Complementarity (molecular biology)

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Match up between two DNA bases (guanine and cytosine) showing hydrogen bonds (dashed lines) holding them together GC base pair jypx3.png
Match up between two DNA bases (guanine and cytosine) showing hydrogen bonds (dashed lines) holding them together
Match up between two DNA bases (adenine and thymine) showing hydrogen bonds (dashed lines) holding them together AT base pair jypx3.png
Match up between two DNA bases (adenine and thymine) showing hydrogen bonds (dashed lines) holding them together

In molecular biology, complementarity describes a relationship between two structures each following the lock-and-key principle. In nature complementarity is the base principle of DNA replication and transcription as it is a property shared between two DNA or RNA sequences, such that when they are aligned antiparallel to each other, the nucleotide bases at each position in the sequences will be complementary, much like looking in the mirror and seeing the reverse of things. This complementary base pairing allows cells to copy information from one generation to another and even find and repair damage to the information stored in the sequences.

Contents

The degree of complementarity between two nucleic acid strands may vary, from complete complementarity (each nucleotide is across from its opposite) to no complementarity (each nucleotide is not across from its opposite) and determines the stability of the sequences to be together. Furthermore, various DNA repair functions as well as regulatory functions are based on base pair complementarity. In biotechnology, the principle of base pair complementarity allows the generation of DNA hybrids between RNA and DNA, and opens the door to modern tools such as cDNA libraries. While most complementarity is seen between two separate strings of DNA or RNA, it is also possible for a sequence to have internal complementarity resulting in the sequence binding to itself in a folded configuration.

DNA and RNA base pair complementarity

Complementarity between two antiparallel strands of DNA. The top strand goes from the left to the right and the lower strand goes from the right to the left lining them up. DNA chemical structure.svg
Complementarity between two antiparallel strands of DNA. The top strand goes from the left to the right and the lower strand goes from the right to the left lining them up.
Left: the nucleotide base pairs that can form in double-stranded DNA. Between A and T there are two hydrogen bonds, while there are three between C and G. Right: two complementary strands of DNA. Complementarity (DNA).png
Left: the nucleotide base pairs that can form in double-stranded DNA. Between A and T there are two hydrogen bonds, while there are three between C and G. Right: two complementary strands of DNA.

Complementarity is achieved by distinct interactions between nucleobases: adenine, thymine (uracil in RNA), guanine and cytosine. Adenine and guanine are purines, while thymine, cytosine and uracil are pyrimidines. Purines are larger than pyrimidines. Both types of molecules complement each other and can only base pair with the opposing type of nucleobase. In nucleic acid, nucleobases are held together by hydrogen bonding, which only works efficiently between adenine and thymine and between guanine and cytosine. The base complement A = T shares two hydrogen bonds, while the base pair G ≡ C has three hydrogen bonds. All other configurations between nucleobases would hinder double helix formation. DNA strands are oriented in opposite directions, they are said to be antiparallel. [1]

Nucleic Acid Nucleobases Base complement
DNA adenine(A), thymine(T), guanine(G), cytosine(C)A = T, G ≡ C
RNA adenine(A), uracil(U), guanine(G), cytosine(C)A = U, G ≡ C

A complementary strand of DNA or RNA may be constructed based on nucleobase complementarity. [2] Each base pair, A = T vs. G ≡ C, takes up roughly the same space, thereby enabling a twisted DNA double helix formation without any spatial distortions. Hydrogen bonding between the nucleobases also stabilizes the DNA double helix. [3]

Complementarity of DNA strands in a double helix make it possible to use one strand as a template to construct the other. This principle plays an important role in DNA replication, setting the foundation of heredity by explaining how genetic information can be passed down to the next generation. Complementarity is also utilized in DNA transcription, which generates an RNA strand from a DNA template. [4] In addition, human immunodeficiency virus, a single-stranded RNA virus, encodes an RNA-dependent DNA polymerase (reverse transcriptase) that uses complementarity to catalyze genome replication. The reverse transcriptase can switch between two parental RNA genomes by copy-choice recombination during replication. [5]

DNA repair mechanisms such as proof reading are complementarity based and allow for error correction during DNA replication by removing mismatched nucleobases. [1] In general, damages in one strand of DNA can be repaired by removal of the damaged section and its replacement by using complementarity to copy information from the other strand, as occurs in the processes of mismatch repair, nucleotide excision repair and base excision repair. [6]

Nucleic acids strands may also form hybrids in which single stranded DNA may readily anneal with complementary DNA or RNA. This principle is the basis of commonly performed laboratory techniques such as the polymerase chain reaction, PCR. [1]

Two strands of complementary sequence are referred to as sense and anti-sense. The sense strand is, generally, the transcribed sequence of DNA or the RNA that was generated in transcription, while the anti-sense strand is the strand that is complementary to the sense sequence.

Self-complementarity and hairpin loops

A sequence of RNA that has internal complementarity which results in it folding into a hairpin Stem-loop.svg
A sequence of RNA that has internal complementarity which results in it folding into a hairpin

Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double-strand like structure. Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, junctions, bulges or internal loops. [1] RNA is more likely to form these kinds of structures due to base pair binding not seen in DNA, such as guanine binding with uracil. [1]

A sequence of RNA showing hairpins (far right and far upper left), and internal loops (lower left structure) ATPC secondary structure.jpg
A sequence of RNA showing hairpins (far right and far upper left), and internal loops (lower left structure)

Regulatory functions

Complementarity can be found between short nucleic acid stretches and a coding region or a transcribed gene, and results in base pairing. These short nucleic acid sequences are commonly found in nature and have regulatory functions such as gene silencing. [1]

Antisense transcripts

Antisense transcripts are stretches of non coding mRNA that are complementary to the coding sequence. [7] Genome wide studies have shown that RNA antisense transcripts occur commonly within nature. They are generally believed to increase the coding potential of the genetic code and add an overall layer of complexity to gene regulation. So far, it is known that 40% of the human genome is transcribed in both directions, underlining the potential significance of reverse transcription. [8] It has been suggested that complementary regions between sense and antisense transcripts would allow generation of double stranded RNA hybrids, which may play an important role in gene regulation. For example, hypoxia-induced factor 1α mRNA and β-secretase mRNA are transcribed bidirectionally, and it has been shown that the antisense transcript acts as a stabilizer to the sense script. [9]

miRNAs and siRNAs

Formation and function of miRNAs in a cell MiRNA.svg
Formation and function of miRNAs in a cell

miRNAs, microRNA, are short RNA sequences that are complementary to regions of a transcribed gene and have regulatory functions. Current research indicates that circulating miRNA may be utilized as novel biomarkers, hence show promising evidence to be utilized in disease diagnostics. [10] MiRNAs are formed from longer sequences of RNA that are cut free by a Dicer enzyme from an RNA sequence that is from a regulator gene. These short strands bind to a RISC complex. They match up with sequences in the upstream region of a transcribed gene due to their complementarity to act as a silencer for the gene in three ways. One is by preventing a ribosome from binding and initiating translation. Two is by degrading the mRNA that the complex has bound to. And three is by providing a new double-stranded RNA (dsRNA) sequence that Dicer can act upon to create more miRNA to find and degrade more copies of the gene. Small interfering RNAs (siRNAs) are similar in function to miRNAs; they come from other sources of RNA, but serve a similar purpose to miRNAs. [1] Given their short length, the rules for complementarity means that they can still be very discriminating in their targets of choice. Given that there are four choices for each base in the strand and a 20bp - 22bp length for a mi/siRNA, that leads to more than 1×1012 possible combinations. Given that the human genome is ~3.1 billion bases in length, [11] this means that each miRNA should only find a match once in the entire human genome by accident.

Kissing hairpins

Kissing hairpins are formed when a single strand of nucleic acid complements with itself creating loops of RNA in the form of a hairpin. [12] When two hairpins come into contact with each other in vivo, the complementary bases of the two strands form up and begin to unwind the hairpins until a double-stranded RNA (dsRNA) complex is formed or the complex unwinds back to two separate strands due to mismatches in the hairpins. The secondary structure of the hairpin prior to kissing allows for a stable structure with a relatively fixed change in energy. [13] The purpose of these structures is a balancing of stability of the hairpin loop vs binding strength with a complementary strand. Too strong an initial binding to a bad location and the strands will not unwind quickly enough; too weak an initial binding and the strands will never fully form the desired complex. These hairpin structures allow for the exposure of enough bases to provide a strong enough check on the initial binding and a weak enough internal binding to allow the unfolding once a favorable match has been found. [13] 

---C G---    C G                 ---C G---    U A                    C G     G C                    U A    C G                    G C    A G                    C G   A   A                   A G    C U                   A   A     U                     CUU              ---CCUGCAACUUAGGCAGG---     A                     GAA              ---GGACGUUGAAUCCGUCC---    G A                   U   U   U   U                  U   C    U C                    G C    G C                    C G    C G                    A U    A U                    G C    G C                 ---G C--- ---G C--- Kissing hairpins meeting up at the top of the loops. The complementarity  of the two heads encourages the hairpin to unfold and straighten out to become one flat sequence of two strands rather than two hairpins.

Bioinformatics

Complementarity allows information found in DNA or RNA to be stored in a single strand. The complementing strand can be determined from the template and vice versa as in cDNA libraries. This also allows for analysis, like comparing the sequences of two different species. Shorthands have been developed for writing down sequences when there are mismatches (ambiguity codes) or to speed up how to read the opposite sequence in the complement (ambigrams).

cDNA Library

A cDNA library is a collection of expressed DNA genes that are seen as a useful reference tool in gene identification and cloning processes. cDNA libraries are constructed from mRNA using RNA-dependent DNA polymerase reverse transcriptase (RT), which transcribes an mRNA template into DNA. Therefore, a cDNA library can only contain inserts that are meant to be transcribed into mRNA. This process relies on the principle of DNA/RNA complementarity. The end product of the libraries is double stranded DNA, which may be inserted into plasmids. Hence, cDNA libraries are a powerful tool in modern research. [1] [14]

Ambiguity codes

When writing sequences for systematic biology it may be necessary to have IUPAC codes that mean "any of the two" or "any of the three". The IUPAC code R (any purine) is complementary to Y (any pyrimidine) and M (amino) to K (keto). W (weak) and S (strong) are usually not swapped [15] but have been swapped in the past by some tools. [16] W and S denote "weak" and "strong", respectively, and indicate a number of the hydrogen bonds that a nucleotide uses to pair with its complementing partner. A partner uses the same number of the bonds to make a complementing pair. [17]

An IUPAC code that specifically excludes one of the three nucleotides can be complementary to an IUPAC code that excludes the complementary nucleotide. For instance, V (A, C or G - "not T") can be complementary to B (C, G or T - "not A").

Symbol [18] DescriptionBases represented
A adenine A1
C cytosine C
G guanine G
T thymine T
U uracil U
WweakAT2
SstrongCG
M amino AC
K keto GT
R purine AG
Y pyrimidine CT
Bnot A (B comes after A)CGT3
Dnot C (D comes after C)AGT
Hnot G (H comes after G)ACT
Vnot T (V comes after T and U)ACG
N or -any base (not a gap)ACGT4

Ambigrams

Specific characters may be used to create a suitable (ambigraphic) nucleic acid notation for complementary bases (i.e. guanine = b, cytosine = q, adenine = n, and thymine = u), which makes it is possible to complement entire DNA sequences by simply rotating the text "upside down". [19] For instance, with the previous alphabet, buqn (GTCA) would read as ubnq (TGAC, reverse complement) if turned upside down.

qqubqnnquunbbqnbb
bbnqbuubnnuqqbuqq

Ambigraphic notations readily visualize complementary nucleic acid stretches such as palindromic sequences. [20] This feature is enhanced when utilizing custom fonts or symbols rather than ordinary ASCII or even Unicode characters. [20]

See also

Related Research Articles

<span class="mw-page-title-main">Base pair</span> Unit consisting of two nucleobases bound to each other by hydrogen bonds

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, "Watson–Crick" base pairs allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. 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.

<span class="mw-page-title-main">DNA</span> Molecule that carries genetic information

Deoxyribonucleic acid is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

<span class="mw-page-title-main">Nucleic acid</span> Class of large biomolecules essential to all known life

Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is deoxyribose, a variant of ribose, the polymer is DNA.

<span class="mw-page-title-main">Nucleotide</span> Biological molecules constituting nucleic acids

Nucleotides are organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver.

An inverted repeat is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, 5'---TTACGnnnnnnCGTAA---3' is an inverted repeat sequence. When the intervening length is zero, the composite sequence is a palindromic sequence.

<span class="mw-page-title-main">Nucleobase</span> Nitrogen-containing biological compounds that form nucleosides

Nucleobases are nitrogen-containing biological compounds that form nucleosides, which, in turn, are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. The ability of nucleobases to form base pairs and to stack one upon another leads directly to long-chain helical structures such as ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). Five nucleobases—adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U)—are called primary or canonical. They function as the fundamental units of the genetic code, with the bases A, G, C, and T being found in DNA while A, G, C, and U are found in RNA. Thymine and uracil are distinguished by merely the presence or absence of a methyl group on the fifth carbon (C5) of these heterocyclic six-membered rings. In addition, some viruses have aminoadenine (Z) instead of adenine. It differs in having an extra amine group, creating a more stable bond to thymine.

<span class="mw-page-title-main">Transcription (biology)</span> Process of copying a segment of DNA into RNA

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins produce messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs).

Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small fragments of nucleic acids can be manufactured as single-stranded molecules with any user-specified sequence, and so are vital for artificial gene synthesis, polymerase chain reaction (PCR), DNA sequencing, molecular cloning and as molecular probes. In nature, oligonucleotides are usually found as small RNA molecules that function in the regulation of gene expression, or are degradation intermediates derived from the breakdown of larger nucleic acid molecules.

<span class="mw-page-title-main">Nucleic acid sequence</span> Succession of nucleotides in a nucleic acid

A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.

In a chain-like biological molecule, such as a protein or nucleic acid, a structural motif is a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules. A structural motif does not have to be associated with a sequence motif; it can be represented by different and completely unrelated sequences in different proteins or RNA.

<span class="mw-page-title-main">Chargaff's rules</span> Two rules about the percentage of A, C, G, and T in DNA strands

Chargaff's rules state that in the DNA of any species and any organism, the amount of guanine should be equal to the amount of cytosine and the amount of adenine should be equal to the amount of thymine. Further, a 1:1 stoichiometric ratio of purine and pyrimidine bases should exist. This pattern is found in both strands of the DNA. They were discovered by Austrian-born chemist Erwin Chargaff in the late 1940s.

In molecular biology and genetics, the sense of a nucleic acid molecule, particularly of a strand of DNA or RNA, refers to the nature of the roles of the strand and its complement in specifying a sequence of amino acids. Depending on the context, sense may have slightly different meanings. For example, the negative-sense strand of DNA is equivalent to the template strand, whereas the positive-sense strand is the non-template strand whose nucleotide sequence is equivalent to the sequence of the mRNA transcript.

<span class="mw-page-title-main">Palindromic sequence</span> DNA or RNA sequence that matches its complement when read backwards

A palindromic sequence is a nucleic acid sequence in a double-stranded DNA or RNA molecule whereby reading in a certain direction on one strand is identical to the sequence in the same direction on the complementary strand. This definition of palindrome thus depends on complementary strands being palindromic of each other.

<span class="mw-page-title-main">Nucleic acid analogue</span> Compound analogous to naturally occurring RNA and DNA

Nucleic acid analogues are compounds which are analogous to naturally occurring RNA and DNA, used in medicine and in molecular biology research. Nucleic acids are chains of nucleotides, which are composed of three parts: a phosphate backbone, a pentose sugar, either ribose or deoxyribose, and one of four nucleobases. An analogue may have any of these altered. Typically the analogue nucleobases confer, among other things, different base pairing and base stacking properties. Examples include universal bases, which can pair with all four canonical bases, and phosphate-sugar backbone analogues such as PNA, which affect the properties of the chain . Nucleic acid analogues are also called xeno nucleic acids and represent one of the main pillars of xenobiology, the design of new-to-nature forms of life based on alternative biochemistries.

Natural antisense transcripts (NATs) are a group of RNAs encoded within a cell that have transcript complementarity to other RNA transcripts. They have been identified in multiple eukaryotes, including humans, mice, yeast and Arabidopsis thaliana. This class of RNAs includes both protein-coding and non-coding RNAs. Current evidence has suggested a variety of regulatory roles for NATs, such as RNA interference (RNAi), alternative splicing, genomic imprinting, and X-chromosome inactivation. NATs are broadly grouped into two categories based on whether they act in cis or in trans. Trans-NATs are transcribed from a different location than their targets and usually have complementarity to multiple transcripts with some mismatches. MicroRNAs (miRNA) are an example of trans-NATs that can target multiple transcripts with a few mismatches. Cis-natural antisense transcripts (cis-NATs) on the other hand are transcribed from the same genomic locus as their target but from the opposite DNA strand and form perfect pairs.

<span class="mw-page-title-main">Nucleic acid structure</span> Biomolecular structure of nucleic acids such as DNA and RNA

Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.

<span class="mw-page-title-main">Nucleic acid secondary structure</span>

Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.

<span class="mw-page-title-main">Polypurine reverse-Hoogsteen hairpin</span>

Polypurine reverse-Hoogsteen hairpins (PPRHs) are non-modified oligonucleotides containing two polypurine domains, in a mirror repeat fashion, linked by a pentathymidine stretch forming double-stranded DNA stem-loop molecules. The two polypurine domains interact by intramolecular reverse-Hoogsteen bonds allowing the formation of this specific hairpin structure.

This glossary of cellular and molecular biology is a list of definitions of terms and concepts commonly used in the study of cell biology, molecular biology, and related disciplines, including genetics, biochemistry, and microbiology. It is split across two articles:

This glossary of cellular and molecular biology is a list of definitions of terms and concepts commonly used in the study of cell biology, molecular biology, and related disciplines, including genetics, biochemistry, and microbiology. It is split across two articles:

References

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