid (meaning simple in Greek) cells have only one copy of each chromosome. ... A graphical representation of the normal human karyotype. ... This article is about the biological chromosome. ...


A Kilobase is a unit of measurement in molecular biology denoting 1000 base pairs of DNA or RNA. Molecular biology is the study of biology at a molecular level. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... For other uses, see RNA (disambiguation). ...

Contents

Examples

The following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5' end to the 3' end; thus the bottom strand is written 3' to 5'. In molecular biology, the 5 end and the 3 end (pronounced 5-prime and 3-prime) are respectively the leading and tail ends of a strand of nucleic acid. ... In molecular biology, the 5 end and the 3 end (pronounced 5-prime and 3-prime) are respectively the leading and tail ends of a strand of nucleic acid. ...

A base-paired DNA sequence:
 ATCGAT TAGCTA 
The corresponding base-paired RNA sequence, in which uracil is substituted for thymine:
 ATCGAT UAGCUA 

Uracil is a pyrimidine which is common and naturally occurring. ...

Length measurements

The following abbreviations are commonly used to describe the length of a DNA/RNA molecule:

  • bp = base pair(s)—one bp corresponds to ca 3.4 Å of length along the strand
  • kb (= kbp) = kilo base pairs = 1,000 bp
  • Mb = mega base pairs = 1,000,000 bp
  • Gb = giga base pairs = 1,000,000,000 bp

In case of single stranded DNA/RNA we talk about nucleotides, abbreviated nt (or knt, Mnt, Gnt), rather than base pairs, as they are not paired. For distinction between units of computer storage and bases kbp, Mbp, Gbp etc may be used for disambiguation. An angstrom, angström, or ångström (symbol Å) is a unit of length. ... A nucleotide is a chemical compound that consists of 3 portions: a heterocyclic base, a sugar, and one or more phosphate groups. ... This article does not cite any references or sources. ...


The Centimorgan is also often used to imply distance along a chromosome, but the number of base-pairs it corresponds to varies widely. In the Human genome, it is about 1 million base pairs[2] [3]. . In genetics, a centimorgan (abbreviated cM) is a unit of recombinant frequency. ...


Hydrogen bonding and stability

A GC base pair demonstrating three intermolecular hydrogen bonds
A GC base pair demonstrating three intermolecular hydrogen bonds
An AT base pair demonstrating two intermolecular hydrogen bonds
An AT base pair demonstrating two intermolecular hydrogen bonds

Hydrogen bonding is the chemical mechanism that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. The GC base pair has three hydrogen bonds, whereas the AT base pair has only two; as a consequence, the GC pair is more stable. Image File history File links This is a lossless scalable vector image. ... Image File history File links This is a lossless scalable vector image. ... An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... Image File history File links This is a lossless scalable vector image. ... Image File history File links This is a lossless scalable vector image. ... An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ... An example of a quadruple hydrogen bond between a self-assembled dimer complex reported by Meijer and coworkers. ...


The larger nucleic acids, adenine and guanine, are members of a class of doubly-ringed chemical structures called purines; the smaller nucleic acids, cytosine and thymine (and uracil), are members of a class of singly-ringed chemical structures called pyrimidines. Purines are only complementary with pyrimidines: pyrimidine-pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine-purine pairings are energetically unfavorable because the molecules are too close, leading to electrostatic repulsion. The only other possible pairings are GT and AC; these pairings are mismatches because the pattern of hydrogen donors and acceptors do not correspond. (It should be noted that the GU pairing, with two hydrogen bonds, does occur fairly often in RNA but rarely in DNA.) Purine (1) is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. ... Pyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring [1]. It is isomeric with two other forms of diazine. ... For other uses, see RNA (disambiguation). ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ...


Paired DNA and RNA molecules are comparatively stable at room temperature but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and the GC content. Higher GC content results in higher melting temperatures; it is therefore unsurprising that the genomes of extremophile organisms such as Thermus thermophilus are particularly GC-rich. Conversely, regions of a genome that need to separate frequently - for example, the promoter regions for often-transcribed genes - are comparatively GC-poor (for example, see TATA box). GC content and melting temperature must also be taken into account when designing primers for PCR reactions. DNA melting, also called DNA denaturation, 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. ... Binomial name Thermus thermophilus Thermus thermophilus is a gram negative eubacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation and systems biology. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... A TATA box (also called Goldberg-Hogness box)[1] is a DNA sequence (Cis-regulatory element) found in the promoter region of most genes (it is considered to be the core promoter sequence) in eukaryotes [2]. It is the binding site of either transcription factors or histones (binding of a... A primer is a nucleic acid strand, or a related molecule that serves as a starting point for DNA replication. ... Wikipedia does not yet have an article with this exact name. ...


Base stacking

Base stacking interactions between the pi orbitals of the bases' aromatic rings also contribute to stability, and again GC stacking interactions with adjacent bases tend to be more favorable. (Note, though, that a GC stacking interaction with the next base pair is geometrically different from a CG interaction.) Base stacking effects are especially important in the secondary structure of RNA; for example, RNA stem-loop structures are stabilized by base stacking in the loop region. Stacking in supramolecular chemistry referes to a stacked arrangement of aromatic molecules, which interact through aromatic interactions. ... Electron atomic and molecular orbitals, showing a Pi-bond at the bottom right of the picture. ... In chemistry, an aromatic molecule is one in which electrons are free to cycle around circular arrangements of atoms, which are alternately singly and doubly bonded to one another. ... An example of an RNA stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. It occurs when two regions of the same molecule base-pair to form a double helix that ends in a short unpaired loop...

Further information: pi stacking

It has been suggested that this article or section be merged into Stacking (chemistry). ...

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. One common mutagenic base analog is 5-bromouracil, which resembles thymine but can base-pair to guanine in its enol form. Nucleic acid analogues are compounds structurally similar to naturally occuring RNA and DNA, used as a research tool in molecular biology and/or as cure in medicine. ... A point mutation, or substitution, is a type of mutation that causes the replacement of a single base nucleotide with another nucleotide. ... DNA replication. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... 5-Bromouracil (or 5-bromo-2,4(1H,3H)-pyrimidinedione or 5-BrU or 5-BU) is a component of 5-bromo-2-deoxy-uridine. ... Enol (or, more officially, but less commonly: alkenol) is an alkene with hydroxyl group on one of the carbon atoms of the double bond. ...


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. Intercalation induces structural distortions. ... A frameshift mutation (also called a frameshift or a framing error) is a genetic mutation that inserts or deletes a number of nucleotides that is not evenly divisible by three from a DNA sequence. ... In chemistry, an aromatic molecule is one in which electrons are free to cycle around circular arrangements of atoms, which are alternately singly and doubly bonded to one another. ... Look up carcinogen in Wiktionary, the free dictionary. ... R-phrases , S-phrases , , , , , Flash point > 100 °C Except where noted otherwise, data are given for materials in their standard state (at 25 Â°C, 100 kPa) Infobox disclaimer and references Absorption spectrum of ethidium bromide Ethidium bromide (sometimes abbreviated as EtBr) is an intercalating agent commonly used as a nucleic... Acridine, C13H9N, is an organic compound and a nitrogen heterocycle. ...


See also

The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... Adenine Guanine Thymine Cytosine ... Wobble base pairs for inosine Wobble base pairs for Uracil A wobble base pair is a G-U and I-U / I-A / I-C pair fundamental in RNA secondary structure. ... A Hoogsteen base pair is a minor variation of base-pairing in nucleic acids such as the A•T pair shown in the figure. ... ISOGG Y-DNA SNP Index - 2007 Single nucleotide polymorphism Unique event polymorphism Human Y-chromosome DNA haplogroups List of DYS markers Categories: | | | | | | | | ...

External links

  • DAN - webserver version of the EMBOSS tool for calculating melting temperatures

Cited references

  1. ^ International Human Genome Sequencing Consortium (2004). "Finishing the euchromatic sequence of the human genome.". Nature 431 (7011): 931–45. doi:10.1038/nature03001. PMID 15496913.  [1]
  2. ^ The Genetic and Rare Diseases Information Center - Office of Rare Diseases redirect
  3. ^ Matthew P Scott, Paul Matsudaira, Harvey Lodish, James Darnell, Lawrence Zipursky, Chris A Kaiser, Arnold Berk, Monty Krieger (2004). Molecular Cell Biology, Fifth Edition. San Francisco: W. H. Freeman, 396. ISBN 0-7167-4366-3. “"...in humans 1 centimorgan on average represents a distance of about 7.5x10E5 base pairs"” 

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ...

General references

  • Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene. 5th ed. Pearson Benjamin Cummings: CSHL Press. See esp. ch. 6 and 9.

  Results from FactBites:
 
Genomics and Its Impact on Science and Society: 2003 Primer (7072 words)
A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA).
A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end.
Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the human genome and whose location and base sequence are known.
  More results at FactBites »

 
 

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