Isolation of DNA

In phenol-chloroform many proteins move to the organic phase or interface. DNA can remain in the aqueous phase.

In phenol-chloroform extraction DNA usually remains in the aqueous phase. That layer is collected carefully.

The direct answer is D: DNA can shear. Shearing means that long DNA molecules break into shorter pieces because of strong mechanical force. Genomic DNA is especially vulnerable because its molecules are very long. The reasoning is: a long DNA molecule is placed in a liquid; harsh vortexing creates strong mixing forces; those forces can pull or break the long molecules; the sample then contains fragments of different sizes instead of intact high-molecular-weight DNA. Option D is correct because vigorous vortexing can damage long genomic DNA and reduce its quality for applications needing intact molecules. Option A is wrong because mechanical mixing does not make DNA longer; at most it can break it into shorter pieces. Option B is wrong because DNA does not produce light merely from vortexing. Option C is wrong because salt does not disappear; mixing may distribute it, but it does not remove it. Small circular plasmids may tolerate some mixing better than long genomic DNA, but “harsh” handling can still be undesirable. Gentle pipetting and slow mixing are safer when intact DNA is required. Memory cue: “long DNA plus strong force equals possible shearing.”

During DNA isolation, nucleases released from cells can cut and degrade DNA. Low temperature slows the activity of these enzymes, helping to preserve the DNA. Increased DNA replication is not the reason, because DNA is not replicated during the isolation procedure. Exam tip: Cold conditions and nuclease inhibitors are used to protect DNA from degradation.

A spectrophotometer estimates DNA amount and purity using absorbance. Link it with quality check.

DNA absorbs ultraviolet light around 260 nm. Therefore 260 nm is important for DNA quantification.

The governing concept is spectrophotometric assessment of nucleic-acid purity. Nucleic acids absorb strongly near 260 nm, whereas proteins, particularly because of aromatic amino acids, contribute substantially near 280 nm. The A260/A280 ratio therefore provides a practical indication of DNA purity. A lower-than-expected value for a DNA preparation can suggest protein or other absorbing contaminants, although interpretation also depends on buffer and sample conditions. Option D is correct. The other listed wavelength ratios are not the standard purity index used for detecting protein contamination in a routine DNA preparation. This measurement assesses quality; it does not itself remove the contaminant.

The governing concept is the absorbance ratio used to estimate DNA purity. At 260 nm, DNA absorbs strongly, while protein contributes more strongly near 280 nm. For relatively pure double-stranded DNA, the A260/A280 value is commonly close to 1.8 under standard measurement conditions. A substantially lower value may indicate protein or reagent contamination, whereas an unusually high value can suggest other contaminants or measurement effects. Therefore option A is correct. Values of 0.2, 5.0, and 10.0 are not the usual exam reference for pure DNA. The ratio is an approximate quality indicator, not an absolute proof that every contaminant has been removed.

In agarose gel electrophoresis, DNA migrates through the gel according to its size and becomes visible as bands. A clear, expected band indicates the presence of intact, good-quality DNA, whereas a smear may indicate fragmented or degraded DNA. Spectrophotometry or fluorometry is more suitable for measuring the exact DNA quantity. Exam tip: associate a clear gel band with generally good DNA integrity.

A smear can indicate broken DNA fragments. Gentle handling and nuclease protection are necessary.

Skin on the hands may carry human DNA, microorganisms, and nucleases—enzymes that can degrade DNA. Gloves prevent these materials from entering the sample, helping to obtain purer, protected DNA. DNA staining is done separately with appropriate dyes; gloves do not colour DNA. Exam tip: For preventing contamination during DNA isolation, remember gloves, clean tools, and nuclease-free materials.

Sterile, nuclease-free tubes are used to keep isolated DNA safe and reliable. Nucleases are enzymes that can cut or digest DNA, so their absence reduces unwanted DNA breakdown. Sterility also prevents outside microorganisms, DNA, proteins, or other material from entering the sample. This is especially important when the extracted DNA will be tested, amplified, or used in recombinant-DNA work.

Therefore, option A is correct because it combines the two main benefits: less nuclease-mediated degradation and less contamination. Options B, C, and D describe unrelated processes. A tube does not make DNA into protein, fill cells with starch, or convert ethanol into water. Proper tubes alone are not enough; clean handling and suitable storage are also needed.

The governing concept is that DNA purification must remove substances that interfere with downstream enzymes. Ethanol is commonly used during precipitation or washing, but if the DNA pellet is not dried adequately, residual ethanol remains in the sample. It can alter the reaction environment and inhibit DNA polymerase in PCR or other enzymes used for digestion, ligation, or measurement. Therefore option B is correct. Option A is wrong because ethanol does not reliably improve reactions. Options C and D describe biologically impossible transformations and are unrelated to purification. The pellet should be dried sufficiently, without excessive drying that makes DNA difficult to redissolve.

When a DNA pellet is over-dried, it can become hard and compact, making it slow or difficult to resuspend in TE buffer or water. DNA does not spontaneously convert into RNA, and drying does not increase protein content. Exam tip: Dry the pellet only enough to remove residual alcohol; avoid excessive drying before resuspension.

Genomic DNA is whole chromosomal DNA while plasmid DNA is small circular extra-chromosomal DNA. The method goal can differ.

Alkaline lysis is a common method in bacterial plasmid DNA isolation. Link it with plasmid preparation.

The governing concept is cell lysis: DNA is enclosed within cells, and the first practical step in extraction is to disrupt the cell membrane and, when present, the nuclear membrane. A lysis buffer usually provides a suitable pH and salt environment and may contain detergents that dissolve membrane lipids. It may also include agents that help protect DNA from nucleases. Thus option A is correct because the buffer makes cellular contents, including DNA, accessible for later purification. Option B is wrong because DNA is not converted into peptide. Options C and D are unrelated to the function of a lysis buffer. The exact composition varies with the organism and extraction method.

After alkaline lysis neutralization helps plasmid DNA remain in solution. Genomic DNA and debris can precipitate.

The direct answer is A: DNA binding on a silica surface. In a common silica-column purification method, cells are lysed and unwanted material is removed or separated. Under suitable salt and pH conditions, DNA binds to the silica membrane. The reasoning is: add binding buffer; DNA attaches to silica; contaminants are washed away while DNA remains bound; change the conditions with an elution buffer, usually reducing salt, and DNA comes off into a clean solution. This is an adsorption-based purification principle, and the exact binding strength depends on the buffer conditions. Option A is correct because silica binding is the central principle of many DNA spin columns. Option B is wrong because protein smell is not used to purify DNA. Option C is incomplete and wrong: boiling water alone does not selectively bind, wash, and elute DNA. Option D is unrelated because cell growth is a biological process, not column purification. Exam cue: bind DNA, wash contaminants, elute DNA.

Elution buffer or water releases DNA from the column. It can be the final step of purified DNA recovery.

The governing concept is that lower temperature slows chemical reactions and nuclease activity, thereby helping preserve isolated DNA. For routine short-term storage, purified DNA is commonly kept at about 4°C, provided the sample is clean and the storage period is limited. Therefore option A is the best answer. Heating at 100°C or placing DNA in boiling water can denature or damage the molecule and is not a storage method. Leaving a tube open at room temperature increases the risk of contamination, evaporation, and degradation, so option C is also unsuitable. For longer storage, DNA is generally kept frozen, often at -20°C or lower depending on the protocol.

Low temperature increases DNA stability in long-term storage. Repeated freeze-thaw should be avoided.

A label records details such as sample identity, source, date, or experiment number. It prevents confusion or interchange between DNA samples and allows results to be linked to the correct sample. DNA is cut by restriction endonucleases, not by labeling. Exam tip: the main purpose of sample labeling is identification and traceability.

In DNA isolation cells are broken and DNA is purified. The final DNA can be used in cloning or PCR.

DNA isolation is a sequential process. Cells are first lysed to release DNA, and impurities such as proteins and often RNA are removed. DNA is then precipitated and checked for purity and quantity. Water and light alone cannot isolate DNA. Exam tip: remember the sequence—lysis, impurity removal, precipitation, and quality check.