What is a Base Pair?

In molecular biology, a Base pair is defined as two complementary nitrogenous molecules, which are connected by hydrogen bonds. Base pairs can be found in both double-stranded DNA and RNA, in which the bonds between them connect the two strands by making the possible double-stranded structures. Base pairs themselves can be formed from bases that are complementary nitrogen-rich organic compounds called either pyrimidines or purines.

Complementary Base Pairing

Complementary base pairing is defined as the phenomenon where in the DNA guanine always hydrogen bonds to the cytosine and adenine binds to thymine always.

About Base Pair

The Watson crick base pairing, which is the foundation for the helical structure of double-stranded DNA, states that DNA comprises four bases: adenine (A) thymine (T) (adenine thymine) guanine (G), the two pyrimidines cytosine including guanine (C); or adenine thymine guanine cytosine. A bonds only with T and C bonds only with G inside the DNA molecule. In RNA, thymine is replaced by uracil (U). The base-pairing models of Non-Watson-Crick display alternative hydrogen-bonding patterns. A few examples are Hoogsteen base pairs: C-G or A-T analogs.

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Intramolecular base pairs can take place within the single-stranded nucleic acids. Particularly, this is essential in RNA molecules (for example, transfer RNA), where the Watson–Crick base pairs (adenine–uracil and guanine-cytosine) permit the formation of the short double-stranded helices, and also a wide variety of non–Watson–Crick interactions (for example, A–A or G–U) allows the RNAs to fold into a vast range of particular three-dimensional structures.

Additionally, the base-pairing between the messenger RNA (mRNA) and transfer RNA (tRNA) forms the basis for the molecular recognition events, which result in the nucleotide sequence of the mRNA becoming translated into the amino acid sequence of proteins through the genetic code.

Often, the size of either an entire genome or an individual gene of the organism is measured in the base pairs because usually, DNA is double-stranded. Thus, the total base pairs count is equal to the nucleotides count in one of the strands (including the exception of non-coding single-stranded telomeres' regions).

The haploid human genome (23 chromosomes) can be estimated to be nearly 3.2 billion bases long and to have 20,000–25,000 distinct protein-coding genes. In molecular biology, a kilobase (kb) is a unit of measurement equivalent to 1000 base pairs of RNA or DNA. The total DNA pairs or base pairs count on Earth is estimated at 5.0×1037, having a weight of 50 billion tonnes. In comparison, the biosphere's total mass has been expected as much as 4 TTC (trillion tons of carbon).

Hydrogen Bonding and Stability

Hydrogen bonding is given as the chemical interaction, which underlies the base-pairing rules. Only the "right" pairs will produce stability due to an effective geometrical correspondence of both hydrogen bond donors and acceptors. DNA pairs having high GC content is stable compared to the DNA with low GC content. But, contrary to popular belief, the hydrogen bonds do not significantly stabilize the DNA; stabilization is primarily because of stacking interactions.

The bigger nucleobases, guanine and adenine, are the members of the double-ringed chemical structures class known as purines; the smaller nucleobases, thymine, and cytosine (including uracil) are the members of a single-ringed chemical structure's class known as pyrimidines. And, purines are only complementary with the pyrimidines: pairings of pyrimidine-pyrimidine are energetically unfavourable due to the molecules are too far apart for hydrogen bonding that is to be established; purine-purine pairings are energetically unfavourable since the molecules are too close together, resulting in overlap repulsion.

Purine-pyrimidine base-pairing of either GC or AT, or UA (in the RNA) results in the proper duplex structure. The only other purine-pyrimidine pairings would be AC, GT, and UG (in the RNA); these specific pairings are mismatches due to the patterns of hydrogen donors, and acceptors do not correspond. With two hydrogen bonds, the GU pairing does take place fairly often in RNA.

Paired RNA and DNA molecules are relatively stable at room temperature, whereas the two nucleotide strands will separate over a melting point, which is defined by the molecule's length, the mispairing extent (if any), and the GC content. A high GC content results in higher melting temperatures; thus, it is unsurprising that genomes of extremophile organisms like Thermus thermophilus are specifically GC-rich.

Conversely, the genome regions need to separate frequently. The promoter regions of frequently transcribed genes, for example, have a low GC content. When developing primers for PCR reactions, GC material, as well as melting temperature, should be taken into account.

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The first figure - a GC base-pair is having three hydrogen bonds, and the second - an AT base pair with two hydrogen bonds. The non-covalent hydrogen bonds between the bases are represented in dashed lines. The relation to both the pentose sugar and the minor groove direction is represented by these unique wiggly lines.


Base pairs can often be used to measure the size of an individual gene within the DNA molecule. The number of nucleotides in one of the strands is equal to the total number of base pairs (each nucleotide has a base pair, a phosphate group, and a deoxyribose sugar). The detailing of base pairs can be complicated with extremely complex genomes.

FAQs (Frequently Asked Questions)

1. Give an Example of a Base Pair?

Answer: The human genome is formed with an estimated three billion base pairs, ranging from 20,000 to 25,000 distinct genes. Dealing with these large numbers, scientists use measures like kilobase pairs (either kb or kbp), which is equivalent to 1,000 base pairs.

2. What is a Conjugate Acid-Base Pair and Wobble Base Pair?

Answer: A conjugate acid with its conjugate base is also called conjugate acid-base pair is pair, which differs by either only +1 charge or one H+ ion. A wobble base pair is defined as a pairing between the two nucleotides in RNA molecules, which does not follow the rules of Watson-Crick base pair.

3. What is an Unnatural Base Pair?

Answer: UBP, an Unnatural Base Pair, is a designed nucleobase or subunit of DNA that is created in a laboratory and does not take place in nature. The DNA sequences that use the newly formed nucleobases to create a third base pair, including the two base pairs found in nature, G-C (guanine-cytosine) and A-T (adenine-thymine), have also been identified.

4. What are RNA Base Pairs?

Answer: An RNA base pair forms when the two complementary RNA bases find themselves over one another. The complementary base pairs for RNA are C=G (2 hydrogen bonds) and A-U (1 hydrogen bond).